From 0ff639a29c6179e530c977b358cebf229c76139d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 13 Oct 2017 20:43:24 -0400
Subject: [PATCH 01/22] More debugging in workflows API tests.

---
 test/api/test_workflows.py | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 4b8c481043e..ea539743e21 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -734,8 +734,8 @@ steps:
     def test_workflow_run_dynamic_output_collections_2(self):
         # A more advanced output collection workflow, testing regression of
         # https://github.com/galaxyproject/galaxy/issues/776
-        history_id = self.dataset_populator.new_history()
-        workflow_id = self._upload_yaml_workflow("""
+        with self.dataset_populator.test_history() as history_id:
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   - label: test_input_1
@@ -759,19 +759,19 @@ steps:
         - input2:
             $link: split_up#split_output
 """)
-        hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
-        hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
-        hda3 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t60.0\n")
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        inputs = {
-            '0': self._ds_entry(hda1),
-            '1': self._ds_entry(hda2),
-            '2': self._ds_entry(hda3),
-        }
-        invocation_id = self.__invoke_workflow(history_id, workflow_id, inputs)
-        self.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
-        content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
-        self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0")
+            hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
+            hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
+            hda3 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t60.0\n")
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            inputs = {
+                '0': self._ds_entry(hda1),
+                '1': self._ds_entry(hda2),
+                '2': self._ds_entry(hda3),
+            }
+            invocation_id = self.__invoke_workflow(history_id, workflow_id, inputs)
+            self.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
+            content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
+            self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0")
 
     @skip_without_tool("collection_split_on_column")
     def test_workflow_run_dynamic_output_collections_3(self):

From 4e9ee22ebcd5cc358d1b86f60e957846f35765a5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 Oct 2017 18:58:37 -0400
Subject: [PATCH 02/22] More verbose workflow extraction test cases.

---
 test/api/test_workflow_extraction.py |  6 +++++-
 test/base/populators.py              | 12 ++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/test/api/test_workflow_extraction.py b/test/api/test_workflow_extraction.py
index ac763f36df5..57008511576 100644
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -5,7 +5,7 @@ import operator
 from collections import namedtuple
 from json import dumps, loads
 
-from base.populators import skip_without_tool
+from base.populators import skip_without_tool, summarize_instance_history_on_error
 
 from .test_workflows import BaseWorkflowsApiTestCase
 
@@ -17,6 +17,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
         self.history_id = self.dataset_populator.new_history()
 
     @skip_without_tool("cat1")
+    @summarize_instance_history_on_error
     def test_extract_from_history(self):
         # Run the simple test workflow and extract it back out from history
         cat1_job_id = self.__setup_and_run_cat1_workflow(history_id=self.history_id)
@@ -29,6 +30,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
         self.assertEqual(downloaded_workflow["name"], "test import from history")
         self.__assert_looks_like_cat1_example_workflow(downloaded_workflow)
 
+    @summarize_instance_history_on_error
     def test_extract_with_copied_inputs(self):
         old_history_id = self.dataset_populator.new_history()
         # Run the simple test workflow and extract it back out from history
@@ -54,6 +56,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
         self.__assert_looks_like_cat1_example_workflow(downloaded_workflow)
 
     @skip_without_tool("random_lines1")
+    @summarize_instance_history_on_error
     def test_extract_mapping_workflow_from_history(self):
         hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair(self.history_id)
         downloaded_workflow = self._extract_and_download_workflow(
@@ -232,6 +235,7 @@ test_data:
         )
 
     @skip_without_tool("collection_creates_pair")
+    @summarize_instance_history_on_error
     def test_extract_with_mapped_output_collections(self):
         jobs_summary = self._run_jobs("""
 class: GalaxyWorkflow
diff --git a/test/base/populators.py b/test/base/populators.py
index c6e364217aa..2beaaf0b29f 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -92,6 +92,18 @@ def skip_without_datatype(extension):
     return method_wrapper
 
 
+def summarize_instance_history_on_error(method):
+    @wraps(method)
+    def wrapped_method(api_test_case, *args, **kwds):
+        try:
+            method(api_test_case, *args, **kwds)
+        except Exception:
+            api_test_case.dataset_populator._summarize_history(api_test_case.history_id)
+            raise
+
+    return wrapped_method
+
+
 def _raise_skip_if(check):
     if check:
         from nose.plugins.skip import SkipTest

From 0e0894bbba8ee1d8b7c6946a5a42695fa6bd0858 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 18 Oct 2017 13:20:55 -0400
Subject: [PATCH 03/22] Refactoring history contents API.

---
 .../webapps/galaxy/api/history_contents.py    | 52 +++++++++----------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index f881fd8822f..87954ef4542 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -133,26 +133,33 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
     @expose_api_anonymous
     def show(self, trans, id, history_id, **kwd):
         """
-        show( self, trans, id, history_id, **kwd )
         * GET /api/histories/{history_id}/contents/{id}
-            return detailed information about an HDA within a history
+        * GET /api/histories/{history_id}/contents/{type}/{id}
+            return detailed information about an HDA or HDCA within a history
         .. note:: Anonymous users are allowed to get their current history contents
 
         :type   id:         str
-        :param  id:        the encoded id of the HDA to return
+        :param  id:         the encoded id of the HDA or HDCA to return
+        :type   type:       str
+        :param  id:         'dataset' or 'dataset_collection'
         :type   history_id: str
-        :param  history_id: encoded id string of the HDA's History
+        :param  history_id: encoded id string of the HDA's or HDCA's History
 
         :rtype:     dict
-        :returns:   dictionary containing detailed HDA information
+        :returns:   dictionary containing detailed HDA or HDCA information
         """
-        contents_type = kwd.get('type', 'dataset')
+        contents_type = self.__get_contents_type(trans, kwd)
         if contents_type == 'dataset':
             return self.__show_dataset(trans, id, **kwd)
         elif contents_type == 'dataset_collection':
             return self.__show_dataset_collection(trans, id, history_id, **kwd)
-        else:
-            return self.__handle_unknown_contents_type(trans, contents_type)
+
+    def __get_contents_type(self, trans, kwd):
+        contents_type = kwd.get('type', 'dataset')
+        if contents_type not in ['dataset', 'dataset_collection']:
+            self.__handle_unknown_contents_type(trans, contents_type)
+
+        return contents_type
 
     def __show_dataset(self, trans, id, **kwd):
         hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
@@ -162,18 +169,15 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
                                                      **self._parse_serialization_params(kwd, 'detailed'))
 
     def __show_dataset_collection(self, trans, id, history_id, **kwd):
-        try:
-            service = trans.app.dataset_collections_service
-            dataset_collection_instance = service.get_dataset_collection_instance(
-                trans=trans,
-                instance_type='history',
-                id=id,
-            )
-            return self.__collection_dict(trans, dataset_collection_instance, view="element")
-        except Exception as e:
-            log.exception("Error in history API at listing dataset collection")
-            trans.response.status = 500
-            return {'error': str(e)}
+        dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
+        return self.__collection_dict(trans, dataset_collection_instance, view="element")
+
+    def __get_accessible_collection(self, trans, id, history_id):
+        return trans.app.dataset_collections_service.get_dataset_collection_instance(
+            trans=trans,
+            instance_type="history",
+            id=id
+        )
 
     @expose_api_raw_anonymous
     def download_dataset_collection(self, trans, id, history_id=None, **kwd):
@@ -188,14 +192,8 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         :param history_id: encoded id string of the HDCA's History
         """
         try:
-            service = trans.app.dataset_collections_service
-            dataset_collection_instance = service.get_dataset_collection_instance(
-                trans=trans,
-                instance_type='history',
-                id=id,
-            )
+            dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
             return self.__stream_dataset_collection(trans, dataset_collection_instance)
-
         except Exception as e:
             log.exception("Error in API while creating dataset collection archive")
             trans.response.status = 500

From 8c1658f61a12b9c1e2efdb04ee3530c1272b0bde Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 Oct 2017 22:14:06 -0400
Subject: [PATCH 04/22] Mixin for uses create and update time.

---
 lib/galaxy/jobs/__init__.py  |  2 +-
 lib/galaxy/model/__init__.py | 26 +++++++++++++++-----------
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 8c82a17da06..3afd5657a3a 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1040,7 +1040,7 @@ class JobWrapper(object, HasResourceParameters):
         destination_params = job.destination_params
         if "__resubmit_delay_seconds" in destination_params:
             delay = float(destination_params["__resubmit_delay_seconds"])
-            if job.seconds_since_update < delay:
+            if job.seconds_since_updated < delay:
                 return False
 
         return True
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 01689a1a555..f054edac4e3 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -117,6 +117,19 @@ class HasName:
         return name
 
 
+class UsesCreateAndUpdateTime:
+
+    @property
+    def seconds_since_updated(self):
+        update_time = self.update_time or galaxy.model.orm.now.now()  # In case not yet flushed
+        return (galaxy.model.orm.now.now() - update_time).total_seconds()
+
+    @property
+    def seconds_since_created(self):
+        create_time = self.create_time or galaxy.model.orm.now.now()  # In case not yet flushed
+        return (galaxy.model.orm.now.now() - create_time).total_seconds()
+
+
 class JobLike:
 
     def _init_metrics(self):
@@ -424,7 +437,7 @@ class TaskMetricNumeric(BaseJobMetric):
     pass
 
 
-class Job(object, JobLike, Dictifiable):
+class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable):
     dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time']
     dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time']
 
@@ -805,10 +818,6 @@ class Job(object, JobLike, Dictifiable):
             config_value = default
         return config_value
 
-    @property
-    def seconds_since_update(self):
-        return (galaxy.model.orm.now.now() - self.update_time).total_seconds()
-
 
 class Task(object, JobLike):
     """
@@ -3952,7 +3961,7 @@ class StoredWorkflowMenuEntry(object):
         self.order_index = None
 
 
-class WorkflowInvocation(object, Dictifiable):
+class WorkflowInvocation(object, UsesCreateAndUpdateTime, Dictifiable):
     dict_collection_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']
     dict_element_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']
     states = Bunch(
@@ -4121,11 +4130,6 @@ class WorkflowInvocation(object, Dictifiable):
                 return True
         return False
 
-    @property
-    def seconds_since_created(self):
-        create_time = self.create_time or galaxy.model.orm.now.now()  # In case not flushed yet
-        return (galaxy.model.orm.now.now() - create_time).total_seconds()
-
 
 class WorkflowInvocationToSubworkflowInvocationAssociation(object, Dictifiable):
     dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']

From c076b3b6c5bf5ac9d374d56d42c9a91c352688ce Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 17 Oct 2017 08:41:18 -0400
Subject: [PATCH 05/22] Refactor workflow testing toward reuse via
 "populators".

Should allow more functionality to be shared between vanilla API tests and integration tests for various workflow scheduling options.
---
 test/api/test_workflows.py | 15 ++-------------
 test/base/populators.py    | 16 +++++++++++++++-
 2 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index ea539743e21..f875c2c9fa9 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -2040,19 +2040,8 @@ steps:
         self._assert_status_code_is(hda_info_response, 200)
         self.assertEqual(hda_info_response.json()["metadata_data_lines"], lines)
 
-    def __invoke_workflow(self, history_id, workflow_id, inputs={}, request={}, assert_ok=True):
-        request["history"] = "hist_id=%s" % history_id,
-        if inputs:
-            request["inputs"] = dumps(inputs)
-            request["inputs_by"] = 'step_index'
-        url = "workflows/%s/usage" % (workflow_id)
-        invocation_response = self._post(url, data=request)
-        if assert_ok:
-            self._assert_status_code_is(invocation_response, 200)
-            invocation_id = invocation_response.json()["id"]
-            return invocation_id
-        else:
-            return invocation_response
+    def __invoke_workflow(self, *args, **kwds):
+        return self.workflow_populator.invoke_workflow(*args, **kwds)
 
     def __import_workflow(self, workflow_id, deprecated_route=False):
         if deprecated_route:
diff --git a/test/base/populators.py b/test/base/populators.py
index 2beaaf0b29f..e382ace1ead 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -383,7 +383,21 @@ class BaseWorkflowPopulator(object):
         """ Wait for a workflow invocation to completely schedule and then history
         to be complete. """
         self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok, timeout=timeout)
+        self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=assert_ok, timeout=timeout)
+
+    def invoke_workflow(self, history_id, workflow_id, inputs={}, request={}, assert_ok=True):
+        request["history"] = "hist_id=%s" % history_id,
+        if inputs:
+            request["inputs"] = json.dumps(inputs)
+            request["inputs_by"] = 'step_index'
+        url = "workflows/%s/usage" % (workflow_id)
+        invocation_response = self._post(url, data=request)
+        if assert_ok:
+            api_asserts.assert_status_code_is(invocation_response, 200)
+            invocation_id = invocation_response.json()["id"]
+            return invocation_id
+        else:
+            return invocation_response
 
 
 class WorkflowPopulator(BaseWorkflowPopulator, ImporterGalaxyInterface):

From 55aa7bce5540469fad266f1166c9a2e7365030d4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 Oct 2017 21:11:11 -0400
Subject: [PATCH 06/22] Test cases for mapping for outputs with filter
 statements.

Checked through tools-iuc and I couldn't find any tools that use the actual input data parameters in filter statements so I think it is a fairly good approximation to assume that all mapped jobs will either filter or not at least with current execution model.
---
 test/api/test_tools.py                        | 38 +++++++++++++++++++
 .../tools/output_filter_with_input.xml        | 29 ++++++++++++++
 test/functional/tools/samples_tool_conf.xml   |  1 +
 3 files changed, 68 insertions(+)
 create mode 100644 test/functional/tools/output_filter_with_input.xml

diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 306bfdca96f..e11ce93c8be 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -704,6 +704,38 @@ class ToolsTestCase(api.ApiTestCase):
             assert output1_details["file_ext"] == "txt" if (use_action == "do") else "data"
             assert output2_details["file_ext"] == "txt" if (use_action == "do") else "data"
 
+    @skip_without_tool("output_filter_with_input")
+    def test_map_over_with_output_filter_no_filtering(self):
+        with self.dataset_populator.test_history() as history_id:
+            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
+            inputs = {
+                "input_1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+                "produce_out_1": "true",
+                "filter_text_1": "foo",
+            }
+            create = self._run('output_filter_with_input', history_id, inputs).json()
+            jobs = create['jobs']
+            implicit_collections = create['implicit_collections']
+            self.assertEquals(len(jobs), 3)
+            self.assertEquals(len(implicit_collections), 3)
+            self._check_implicit_collection_populated(create)
+
+    @skip_without_tool("output_filter_with_input")
+    def test_map_over_with_output_filter_one_filtered(self):
+        with self.dataset_populator.test_history() as history_id:
+            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
+            inputs = {
+                "input_1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+                "produce_out_1": "true",
+                "filter_text_1": "bar",
+            }
+            create = self._run('output_filter_with_input', history_id, inputs).json()
+            jobs = create['jobs']
+            implicit_collections = create['implicit_collections']
+            self.assertEquals(len(jobs), 3)
+            self.assertEquals(len(implicit_collections), 2)
+            self._check_implicit_collection_populated(create)
+
     @skip_without_tool("Cut1")
     def test_map_over_with_complex_output_actions(self):
         history_id = self.dataset_populator.new_history()
@@ -1297,6 +1329,12 @@ class ToolsTestCase(api.ApiTestCase):
         assert output1_content.strip() == "123\n456\nxxx", output1_content
         assert output2_content.strip() == "789\n0ab\nyyy", output2_content
 
+    def _check_implicit_collection_populated(self, run_response):
+        implicit_collections = run_response["implicit_collections"]
+        assert implicit_collections
+        for implicit_collection in implicit_collections:
+            assert implicit_collection["populated_state"] == "ok"
+
     def _cat1_outputs(self, history_id, inputs):
         return self._run_outputs(self._run_cat1(history_id, inputs))
 
diff --git a/test/functional/tools/output_filter_with_input.xml b/test/functional/tools/output_filter_with_input.xml
new file mode 100644
index 00000000000..9eb7dbc20d1
--- /dev/null
+++ b/test/functional/tools/output_filter_with_input.xml
@@ -0,0 +1,29 @@
+<tool id="output_filter_with_input" name="output_filter_with_input" version="1.0.0">
+  <!-- output_filter.xml but with an input -->
+  <command>
+    echo "test" > 1;
+    echo "test" > 2;
+    echo "test" > 3;
+    echo "test" > 4;
+    echo "test" > 5;
+  </command>
+  <inputs>
+    <param name="input_1" type="data" />
+    <param name="produce_out_1" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do Filter 1" />
+    <param name="filter_text_1" type="text" value="1" />
+  </inputs>
+  <outputs>
+    <data format="txt" from_work_dir="1" name="out_1">
+      <filter>produce_out_1 is True</filter>
+    </data>
+    <data format="txt" from_work_dir="2" name="out_2">
+      <filter>filter_text_1 in ["foo", "bar"]</filter>
+      <!-- Must pass all filters... -->
+      <filter>filter_text_1 == "foo"</filter>
+    </data>
+    <data format="txt" from_work_dir="3" name="out_3">
+    </data>
+  </outputs>
+  <tests>
+  </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index fa5c8ed5cd6..88ecc25f816 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -60,6 +60,7 @@
   <tool file="output_format_deprecated_when.xml" />
   <tool file="output_format_collection.xml" />
   <tool file="output_filter.xml" />
+  <tool file="output_filter_with_input.xml" />
   <tool file="output_filter_exception_1.xml" />
   <tool file="output_collection_filter.xml" />
   <tool file="output_auto_format.xml" />

From d5f98f49045bca351e982f17cac9386308089eeb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 25 Jul 2017 12:41:54 +0200
Subject: [PATCH 07/22] Formalize workflow invocation and invocation step
 outputs.

Workflow Invocations
--------------------

The workflow invocation outputs half of this is relatively straight forward. It is modelled somewhat on job outputs, output datasets and output dataset collections are now tracked for each workflow invocation and exposed via the workflow invocation API. This required adding new tables (linked to WorkflowInvocations and WorkflowOutputs) that track these output associations.

Previously one could imagine backtracking this information for simple tool steps via the WorkflowInvocationStep -> Job table, but for steps that have many jobs (i.e. mapping over a collection) or for non-tool steps such information was more difficult to recover (and simply couldn't be recovered from the API at all or even internally without significant knowledge of the underlying workflow).

Workflow Invocation Steps
-------------------------

Tracking the outputs of WorkflowInvocationSteps was not previously done at all, one would have to follow the Job table as well. A signficant downside to this is that one cannot map over empty collections in a workflow - since no such job would exist. Tracking job outputs for WorkflowInvocationSteps is not a simple matter of just attaching outputs to an existing table because we had no concept of a workflow step tracked - since there could be many WorklfowInvocationSteps corresponding to the same combination of WorkflowInvocation and WorkflowStep. That should feel wrong and that is because it is - when collections were added the possiblity of having many jobs for the same combination of WorkflowInvocation and WorkflowStep was added. I should have split WorkflowInvocationSteps into WorkflowInvocationSteps and WorkflowInvocationStepJobAssociations at that time but didn't. This commit now does it - effectively normalizing the ``workflow_invocation_step`` table by introducing the new ``workflow_invocation_step_job_association`` table.

Splitting up the WorkflowInvocationStep table this way allows recovering the mapped over output (e.g. the implicitly created collection from all the jobs) as well the outputs from the individual jobs (by walking WorkflowInvocationStep -> WorkflowInvocationStepJobAssociation -> Job -> JobToOutput*Association).

This split up involves failrly substantial changes to the workflow module interface. Any place a list of WorkflowInvocationSteps was assumed, I reworked it to just expect a single WorkflowInvocationStep. I vastly simplified recover_mapping to just use the persisted outputs (this was needed in order to also implment empty collection mapping in workflows). This also fixes a bug (or implements a missing feature) where Subworkflow moudles had no recover_mapping methods - so for instance if a tool that produces dynamic collections appeared anywhere in a workflow after a subworkflow step - that workflow would not complete scheduling properly.

Now that we have a way to reference the set of jobs corresponding to a workflow step within an invocation, we can start to track partial scheduling of such steps. This is outlined in https://github.com/galaxyproject/galaxy/issues/3883 and refactoring toward this goal is included here - including adding a state to WorkflowInvocationStep so Galaxy can determine if it has started scheduling this step and an index when scheduling jobs so it can tell how far into a scheduling things have gone as well as augmenting the tool executor to take a maximum number of jobs to execute and allow recovery of existing jobs for collection building purposes.

*Applications*

These changes will enable:

- A simple, consistent API for finding workflow outputs that can be consumed by Planemo for testing workflows.
- Mapping over empty collections in workflows.
- Re-scheduling workflow invocations that include subworkflow steps.
- Partial scheduling within steps requiring a large number of jobs when scheduling workflow invocations.
---
 lib/galaxy/jobs/actions/post.py               |  12 +-
 lib/galaxy/model/__init__.py                  | 172 ++++++++++++----
 lib/galaxy/model/mapping.py                   |  97 ++++++++-
 .../versions/0136_record_workflow_outputs.py  | 185 ++++++++++++++++++
 lib/galaxy/tools/execute.py                   |  58 +++++-
 lib/galaxy/workflow/modules.py                | 124 +++++++-----
 lib/galaxy/workflow/run.py                    | 108 +++++++---
 test/api/test_workflows.py                    |  71 +++++++
 test/base/populators.py                       |   2 +
 test/unit/workflows/test_workflow_progress.py |  65 +++---
 10 files changed, 738 insertions(+), 156 deletions(-)
 create mode 100644 lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py

diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py
index 267a765e66f..138d4b8005b 100644
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -269,10 +269,10 @@ class DeleteIntermediatesAction(DefaultJobAction):
         # concurrently, sometimes non-terminal steps won't be cleaned up
         # because of the lag in job state updates.
         sa_session.flush()
-        if not job.workflow_invocation_step:
+        if not job.workflow_invocation_step_assoc.workflow_invocation_step:
             log.debug("This job is not part of a workflow invocation, delete intermediates aborted.")
             return
-        wfi = job.workflow_invocation_step.workflow_invocation
+        wfi = job.workflow_invocation_step_assoc.workflow_invocation_step.workflow_invocation
         sa_session.refresh(wfi)
         if wfi.active:
             log.debug("Workflow still scheduling so new jobs may appear, skipping deletion of intermediate files.")
@@ -285,9 +285,9 @@ class DeleteIntermediatesAction(DefaultJobAction):
             jobs_to_check = []
             for wfi_step in wfi_steps:
                 sa_session.refresh(wfi_step)
-                wfi_step_job = wfi_step.job
-                if wfi_step_job:
-                    jobs_to_check.append(wfi_step_job)
+                wfi_step_job_assocs = wfi_step.jobs
+                if wfi_step_job_assocs:
+                    jobs_to_check.extend(map(lambda j: j.job, wfi_step_job_assocs))
                 else:
                     log.debug("No job found yet for wfi_step %s, (step %s)" % (wfi_step, wfi_step.workflow_step))
             for j2c in jobs_to_check:
@@ -302,7 +302,7 @@ class DeleteIntermediatesAction(DefaultJobAction):
                 for (input_dataset, creating_job) in creating_jobs:
                     sa_session.refresh(creating_job)
                     sa_session.refresh(input_dataset)
-                for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
+                for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step_assoc and creating_job.workflow_invocation_step_assoc.workflow_invocation_step.workflow_invocation == wfi]:
                     # note that the above input_dataset is a reference to a
                     # job.input_dataset.dataset at this point
                     safe_to_delete = True
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index f054edac4e3..707f96cbdbf 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -803,8 +803,9 @@ class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable):
 
     def set_final_state(self, final_state):
         self.set_state(final_state)
-        if self.workflow_invocation_step:
-            self.workflow_invocation_step.update()
+        workflow_invocation_step_assoc = self.workflow_invocation_step_assoc
+        if workflow_invocation_step_assoc:
+            workflow_invocation_step_assoc.workflow_invocation_step.update()
 
     def get_destination_configuration(self, config, key, default=None):
         """ Get a destination parameter that can be defaulted back
@@ -4036,17 +4037,16 @@ class WorkflowInvocation(object, UsesCreateAndUpdateTime, Dictifiable):
         step_invocations = {}
         for invocation_step in self.steps:
             step_id = invocation_step.workflow_step_id
-            if step_id not in step_invocations:
-                step_invocations[step_id] = []
-            step_invocations[step_id].append(invocation_step)
+            assert step_id not in step_invocations
+            step_invocations[step_id] = invocation_step
         return step_invocations
 
-    def step_invocations_for_step_id(self, step_id):
-        step_invocations = []
+    def step_invocation_for_step_id(self, step_id):
+        target_invocation_step = None
         for invocation_step in self.steps:
             if step_id == invocation_step.workflow_step_id:
-                step_invocations.append(invocation_step)
-        return step_invocations
+                target_invocation_step = invocation_step
+        return target_invocation_step
 
     @staticmethod
     def poll_active_workflow_ids(
@@ -4072,6 +4072,24 @@ class WorkflowInvocation(object, UsesCreateAndUpdateTime, Dictifiable):
         # is relatively intutitive.
         return [wid for wid in query.all()]
 
+    def add_output(self, workflow_output, step, output_object):
+        if output_object.history_content_type == "dataset":
+            output_assoc = WorkflowInvocationOutputDatasetAssociation()
+            output_assoc.workflow_invocation = self
+            output_assoc.workflow_output = workflow_output
+            output_assoc.workflow_step = step
+            output_assoc.dataset = output_object
+            self.output_datasets.append(output_assoc)
+        elif output_object.history_content_type == "dataset_collection":
+            output_assoc = WorkflowInvocationOutputDatasetCollectionAssociation()
+            output_assoc.workflow_invocation = self
+            output_assoc.workflow_output = workflow_output
+            output_assoc.workflow_step = step
+            output_assoc.dataset_collection = output_object
+            self.output_dataset_collections.append(output_assoc)
+        else:
+            raise Exception("Uknown output type encountered")
+
     def to_dict(self, view='collection', value_mapper=None, step_details=False):
         rval = super(WorkflowInvocation, self).to_dict(view=view, value_mapper=value_mapper)
         if view == 'element':
@@ -4087,17 +4105,43 @@ class WorkflowInvocation(object, UsesCreateAndUpdateTime, Dictifiable):
             inputs = {}
             for step in self.steps:
                 if step.workflow_step.type == 'tool':
-                    for step_input in step.workflow_step.input_connections:
-                        output_step_type = step_input.output_step.type
-                        if output_step_type in ['data_input', 'data_collection_input']:
-                            src = "hda" if output_step_type == 'data_input' else 'hdca'
-                            for job_input in step.job.input_datasets:
-                                if job_input.name == step_input.input_name:
-                                    inputs[str(step_input.output_step.order_index)] = {
-                                        "id": job_input.dataset_id, "src": src,
-                                        "uuid" : str(job_input.dataset.dataset.uuid) if job_input.dataset.dataset.uuid is not None else None
-                                    }
+                    for step_job_assoc in step.jobs:
+                        for step_input in step.workflow_step.input_connections:
+                            output_step_type = step_input.output_step.type
+                            if output_step_type in ['data_input', 'data_collection_input']:
+                                src = "hda" if output_step_type == 'data_input' else 'hdca'
+                                for job_input in step_job_assoc.job.input_datasets:
+                                    if job_input.name == step_input.input_name:
+                                        inputs[str(step_input.output_step.order_index)] = {
+                                            "id": job_input.dataset_id, "src": src,
+                                            "uuid" : str(job_input.dataset.dataset.uuid) if job_input.dataset.dataset.uuid is not None else None
+                                        }
             rval['inputs'] = inputs
+
+            outputs = {}
+            for output_assoc in self.output_datasets:
+                label = output_assoc.workflow_output.label
+                if not label:
+                    continue
+
+                outputs[label] = {
+                    'src': 'hda',
+                    'id': output_assoc.dataset_id,
+                }
+
+            output_collections = {}
+            for output_assoc in self.output_dataset_collections:
+                label = output_assoc.workflow_output.label
+                if not label:
+                    continue
+
+                output_collections[label] = {
+                    'src': 'hdca',
+                    'id': output_assoc.dataset_collection_id,
+                }
+
+            rval['outputs'] = outputs
+            rval['output_collections'] = output_collections
         return rval
 
     def update(self):
@@ -4137,36 +4181,70 @@ class WorkflowInvocationToSubworkflowInvocationAssociation(object, Dictifiable):
 
 
 class WorkflowInvocationStep(object, Dictifiable):
-    dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'action']
-    dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'action']
+    dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
+    dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
+    states = Bunch(
+        NEW='new',  # Brand new workflow invocation step
+        READY='ready',  # Workflow invocation step ready for another iteration of scheduling.
+        SCHEDULED='scheduled',  # Workflow invocation step has been scheduled.
+        # CANCELLED='cancelled',  TODO: implement and expose
+        # FAILED='failed',  TODO: implement and expose
+    )
 
     def update(self):
         self.workflow_invocation.update()
 
+    def add_output(self, output_name, output_object):
+        if output_object.history_content_type == "dataset":
+            output_assoc = WorkflowInvocationStepOutputDatasetAssociation()
+            output_assoc.workflow_invocation_step = self
+            output_assoc.dataset = output_object
+            output_assoc.output_name = output_name
+            self.output_datasets.append(output_assoc)
+        elif output_object.history_content_type == "dataset_collection":
+            output_assoc = WorkflowInvocationStepOutputDatasetCollectionAssociation()
+            output_assoc.workflow_invocation_step = self
+            output_assoc.dataset_collection = output_object
+            output_assoc.output_name = output_name
+            self.output_dataset_collections.append(output_assoc)
+        else:
+            raise Exception("Uknown output type encountered")
+
     def to_dict(self, view='collection', value_mapper=None):
         rval = super(WorkflowInvocationStep, self).to_dict(view=view, value_mapper=value_mapper)
         rval['order_index'] = self.workflow_step.order_index
         rval['workflow_step_label'] = self.workflow_step.label
         rval['workflow_step_uuid'] = str(self.workflow_step.uuid)
-        rval['state'] = self.job.state if self.job is not None else None
-        if self.job is not None and view == 'element':
-            output_dict = {}
-            for i in self.job.output_datasets:
-                if i.dataset is not None:
-                    output_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "hda",
-                        "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
-                    }
-            for i in self.job.output_library_datasets:
-                if i.dataset is not None:
-                    output_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "ldda",
-                        "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
-                    }
-            rval['outputs'] = output_dict
+        # Following no longer makes sense...
+        # rval['state'] = self.job.state if self.job is not None else None
+        if view == 'element':
+            outputs = {}
+            for output_assoc in self.output_datasets:
+                name = output_assoc.output_name
+                outputs[name] = {
+                    'src': 'hda',
+                    'id': output_assoc.dataset.id,
+                    'uuid': str(output_assoc.dataset.dataset.uuid) if output_assoc.dataset.dataset.uuid is not None else None
+                }
+
+            output_collections = {}
+            for output_assoc in self.output_dataset_collections:
+                name = output_assoc.output_name
+                output_collections[name] = {
+                    'src': 'hdca',
+                    'id': output_assoc.dataset_collection.id,
+                }
+
+            rval['outputs'] = outputs
+            rval['output_collections'] = output_collections
         return rval
 
 
+class WorkflowInvocationStepJobAssociation(object, Dictifiable):
+    dict_collection_visible_keys = ('id', 'job_id', 'workflow_invocation_step_id')
+    dict_element_visible_keys = ('id', 'job_id', 'workflow_invocation_step_id')
+
+
 class WorkflowRequest(object, Dictifiable):
     dict_collection_visible_keys = ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']
     dict_element_visible_keys = ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']
@@ -4221,6 +4299,26 @@ class WorkflowRequestInputStepParmeter(object, Dictifiable):
     dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']
 
 
+class WorkflowInvocationOutputDatasetAssociation(object, Dictifiable):
+    """Represents links to output datasets for the workflow."""
+    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
+
+
+class WorkflowInvocationOutputDatasetCollectionAssociation(object, Dictifiable):
+    """Represents links to output dataset collections for the workflow."""
+    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
+
+
+class WorkflowInvocationStepOutputDatasetAssociation(object, Dictifiable):
+    """Represents links to output datasets for the workflow."""
+    dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']
+
+
+class WorkflowInvocationStepOutputDatasetCollectionAssociation(object, Dictifiable):
+    """Represents links to output dataset collections for the workflow."""
+    dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']
+
+
 class MetadataFile(StorableObject):
 
     def __init__(self, dataset=None, name=None):
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 97923d892cc..49d6d4ed206 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -901,9 +901,54 @@ model.WorkflowInvocationStep.table = Table(
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
+    Column("state", TrimmedString(64), index=True),
     Column("action", JSONType, nullable=True))
 
+
+model.WorkflowInvocationStepJobAssociation.table = Table(
+    "workflow_invocation_step_job_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
+    Column("order_index", Integer, nullable=True),  # recovering partially complete WorkflowInvocationSteps requires knowing which jobs have been scheduled
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+)
+
+
+model.WorkflowInvocationOutputDatasetAssociation.table = Table(
+    "workflow_invocation_output_dataset_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
+)
+
+model.WorkflowInvocationOutputDatasetCollectionAssociation.table = Table(
+    "workflow_invocation_output_dataset_collection_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
+)
+
+model.WorkflowInvocationStepOutputDatasetAssociation.table = Table(
+    "workflow_invocation_step_output_dataset_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("output_name", String(255), nullable=True),
+)
+
+model.WorkflowInvocationStepOutputDatasetCollectionAssociation.table = Table(
+    "workflow_invocation_step_output_dataset_collection_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("output_name", String(255), nullable=True),
+)
+
 model.WorkflowInvocationToSubworkflowInvocationAssociation.table = Table(
     "workflow_invocation_to_subworkflow_invocation_association", metadata,
     Column("id", Integer, primary_key=True),
@@ -2310,7 +2355,7 @@ mapper(model.WorkflowInvocation, model.WorkflowInvocation.table, properties=dict
         uselist=True,
     ),
     steps=relation(model.WorkflowInvocationStep,
-        backref='workflow_invocation'),
+        backref="workflow_invocation"),
     workflow=relation(model.Workflow)
 ))
 
@@ -2323,12 +2368,17 @@ mapper(model.WorkflowInvocationToSubworkflowInvocationAssociation, model.Workflo
     workflow_step=relation(model.WorkflowStep),
 ))
 
-mapper(model.WorkflowInvocationStep, model.WorkflowInvocationStep.table, properties=dict(
-    workflow_step=relation(model.WorkflowStep),
+
+simple_mapping(model.WorkflowInvocationStepJobAssociation,
+    workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="jobs"),
     job=relation(model.Job,
-        backref=backref('workflow_invocation_step',
-            uselist=False))
-))
+        backref=backref('workflow_invocation_step_assoc',
+            uselist=False)))
+
+
+simple_mapping(model.WorkflowInvocationStep,
+    workflow_step=relation(model.WorkflowStep))
+
 
 simple_mapping(model.WorkflowRequestInputParameter,
     workflow_invocation=relation(model.WorkflowInvocation))
@@ -2358,6 +2408,39 @@ mapper(model.MetadataFile, model.MetadataFile.table, properties=dict(
     library_dataset=relation(model.LibraryDatasetDatasetAssociation)
 ))
 
+
+simple_mapping(
+    model.WorkflowInvocationOutputDatasetAssociation,
+    workflow_invocation=relation(model.WorkflowInvocation, backref="output_datasets"),
+    workflow_step=relation(model.WorkflowStep),
+    dataset=relation(model.HistoryDatasetAssociation),
+    workflow_output=relation(model.WorkflowOutput),
+)
+
+
+simple_mapping(
+    model.WorkflowInvocationOutputDatasetCollectionAssociation,
+    workflow_invocation=relation(model.WorkflowInvocation, backref="output_dataset_collections"),
+    workflow_step=relation(model.WorkflowStep),
+    dataset_collection=relation(model.HistoryDatasetCollectionAssociation),
+    workflow_output=relation(model.WorkflowOutput),
+)
+
+
+simple_mapping(
+    model.WorkflowInvocationStepOutputDatasetAssociation,
+    workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="output_datasets"),
+    dataset=relation(model.HistoryDatasetAssociation),
+)
+
+
+simple_mapping(
+    model.WorkflowInvocationStepOutputDatasetCollectionAssociation,
+    workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="output_dataset_collections"),
+    dataset_collection=relation(model.HistoryDatasetCollectionAssociation),
+)
+
+
 mapper(model.PageRevision, model.PageRevision.table)
 
 mapper(model.Page, model.Page.table, properties=dict(
diff --git a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
new file mode 100644
index 00000000000..1b83a49aa31
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
@@ -0,0 +1,185 @@
+"""
+Migration script for workflow request tables.
+"""
+from __future__ import print_function
+
+import datetime
+import logging
+
+from collections import OrderedDict
+
+from migrate.changeset.constraint import ForeignKeyConstraint
+from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table
+
+from galaxy.model.custom_types import JSONType, TrimmedString
+
+
+now = datetime.datetime.utcnow
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+
+def get_new_tables():
+    # Normally we define this globally in the file, but we need to delay the
+    # reading of existing tables because an existing workflow_invocation_step
+    # table exists that we want to recreate.
+
+    workflow_invocation_output_dataset_association_table = Table(
+        "workflow_invocation_output_dataset_association", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+        Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+        Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
+    )
+
+    workflow_invocation_output_dataset_collection_association_table = Table(
+        "workflow_invocation_output_dataset_collection_association", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+        Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+        Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
+    )
+
+    workflow_invocation_step_output_dataset_association_table = Table(
+        "workflow_invocation_step_output_dataset_association", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+        Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+        Column("output_name", String(255), nullable=True),
+    )
+
+    workflow_invocation_step_output_dataset_collection_association_table = Table(
+        "workflow_invocation_step_output_dataset_collection_association", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+        Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+        Column("output_name", String(255), nullable=True),
+    )
+
+    workflow_invocation_step_table = Table(
+        "workflow_invocation_step", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
+        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+        Column("action", JSONType, nullable=True),
+        Column("state", TrimmedString(64), default="new"),
+    )
+
+    workflow_invocation_step_job_association_table = Table(
+        "workflow_invocation_step_job_association", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
+        Column("order_index", Integer, nullable=True),
+        Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+    )
+
+    tables = OrderedDict()
+    tables["workflow_invocation_step"] = workflow_invocation_step_table
+    tables["workflow_invocation_output_dataset_association"] = workflow_invocation_output_dataset_association_table
+    tables["workflow_invocation_output_dataset_collection_association"] = workflow_invocation_output_dataset_collection_association_table
+    tables["workflow_invocation_step_output_dataset_association"] = workflow_invocation_step_output_dataset_association_table
+    tables["workflow_invocation_step_output_dataset_collection_association"] = workflow_invocation_step_output_dataset_collection_association_table
+    tables["workflow_invocation_step_job_association"] = workflow_invocation_step_job_association_table
+
+    return tables
+
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print(__doc__)
+
+    LegacyWorkflowInvocationStep_table = Table("workflow_invocation_step", metadata, autoload=True)
+    ExistingWorkflowInvocation_table = Table("workflow_invocation", metadata, autoload=True)
+
+    cons = ForeignKeyConstraint([LegacyWorkflowInvocationStep_table.c.workflow_invocation_id], [ExistingWorkflowInvocation_table.c.id])
+    cons.drop()
+
+    for index in LegacyWorkflowInvocationStep_table.indexes:
+        index.drop()
+
+    LegacyWorkflowInvocationStep_table.rename("workflow_invocation_step_premigrate135")
+    # Try to deregister that workflow_invocation_step to work around some caching problems
+    # it seems.
+    LegacyWorkflowInvocationStep_table.deregister()
+    metadata._remove_table("workflow_invocation_step", metadata.schema)
+
+    metadata.reflect()
+    tables = get_new_tables()
+    for table in tables.values():
+        __create(table)
+
+    def nextval(table, col='id'):
+        if migrate_engine.name in ['postgres', 'postgresql']:
+            return "nextval('%s_%s_seq')" % (table, col)
+        elif migrate_engine.name in ['mysql', 'sqlite']:
+            return "null"
+        else:
+            raise Exception("Unhandled database type")
+
+    # Skips action - since I can't aggregate (sql needs a RANDOM(col)) that and it is only used by optional
+    # beta extensions.
+    cmd = \
+        "INSERT INTO workflow_invocation_step " + \
+        "(id, create_time, update_time, workflow_invocation_id, workflow_step_id, action, state)" + \
+        "SELECT " + \
+        nextval('workflow_invocation_step') + " AS id, " \
+        "MIN(create_time) AS create_time, " + \
+        "MAX(update_time) AS update_time, " + \
+        "workflow_invocation_step_premigrate135.workflow_invocation_id AS workflow_invocation_id, " +\
+        "workflow_invocation_step_premigrate135.workflow_step_id AS workflow_step_id, " + \
+        "NULL AS action, " + \
+        "'scheduled' AS state " + \
+        "FROM workflow_invocation_step_premigrate135 " + \
+        "WHERE workflow_invocation_step_premigrate135.workflow_step_id IS NOT NULL AND workflow_invocation_step_premigrate135.workflow_invocation_id IS NOT NULL " +\
+        "GROUP BY workflow_invocation_step_premigrate135.workflow_invocation_id, workflow_invocation_step_premigrate135.workflow_step_id " + \
+        ""
+    migrate_engine.execute(cmd)
+
+    cmd = \
+        "INSERT INTO workflow_invocation_step_job_association " + \
+        "(id, workflow_invocation_step_id, order_index, job_id) " + \
+        "SELECT " + \
+        nextval('workflow_invocation_step_job_association') + " AS id, " \
+        "workflow_invocation_step.id AS workflow_invocation_step_id, " + \
+        "NULL AS order_index, " + \
+        "job_id AS job_id " + \
+        "FROM workflow_invocation_step_premigrate135 " + \
+        "LEFT JOIN workflow_invocation_step on (" + \
+        "  workflow_invocation_step.workflow_invocation_id = workflow_invocation_step_premigrate135.workflow_invocation_id " + \
+        "  AND workflow_invocation_step.workflow_step_id = workflow_invocation_step_premigrate135.workflow_step_id" + \
+        ") " + \
+        "WHERE job_id is not NULL "
+    migrate_engine.execute(cmd)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    tables = get_new_tables()
+    for table in tables.values():
+        __drop(table)
+
+    # Drop new workflow invocation step and job association table and restore legacy data.
+    LegacyWorkflowInvocationStep_table = Table("workflow_invocation_step_premigrate135", metadata, autoload=True)
+    LegacyWorkflowInvocationStep_table.rename("workflow_invocation_step")
+
+
+def __create(table):
+    try:
+        table.create()
+    except Exception:
+        log.exception("Creating %s table failed.", table.name)
+
+
+def __drop(table):
+    try:
+        table.drop()
+    except Exception:
+        log.exception("Dropping %s table failed.", table.name)
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index c24a57af1c0..e6d37538110 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -18,7 +18,13 @@ log = logging.getLogger(__name__)
 EXECUTION_SUCCESS_MESSAGE = "Tool [%s] created job [%s] %s"
 
 
-def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None):
+class PartialJobExecution(Exception):
+
+    def __init__(self, jobs):
+        self.jobs = jobs
+
+
+def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None):
     """
     Execute a tool and return object containing summary (output data, number of
     failures, etc...).
@@ -28,6 +34,8 @@ def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, c
     app = trans.app
     execution_cache = ToolExecutionCache(trans)
 
+    new_jobs = []
+
     def execute_single_job(params):
         job_timer = ExecutionTimer()
         if workflow_invocation_uuid:
@@ -41,6 +49,7 @@ def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, c
             message = EXECUTION_SUCCESS_MESSAGE % (tool.id, job.id, job_timer)
             log.debug(message)
             execution_tracker.record_success(job, result)
+            new_jobs.append(job)
         else:
             execution_tracker.record_error(result)
 
@@ -59,11 +68,27 @@ def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, c
                 history
             )
 
+    if invocation_step:
+        execution_tracker.recover_successful_jobs(invocation_step)
+
+    previously_executed_jobs_count = len(execution_tracker.successful_jobs)
     job_count = len(execution_tracker.param_combinations)
-    if job_count < burst_at or burst_threads < 2:
-        for params in execution_tracker.param_combinations:
-            execute_single_job(params)
+
+    jobs_executed = 0
+    has_remaining_jobs = False
+
+    if (job_count < burst_at or burst_threads < 2):
+        for index, params in enumerate(execution_tracker.param_combinations):
+            if index < previously_executed_jobs_count:
+                continue
+            elif max_num_jobs and jobs_executed >= max_num_jobs:
+                has_remaining_jobs = True
+                break
+            else:
+                execute_single_job(params)
+                jobs_executed += 1
     else:
+        # TODO: re-record success...
         q = Queue()
 
         def worker():
@@ -77,11 +102,21 @@ def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, c
             t.daemon = True
             t.start()
 
-        for params in execution_tracker.param_combinations:
-            q.put(params)
+        for index, params in enumerate(execution_tracker.param_combinations):
+            if index < previously_executed_jobs_count:
+                continue
+            elif max_num_jobs and jobs_executed >= max_num_jobs:
+                has_remaining_jobs = True
+                break
+            else:
+                q.put(params)
+                jobs_executed += 1
 
         q.join()
 
+    if has_remaining_jobs:
+        raise PartialJobExecution(new_jobs)
+
     log.debug("Executed %d job(s) for tool %s request: %s" % (job_count, tool.id, all_jobs_timer))
     if collection_info:
         history = history or tool.get_default_history_by_trans(trans)
@@ -110,6 +145,17 @@ class ToolExecutionTracker(object):
         self.outputs_by_output_name = collections.defaultdict(list)
         self.implicit_collections = {}
 
+    def recover_successful_jobs(self, invocation_step):
+        # TODO: Optimize away the need to do this - we should just be dealing with IDs
+        # and such and we shouldn't fetch them until the very end when we need them to create
+        # collections.
+        for job_assoc in invocation_step.jobs:
+            job = job_assoc.job
+            for job_output in job.output_datasets:
+                self.outputs_by_output_name[job_output.name].append(job_output.dataset)
+            for job_output in job.output_dataset_collections:
+                self.outputs_by_output_name[job_output.name].append(job_output.dataset_collection)
+
     def record_success(self, job, outputs):
         self.successful_jobs.append(job)
         self.output_datasets.extend(outputs)
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index d5fcbf641cf..7abc55636a5 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -21,7 +21,7 @@ from galaxy.tools import (
     DefaultToolState,
     ToolInputsNotReadyException
 )
-from galaxy.tools.execute import execute
+from galaxy.tools.execute import execute, PartialJobExecution
 from galaxy.tools.parameters import (
     check_param,
     params_to_incoming,
@@ -214,10 +214,14 @@ class WorkflowModule(object):
         state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs()), self.trans.app)
         return state
 
-    def execute(self, trans, progress, invocation, step):
-        """ Execute the given workflow step in the given workflow invocation.
+    def execute(self, trans, progress, invocation_step):
+        """ Execute the given workflow invocation step.
+
         Use the supplied workflow progress object to track outputs, find
-        inputs, etc...
+        inputs, etc....
+
+        Return jobs created and a boolean indicating if there are additional
+        jobs to create on subsequent workflow scheduling tests.
         """
         raise TypeError("Abstract method")
 
@@ -230,11 +234,19 @@ class WorkflowModule(object):
         """
         raise exceptions.RequestParameterInvalidException("Attempting to perform invocation step action on module that does not support actions.")
 
-    def recover_mapping(self, step, step_invocations, progress):
+    def recover_mapping(self, invocation_step, progress):
         """ Re-populate progress object with information about connections
-        from previously executed steps recorded via step_invocations.
+        from previously executed steps recorded via invocation_steps.
         """
-        raise TypeError("Abstract method")
+        outputs = {}
+
+        for output_dataset_assoc in invocation_step.output_datasets:
+            outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
+
+        for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
+            outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
+
+        progress.set_step_outputs(invocation_step, outputs, already_persisted=True)
 
 
 class SubWorkflowModule(WorkflowModule):
@@ -320,11 +332,12 @@ class SubWorkflowModule(WorkflowModule):
     def get_content_id(self):
         return self.trans.security.encode_id(self.subworkflow.id)
 
-    def execute(self, trans, progress, invocation, step):
+    def execute(self, trans, progress, invocation_step):
         """ Execute the given workflow step in the given workflow invocation.
         Use the supplied workflow progress object to track outputs, find
         inputs, etc...
         """
+        step = invocation_step.workflow_step
         subworkflow_invoker = progress.subworkflow_invoker(trans, step)
         subworkflow_invoker.invoke()
         subworkflow = subworkflow_invoker.workflow
@@ -334,7 +347,7 @@ class SubWorkflowModule(WorkflowModule):
             workflow_output_label = workflow_output.label or "%s:%s" % (step.order_index, workflow_output.output_name)
             replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output)
             outputs[workflow_output_label] = replacement
-        progress.set_step_outputs(step, outputs)
+        progress.set_step_outputs(invocation_step, outputs)
         return None
 
     def get_runtime_state(self):
@@ -353,8 +366,10 @@ class InputModule(WorkflowModule):
     def get_data_inputs(self):
         return []
 
-    def execute(self, trans, progress, invocation, step):
-        job, step_outputs = None, dict(output=step.state.inputs['input'])
+    def execute(self, trans, progress, invocation_step):
+        invocation = invocation_step.workflow_invocation
+        step = invocation_step.workflow_step
+        step_outputs = dict(output=step.state.inputs['input'])
 
         # Web controller may set copy_inputs_to_history, API controller always sets
         # inputs.
@@ -378,11 +393,10 @@ class InputModule(WorkflowModule):
             content = next(iter(step_outputs.values()))
             if content:
                 invocation.add_input(content, step.id)
-        progress.set_outputs_for_input(step, step_outputs)
-        return job
+        progress.set_outputs_for_input(invocation_step, step_outputs)
 
-    def recover_mapping(self, step, step_invocations, progress):
-        progress.set_outputs_for_input(step)
+    def recover_mapping(self, invocation_step, progress):
+        progress.set_outputs_for_input(invocation_step)
 
 
 class InputDataModule(InputModule):
@@ -489,10 +503,10 @@ class InputParameterModule(WorkflowModule):
     def get_data_inputs(self):
         return []
 
-    def execute(self, trans, progress, invocation, step):
-        job, step_outputs = None, dict(output=step.state.inputs['input'])
-        progress.set_outputs_for_input(step, step_outputs)
-        return job
+    def execute(self, trans, progress, invocation_step):
+        step = invocation_step.workflow_step
+        step_outputs = dict(output=step.state.inputs['input'])
+        progress.set_outputs_for_input(invocation_step, step_outputs)
 
 
 class PauseModule(WorkflowModule):
@@ -520,18 +534,18 @@ class PauseModule(WorkflowModule):
         state.inputs = dict()
         return state
 
-    def execute(self, trans, progress, invocation, step):
+    def execute(self, trans, progress, invocation_step):
+        step = invocation_step.workflow_step
         progress.mark_step_outputs_delayed(step, why="executing pause step")
-        return None
 
-    def recover_mapping(self, step, step_invocations, progress):
-        if step_invocations:
-            step_invocation = step_invocations[0]
-            action = step_invocation.action
+    def recover_mapping(self, invocation_step, progress):
+        if invocation_step:
+            step = invocation_step.workflow_step
+            action = invocation_step.action
             if action:
                 connection = step.input_connections_by_name["input"][0]
                 replacement = progress.replacement_for_connection(connection)
-                progress.set_step_outputs(step, {'output': replacement})
+                progress.set_step_outputs(invocation_step, {'output': replacement})
                 return
             elif action is False:
                 raise CancelWorkflowEvaluation()
@@ -790,7 +804,9 @@ class ToolModule(WorkflowModule):
         else:
             raise ToolMissingException("Tool %s missing. Cannot recover runtime state." % self.tool_id)
 
-    def execute(self, trans, progress, invocation, step):
+    def execute(self, trans, progress, invocation_step):
+        invocation = invocation_step.workflow_invocation
+        step = invocation_step.workflow_step
         tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version)
         tool_state = step.state
         # Not strictly needed - but keep Tool state clean by stripping runtime
@@ -855,6 +871,9 @@ class ToolModule(WorkflowModule):
 
             param_combinations.append(execution_state.inputs)
 
+        # Will be set if only a subset of required jobs have been scheduled and the
+        # workflow should be delayed.
+        partial_jobs = None
         try:
             execution_tracker = execute(
                 trans=self.trans,
@@ -862,50 +881,49 @@ class ToolModule(WorkflowModule):
                 param_combinations=param_combinations,
                 history=invocation.history,
                 collection_info=collection_info,
-                workflow_invocation_uuid=invocation.uuid.hex
+                workflow_invocation_uuid=invocation.uuid.hex,
+                invocation_step=invocation_step,
             )
+        except PartialJobExecution as p:
+            partial_jobs = p.jobs
         except ToolInputsNotReadyException:
             delayed_why = "tool [%s] inputs are not ready, this special tool requires inputs to be ready" % tool.id
             raise DelayedWorkflowEvaluation(why=delayed_why)
 
-        if collection_info:
-            step_outputs = dict(execution_tracker.implicit_collections)
+        if partial_jobs is None:
+            if collection_info:
+                step_outputs = dict(execution_tracker.implicit_collections)
+            else:
+                step_outputs = dict(execution_tracker.output_datasets)
+                step_outputs.update(execution_tracker.output_collections)
+            progress.set_step_outputs(invocation_step, step_outputs)
+            jobs = execution_tracker.successful_jobs
         else:
-            step_outputs = dict(execution_tracker.output_datasets)
-            step_outputs.update(execution_tracker.output_collections)
-        progress.set_step_outputs(step, step_outputs)
-        jobs = execution_tracker.successful_jobs
+            jobs = partial_jobs
+
         for job in jobs:
             self._handle_post_job_actions(step, job, invocation.replacement_dict)
+
         if execution_tracker.execution_errors:
             failed_count = len(execution_tracker.execution_errors)
             success_count = len(execution_tracker.successful_jobs)
             all_count = failed_count + success_count
             message = "Failed to create %d out of %s job(s) for workflow step." % (failed_count, all_count)
             raise Exception(message)
-        return jobs
 
-    def recover_mapping(self, step, step_invocations, progress):
-        # Grab a job representing this invocation - for normal workflows
-        # there will be just one job but if this step was mapped over there
-        # may be many.
-        job_0 = step_invocations[0].job
+        complete = partial_jobs is None
+        return jobs, complete
 
+    def recover_mapping(self, invocation_step, progress):
         outputs = {}
-        for job_output in job_0.output_datasets:
-            replacement_name = job_output.name
-            replacement_value = job_output.dataset
-            # If was a mapping step, grab the output mapped collection for
-            # replacement instead.
-            if replacement_value.hidden_beneath_collection_instance:
-                replacement_value = replacement_value.hidden_beneath_collection_instance
-            outputs[replacement_name] = replacement_value
-        for job_output_collection in job_0.output_dataset_collection_instances:
-            replacement_name = job_output_collection.name
-            replacement_value = job_output_collection.dataset_collection_instance
-            outputs[replacement_name] = replacement_value
 
-        progress.set_step_outputs(step, outputs)
+        for output_dataset_assoc in invocation_step.output_datasets:
+            outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
+
+        for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
+            outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
+
+        progress.set_step_outputs(invocation_step, outputs)
 
     def _find_collections_to_match(self, tool, progress, step):
         collections_to_match = matching.CollectionsToMatch()
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 0f6fd041d04..75222d5a46d 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -162,24 +162,46 @@ class WorkflowInvoker(object):
 
         remaining_steps = self.progress.remaining_steps()
         delayed_steps = False
-        for step in remaining_steps:
+        for (step, workflow_invocation_step) in remaining_steps:
             step_delayed = False
             step_timer = ExecutionTimer()
             jobs = None
             try:
                 self.__check_implicitly_dependent_steps(step)
 
-                # TODO: step may fail to invoke, do something about that.
-                jobs = self._invoke_step(step)
-                for job in (util.listify(jobs) or [None]):
-                    # Record invocation
+                if not workflow_invocation_step:
                     workflow_invocation_step = model.WorkflowInvocationStep()
                     workflow_invocation_step.workflow_invocation = workflow_invocation
                     workflow_invocation_step.workflow_step = step
+                    workflow_invocation_step.state = 'new'
+                    previously_executed_jobs_count = 0
+
+                    workflow_invocation.steps.append(workflow_invocation_step)
+                else:
+                    previously_executed_jobs_count = len(workflow_invocation_step.jobs)
+
+                jobs_or_none = self._invoke_step(workflow_invocation_step)
+                if jobs_or_none:
+                    jobs, complete = jobs_or_none
+                else:
+                    jobs, complete = [], True
+
+                for job in (util.listify(jobs) or []):
+                    job_assoc = model.WorkflowInvocationStepJobAssociation()
+                    job_assoc.index = previously_executed_jobs_count
+                    job_assoc.workflow_invocation_step = workflow_invocation_step
                     # Job may not be generated in this thread if bursting is enabled
                     # https://github.com/galaxyproject/galaxy/issues/2259
-                    if job:
-                        workflow_invocation_step.job_id = job.id
+                    job_assoc.job_id = job.id
+
+                    previously_executed_jobs_count += 1
+
+                if not complete:
+                    step_delayed = delayed_steps = True
+                    workflow_invocation_step.state = 'ready'
+                    self.progress.mark_step_outputs_delayed(step, why="Not all jobs scheduled for state.")
+                else:
+                    workflow_invocation_step.state = 'scheduled'
             except modules.DelayedWorkflowEvaluation as de:
                 step_delayed = delayed_steps = True
                 self.progress.mark_step_outputs_delayed(step, why=de.why)
@@ -218,15 +240,19 @@ class WorkflowInvoker(object):
                 self.__check_implicitly_dependent_step(output_id)
 
     def __check_implicitly_dependent_step(self, output_id):
-        step_invocations = self.workflow_invocation.step_invocations_for_step_id(output_id)
+        step_invocation = self.workflow_invocation.step_invocation_for_step_id(output_id)
 
         # No steps created yet - have to delay evaluation.
-        if not step_invocations:
+        if not step_invocation:
             delayed_why = "depends on step [%s] but that step has not been invoked yet" % output_id
             raise modules.DelayedWorkflowEvaluation(why=delayed_why)
 
-        for step_invocation in step_invocations:
-            job = step_invocation.job
+        if step_invocation.state != 'scheduled':
+            delayed_why = "depends on step [%s] job has not finished scheduling yet" % output_id
+            raise modules.DelayedWorkflowEvaluation(delayed_why)
+
+        for job_assoc in step_invocation.jobs:
+            job = job_assoc.job
             if job:
                 # At least one job in incomplete.
                 if not job.finished:
@@ -241,9 +267,9 @@ class WorkflowInvoker(object):
                 # pause steps.
                 pass
 
-    def _invoke_step(self, step):
-        jobs = step.module.execute(self.trans, self.progress, self.workflow_invocation, step)
-        return jobs
+    def _invoke_step(self, invocation_step):
+        jobs_or_none = invocation_step.workflow_step.module.execute(self.trans, self.progress, invocation_step)
+        return jobs_or_none
 
 
 STEP_OUTPUT_DELAYED = object()
@@ -256,11 +282,19 @@ class WorkflowProgress(object):
         self.module_injector = module_injector
         self.workflow_invocation = workflow_invocation
         self.inputs_by_step_id = inputs_by_step_id
+        self.jobs_per_scheduling_iteration = 1
+
+    @property
+    def maximum_jobs_to_schedule(self):
+        return 1
 
     def remaining_steps(self):
         # Previously computed and persisted step states.
         step_states = self.workflow_invocation.step_states_by_step_id()
         steps = self.workflow_invocation.workflow.steps
+
+        # TODO: Wouldn't a generator be much better here so we don't have to reason about
+        # steps we are no where near ready to schedule?
         remaining_steps = []
         step_invocations_by_id = self.workflow_invocation.step_invocations_by_step_id()
         for step in steps:
@@ -274,11 +308,11 @@ class WorkflowProgress(object):
                 runtime_state = step_states[step_id].value
                 step.state = step.module.decode_runtime_state(runtime_state)
 
-            invocation_steps = step_invocations_by_id.get(step_id, None)
-            if invocation_steps:
-                self._recover_mapping(step, invocation_steps)
+            invocation_step = step_invocations_by_id.get(step_id, None)
+            if invocation_step and invocation_step.state == 'scheduled':
+                self._recover_mapping(invocation_step)
             else:
-                remaining_steps.append(step)
+                remaining_steps.append((step, invocation_step))
         return remaining_steps
 
     def replacement_for_tool_input(self, step, input, prefixed_name):
@@ -340,7 +374,9 @@ class WorkflowProgress(object):
         output_name = workflow_output.output_name
         return self.outputs[step.id][output_name]
 
-    def set_outputs_for_input(self, step, outputs=None):
+    def set_outputs_for_input(self, invocation_step, outputs=None):
+        step = invocation_step.workflow_step
+
         if outputs is None:
             outputs = {}
 
@@ -352,10 +388,34 @@ class WorkflowProgress(object):
                 raise ValueError(message)
             outputs['output'] = self.inputs_by_step_id[step_id]
 
-        self.set_step_outputs(step, outputs)
+        self.set_step_outputs(invocation_step, outputs)
 
-    def set_step_outputs(self, step, outputs):
+    def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
+        step = invocation_step.workflow_step
         self.outputs[step.id] = outputs
+        if not already_persisted:
+            for output_name, output_object in outputs.items():
+                if hasattr(output_object, "history_content_type"):
+                    invocation_step.add_output(output_name, output_object)
+                else:
+                    # This is a problem, this non-data, non-collection output
+                    # won't be recovered on a subsequent workflow scheduling
+                    # iteration. This seems to have been a pre-existing problem
+                    # prior to #4584 though.
+                    pass
+            for workflow_output in step.workflow_outputs:
+                output_name = workflow_output.output_name
+                if output_name not in outputs:
+                    raise KeyError("Failed to find [%s] in step outputs [%s]" % (output_name, outputs))
+                output = outputs[output_name]
+                self._record_workflow_output(
+                    step,
+                    workflow_output,
+                    output=output,
+                )
+
+    def _record_workflow_output(self, step, workflow_output, output):
+        self.workflow_invocation.add_output(workflow_output, step, output)
 
     def mark_step_outputs_delayed(self, step, why=None):
         if why:
@@ -414,11 +474,11 @@ class WorkflowProgress(object):
             self.module_injector,
         )
 
-    def _recover_mapping(self, step, step_invocations):
+    def _recover_mapping(self, step_invocation):
         try:
-            step.module.recover_mapping(step, step_invocations, self)
+            step_invocation.workflow_step.module.recover_mapping(step_invocation, self)
         except modules.DelayedWorkflowEvaluation as de:
-            self.mark_step_outputs_delayed(step, de.why)
+            self.mark_step_outputs_delayed(step_invocation.workflow_step, de.why)
 
 
 __all__ = ('invoke', 'WorkflowRunConfig')
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index f875c2c9fa9..214692f1021 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -963,6 +963,77 @@ test_data:
         time.sleep(5)
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
 
+    def test_workflow_output_dataset(self):
+        history_id = self.dataset_populator.new_history()
+        summary = self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+outputs:
+  - id: wf_output_1
+    source: first_cat#out_file1
+steps:
+  - tool_id: cat1
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+
+test_data:
+  input1: "hello world"
+""", history_id=history_id)
+        workflow_id = summary.workflow_id
+        invocation_id = summary.invocation_id
+        invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+        self._assert_status_code_is(invocation_response, 200)
+        invocation = invocation_response.json()
+        self._assert_has_keys(invocation , "id", "outputs", "output_collections")
+        assert len(invocation["output_collections"]) == 0
+        assert len(invocation["outputs"]) == 1
+        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=invocation["outputs"]["wf_output_1"]["id"])
+        assert "hello world" == output_content.strip()
+
+    def test_workflow_output_dataset_collection(self):
+        history_id = self.dataset_populator.new_history()
+        summary = self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+    type: data_collection_input
+    collection_type: list
+outputs:
+  - id: wf_output_1
+    source: first_cat#out_file1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+test_data:
+  input1:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+""", history_id=history_id)
+        workflow_id = summary.workflow_id
+        invocation_id = summary.invocation_id
+        invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+        self._assert_status_code_is(invocation_response, 200)
+        invocation = invocation_response.json()
+        self._assert_has_keys(invocation , "id", "outputs", "output_collections")
+        assert len(invocation["output_collections"]) == 1
+        assert len(invocation["outputs"]) == 0
+        output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+        self._assert_has_keys(output_content , "id", "elements")
+        elements = output_content["elements"]
+        assert len(elements) == 1
+        elements0 = elements[0]
+        assert elements0["element_identifier"] == "el1"
+
     @skip_without_tool("cat")
     def test_cancel_new_workflow_when_history_deleted(self):
         with self.dataset_populator.test_history() as history_id:
diff --git a/test/base/populators.py b/test/base/populators.py
index e382ace1ead..b64b57ff526 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -282,6 +282,8 @@ class BaseDatasetPopulator(object):
         # the last dataset in the history will be fetched.
         if "dataset_id" in kwds:
             history_content_id = kwds["dataset_id"]
+        elif "content_id" in kwds:
+            history_content_id = kwds["content_id"]
         elif "dataset" in kwds:
             history_content_id = kwds["dataset"]["id"]
         else:
diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py
index 21cb2341414..3991cb393a4 100644
--- a/test/unit/workflows/test_workflow_progress.py
+++ b/test/unit/workflows/test_workflow_progress.py
@@ -72,13 +72,17 @@ class WorkflowProgressTestCase(unittest.TestCase):
             self.invocation, self.inputs_by_step_id, MockModuleInjector(self.progress)
         )
 
-    def _set_previous_progress(self, outputs_dict):
-        for step_id, step_value in outputs_dict.items():
+    def _set_previous_progress(self, outputs):
+        for i, (step_id, step_value) in enumerate(outputs):
             if step_value is not UNSCHEDULED_STEP:
                 self.progress[step_id] = step_value
 
                 workflow_invocation_step = model.WorkflowInvocationStep()
                 workflow_invocation_step.workflow_step_id = step_id
+                workflow_invocation_step.state = 'scheduled'
+                workflow_invocation_step.workflow_step = self._step(i)
+                self.assertEqual(step_id, self._step(i).id)
+                # workflow_invocation_step.workflow_invocation = self.invocation
                 self.invocation.steps.append(workflow_invocation_step)
 
             workflow_invocation_step_state = model.WorkflowRequestStepState()
@@ -89,13 +93,21 @@ class WorkflowProgressTestCase(unittest.TestCase):
     def _step(self, index):
         return self.invocation.workflow.steps[index]
 
+    def _invocation_step(self, index):
+        if index < len(self.invocation.steps):
+            return self.invocation.steps[index]
+        else:
+            workflow_invocation_step = model.WorkflowInvocationStep()
+            workflow_invocation_step.workflow_step = self._step(index)
+            return workflow_invocation_step
+
     def test_connect_data_input(self):
         self._setup_workflow(TEST_WORKFLOW_YAML)
         hda = model.HistoryDatasetAssociation()
 
         self.inputs_by_step_id = {100: hda}
         progress = self._new_workflow_progress()
-        progress.set_outputs_for_input(self._step(0))
+        progress.set_outputs_for_input(self._invocation_step(0))
 
         conn = model.WorkflowStepConnection()
         conn.output_name = "output"
@@ -108,7 +120,7 @@ class WorkflowProgressTestCase(unittest.TestCase):
 
         self.inputs_by_step_id = {100: hda}
         progress = self._new_workflow_progress()
-        progress.set_outputs_for_input(self._step(0))
+        progress.set_outputs_for_input(self._invocation_step(0))
 
         replacement = progress.replacement_for_tool_input(self._step(2), MockInput(), "input1")
         assert replacement is hda
@@ -118,7 +130,7 @@ class WorkflowProgressTestCase(unittest.TestCase):
         hda = model.HistoryDatasetAssociation()
 
         progress = self._new_workflow_progress()
-        progress.set_step_outputs(self._step(2), {"out1": hda})
+        progress.set_step_outputs(self._invocation_step(2), {"out1": hda})
 
         conn = model.WorkflowStepConnection()
         conn.output_name = "out1"
@@ -128,17 +140,18 @@ class WorkflowProgressTestCase(unittest.TestCase):
     def test_remaining_steps_with_progress(self):
         self._setup_workflow(TEST_WORKFLOW_YAML)
         hda3 = model.HistoryDatasetAssociation()
-        self._set_previous_progress({
-            100: {"output": model.HistoryDatasetAssociation()},
-            101: {"output": model.HistoryDatasetAssociation()},
-            102: {"out_file1": hda3},
-            103: {"out_file1": model.HistoryDatasetAssociation()},
-            104: UNSCHEDULED_STEP,
-        })
+        self._set_previous_progress([
+            (100, {"output": model.HistoryDatasetAssociation()}),
+            (101, {"output": model.HistoryDatasetAssociation()}),
+            (102, {"out_file1": hda3}),
+            (103, {"out_file1": model.HistoryDatasetAssociation()}),
+            (104, UNSCHEDULED_STEP),
+        ])
         progress = self._new_workflow_progress()
         steps = progress.remaining_steps()
-        assert len(steps) == 1
-        assert steps[0] is self.invocation.workflow.steps[4]
+        assert len(steps) == 1, steps
+        step, invocation_step = steps[0]
+        assert step is self.invocation.workflow.steps[4]
 
         replacement = progress.replacement_for_tool_input(self._step(4), MockInput(), "input1")
         assert replacement is hda3
@@ -151,21 +164,27 @@ class WorkflowProgressTestCase(unittest.TestCase):
     def test_subworkflow_progress(self):
         self._setup_workflow(TEST_SUBWORKFLOW_YAML)
         hda = model.HistoryDatasetAssociation()
-        self._set_previous_progress({
-            100: {"output": hda},
-            101: UNSCHEDULED_STEP,
-        })
+        self._set_previous_progress([
+            (100, {"output": hda}),
+            (101, UNSCHEDULED_STEP),
+        ])
         self.invocation.create_subworkflow_invocation_for_step(
             self.invocation.workflow.step_by_index(1)
         )
         progress = self._new_workflow_progress()
         remaining_steps = progress.remaining_steps()
-        subworkflow_step = remaining_steps[0]
+        (subworkflow_step, subworkflow_invocation_step) = remaining_steps[0]
         subworkflow_progress = progress.subworkflow_progress(subworkflow_step)
         subworkflow = subworkflow_step.subworkflow
         assert subworkflow_progress.workflow_invocation.workflow == subworkflow
+
         subworkflow_input_step = subworkflow.step_by_index(0)
-        subworkflow_progress.set_outputs_for_input(subworkflow_input_step)
+        subworkflow_invocation_step = model.WorkflowInvocationStep()
+        subworkflow_invocation_step.workflow_step_id = subworkflow_input_step.id
+        subworkflow_invocation_step.state = 'new'
+        subworkflow_invocation_step.workflow_step = subworkflow_input_step
+
+        subworkflow_progress.set_outputs_for_input(subworkflow_invocation_step)
 
         subworkflow_cat_step = subworkflow.step_by_index(1)
 
@@ -200,7 +219,7 @@ class MockModule(object):
     def decode_runtime_state(self, runtime_state):
         return True
 
-    def recover_mapping(self, step, step_invocations, progress):
-        step_id = step.id
+    def recover_mapping(self, invocation_step, progress):
+        step_id = invocation_step.workflow_step.id
         if step_id in self.progress:
-            progress.set_step_outputs(step, self.progress[step_id])
+            progress.set_step_outputs(invocation_step, self.progress[step_id])

From 64835c1e72eea545269260256c7a238a4e5ea7fe Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 8 Aug 2017 13:47:28 -0400
Subject: [PATCH 08/22] Three new worklfow test cases to verify mapping over
 workflows is possible.

- Simple mapping over an input dataset.
- Mapping that produces nested collections.
- Mapping over subworkflows.
---
 test/api/test_workflows.py | 138 +++++++++++++++++++++++++++++++++++--
 1 file changed, 132 insertions(+), 6 deletions(-)

diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 214692f1021..b3501adc9a2 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -24,6 +24,9 @@ SIMPLE_NESTED_WORKFLOW_YAML = """
 class: GalaxyWorkflow
 inputs:
   - id: outer_input
+outputs:
+  - id: outer_output
+    source: second_cat#out_file1
 steps:
   - tool_id: cat1
     label: first_cat
@@ -58,11 +61,6 @@ steps:
       queries:
         - input2:
             $link: nested_workflow#workflow_output
-
-test_data:
-  outer_input:
-    value: 1.bed
-    type: File
 """
 
 
@@ -861,7 +859,14 @@ test_data:
 
     def test_run_subworkflow_simple(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs(SIMPLE_NESTED_WORKFLOW_YAML, history_id=history_id)
+        workflow_run_description = """%s
+
+test_data:
+  outer_input:
+    value: 1.bed
+    type: File
+""" % SIMPLE_NESTED_WORKFLOW_YAML
+        self._run_jobs(workflow_run_description, history_id=history_id)
 
         content = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual("chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", content)
@@ -1029,11 +1034,132 @@ test_data:
         assert len(invocation["outputs"]) == 0
         output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
         self._assert_has_keys(output_content , "id", "elements")
+        assert output_content["collection_type"] == "list"
         elements = output_content["elements"]
         assert len(elements) == 1
         elements0 = elements[0]
         assert elements0["element_identifier"] == "el1"
 
+    def test_worklfow_input_mapping(self):
+        history_id = self.dataset_populator.new_history()
+        summary = self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+outputs:
+  - id: wf_output_1
+    source: first_cat#out_file1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+test_data:
+  input1:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+      - identifier: el2
+        value: 1.fastq
+        type: File
+""", history_id=history_id)
+        workflow_id = summary.workflow_id
+        invocation_id = summary.invocation_id
+        invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+        self._assert_status_code_is(invocation_response, 200)
+        invocation = invocation_response.json()
+        self._assert_has_keys(invocation , "id", "outputs", "output_collections")
+        assert len(invocation["output_collections"]) == 1
+        assert len(invocation["outputs"]) == 0
+        output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+        self._assert_has_keys(output_content , "id", "elements")
+        elements = output_content["elements"]
+        assert len(elements) == 2
+        elements0 = elements[0]
+        assert elements0["element_identifier"] == "el1"
+
+    @skip_without_tool("collection_creates_pair")
+    def test_workflow_run_input_mapping_with_output_collections(self):
+        history_id = self.dataset_populator.new_history()
+        summary = self._run_jobs("""
+class: GalaxyWorkflow
+outputs:
+  - id: wf_output_1
+    source: split_up#paired_output
+steps:
+  - label: text_input
+    type: input
+  - label: split_up
+    tool_id: collection_creates_pair
+    state:
+      input1:
+        $link: text_input
+test_data:
+  text_input:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+      - identifier: el2
+        value: 1.fastq
+        type: File
+""", history_id=history_id)
+        workflow_id = summary.workflow_id
+        invocation_id = summary.invocation_id
+        invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+        self._assert_status_code_is(invocation_response, 200)
+        invocation = invocation_response.json()
+        self._assert_has_keys(invocation , "id", "outputs", "output_collections")
+        assert len(invocation["output_collections"]) == 1
+        assert len(invocation["outputs"]) == 0
+        output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+        self._assert_has_keys(output_content , "id", "elements")
+        assert output_content["collection_type"] == "list:paired", output_content
+        elements = output_content["elements"]
+        assert len(elements) == 2
+        elements0 = elements[0]
+        assert elements0["element_identifier"] == "el1"
+
+    def test_workflow_run_input_mapping_with_subworkflows(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_jobs("""%s
+
+test_data:
+  outer_input:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+      - identifier: el2
+        value: 1.fastq
+        type: File
+""" % SIMPLE_NESTED_WORKFLOW_YAML, history_id=history_id)
+            workflow_id = summary.workflow_id
+            invocation_id = summary.invocation_id
+            invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+            self._assert_status_code_is(invocation_response, 200)
+            invocation_response = self._get("workflows/%s/invocations/%s" % (workflow_id, invocation_id))
+            self._assert_status_code_is(invocation_response, 200)
+            invocation = invocation_response.json()
+            self._assert_has_keys(invocation , "id", "outputs", "output_collections")
+            assert len(invocation["output_collections"]) == 1, invocation
+            assert len(invocation["outputs"]) == 0
+            output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["outer_output"]["id"])
+            self._assert_has_keys(output_content , "id", "elements")
+            assert output_content["collection_type"] == "list", output_content
+            elements = output_content["elements"]
+            assert len(elements) == 2
+            elements0 = elements[0]
+            assert elements0["element_identifier"] == "el1"
+
     @skip_without_tool("cat")
     def test_cancel_new_workflow_when_history_deleted(self):
         with self.dataset_populator.test_history() as history_id:

From 0185e04a5beaf951bb20d670d9421d988d70bb29 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 11 Sep 2017 14:28:26 -0400
Subject: [PATCH 09/22] Test recover_mapping in conjunction with subworkflow
 executions.

---
 test/api/test_workflows.py | 112 +++++++++++++++++++++++++++++++++++++
 1 file changed, 112 insertions(+)

diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index b3501adc9a2..47d9820887a 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1160,6 +1160,118 @@ test_data:
             elements0 = elements[0]
             assert elements0["element_identifier"] == "el1"
 
+    @skip_without_tool("cat_list")
+    @skip_without_tool("random_lines1")
+    @skip_without_tool("split")
+    def test_subworkflow_recover_mapping(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: outer_input
+outputs:
+  - id: outer_output
+    source: second_cat#out_file1
+steps:
+  - tool_id: cat1
+    label: first_cat
+    state:
+      input1:
+        $link: outer_input
+  - run:
+      class: GalaxyWorkflow
+      inputs:
+        - id: inner_input
+      outputs:
+        - id: workflow_output
+          source: random_lines#out_file1
+      steps:
+        - tool_id: random_lines1
+          label: random_lines
+          state:
+            num_lines: 2
+            input:
+              $link: inner_input
+            seed_source:
+              seed_source_selector: set_seed
+              seed: asdf
+    label: nested_workflow
+    connect:
+      inner_input: first_cat#out_file1
+  - tool_id: split
+    label: split
+    state:
+      input1:
+        $link: nested_workflow#workflow_output
+  - tool_id: cat_list
+    label: second_cat
+    state:
+      input1:
+        $link: split#output
+
+test_data:
+  outer_input:
+    value: 1.bed
+    type: File
+""", history_id=history_id, wait=True)
+            self.assertEqual("chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
+
+    @skip_without_tool("cat_list")
+    @skip_without_tool("random_lines1")
+    @skip_without_tool("split")
+    def test_recover_mapping_in_subworkflow(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: outer_input
+outputs:
+  - id: outer_output
+    source: second_cat#out_file1
+steps:
+  - tool_id: cat1
+    label: first_cat
+    state:
+      input1:
+        $link: outer_input
+  - run:
+      class: GalaxyWorkflow
+      inputs:
+        - id: inner_input
+      outputs:
+        - id: workflow_output
+          source: split#output
+      steps:
+        - tool_id: random_lines1
+          label: random_lines
+          state:
+            num_lines: 2
+            input:
+              $link: inner_input
+            seed_source:
+              seed_source_selector: set_seed
+              seed: asdf
+        - tool_id: split
+          label: split
+          state:
+            input1:
+              $link: random_lines#out_file1
+    label: nested_workflow
+    connect:
+      inner_input: first_cat#out_file1
+  - tool_id: cat_list
+    label: second_cat
+    state:
+      input1:
+        $link: nested_workflow#workflow_output
+
+test_data:
+  outer_input:
+    value: 1.bed
+    type: File
+""", history_id=history_id, wait=True)
+            self.assertEqual("chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
+
     @skip_without_tool("cat")
     def test_cancel_new_workflow_when_history_deleted(self):
         with self.dataset_populator.test_history() as history_id:

From 9e471d3e97a6d6b6893ed243b6a48108076899c4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 15 Nov 2017 08:54:23 -0500
Subject: [PATCH 10/22] Allow mapping over empty collections.

If one maps a tool over an empty collection, one should get an empty output collection for each of the tool's outputs.

This should have always been a valid operation I think, the code just wasn't quite structured right when the collection work was merged - there were too many places I was assuming the existence of at least one actual output or input that was mapped over to continue going. This reworks all of that and seems to handle empty collections appropriately.

Fixes #4025 (not being informing the user of the operation, but actually by allowing the operation - which it should be allowed I think).
---
 lib/galaxy/dataset_collections/matching.py    |  4 +-
 lib/galaxy/tools/__init__.py                  | 32 +++++---
 lib/galaxy/tools/execute.py                   | 18 ++---
 lib/galaxy/workflow/modules.py                |  5 +-
 test/api/test_tools.py                        | 18 +++++
 test/api/test_workflows.py                    | 80 +++++++++++++++++++
 test/base/populators.py                       |  2 +-
 .../tools/for_workflows/count_list.xml        | 16 ++++
 .../tools/for_workflows/count_multi_file.xml  | 16 ++++
 .../tools/for_workflows/empty_list.xml        | 22 +++++
 test/functional/tools/samples_tool_conf.xml   |  3 +
 11 files changed, 191 insertions(+), 25 deletions(-)
 create mode 100644 test/functional/tools/for_workflows/count_list.xml
 create mode 100644 test/functional/tools/for_workflows/count_multi_file.xml
 create mode 100644 test/functional/tools/for_workflows/empty_list.xml

diff --git a/lib/galaxy/dataset_collections/matching.py b/lib/galaxy/dataset_collections/matching.py
index b8720ccf80b..94b4f2d5d66 100644
--- a/lib/galaxy/dataset_collections/matching.py
+++ b/lib/galaxy/dataset_collections/matching.py
@@ -64,7 +64,9 @@ class MatchingCollections(object):
         effective_structure = leaf
         for unlinked_structure in self.unlinked_structures:
             effective_structure = effective_structure.multiply(unlinked_structure)
-        linked_structure = self.linked_structure or leaf
+        linked_structure = self.linked_structure
+        if linked_structure is None:
+            linked_structure = leaf
         effective_structure = effective_structure.multiply(linked_structure)
         return None if effective_structure.is_leaf else effective_structure
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index f29e2dbf95f..9731214c194 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -84,7 +84,10 @@ from galaxy.web import url_for
 from galaxy.web.form_builder import SelectField
 from galaxy.work.context import WorkRequestContext
 from tool_shed.util import common_util
-from .execute import execute as execute_job
+from .execute import (
+    execute as execute_job,
+    MappingParameters,
+)
 from .loader import (
     imported_macro_paths,
     raw_tool_xml_tree,
@@ -1244,8 +1247,6 @@ class Tool(object, Dictifiable):
         # Fixed set of input parameters may correspond to any number of jobs.
         # Expand these out to individual parameters for given jobs (tool executions).
         expanded_incomings, collection_info = expand_meta_parameters(trans, self, incoming)
-        if not expanded_incomings:
-            raise exceptions.MessageException('Tool execution failed, trying to run a tool over an empty collection.')
 
         # Remapping a single job to many jobs doesn't make sense, so disable
         # remap if multi-runs of tools are being used.
@@ -1295,17 +1296,24 @@ class Tool(object, Dictifiable):
             err_data = {key: value for d in all_errors for (key, value) in d.items()}
             raise exceptions.MessageException(', '.join(msg for msg in err_data.values()), err_data=err_data)
         else:
-            execution_tracker = execute_job(trans, self, all_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info)
-            if execution_tracker.successful_jobs:
-                return dict(out_data=execution_tracker.output_datasets,
-                            num_jobs=len(execution_tracker.successful_jobs),
-                            job_errors=execution_tracker.execution_errors,
-                            jobs=execution_tracker.successful_jobs,
-                            output_collections=execution_tracker.output_collections,
-                            implicit_collections=execution_tracker.implicit_collections)
-            else:
+            mapping_params = MappingParameters(incoming, all_params)
+            execution_tracker = execute_job(trans, self, mapping_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info)
+            # Raise an exception if there were jobs to execute and none of them were submitted,
+            # if at least one is submitted or there are no jobs to execute - return aggregate
+            # information including per-job errors. Arguably we should just always return the
+            # aggregate information - we just haven't done that historically.
+            raise_execution_exception = not execution_tracker.successful_jobs and len(all_params) > 0
+
+            if raise_execution_exception:
                 raise exceptions.MessageException(execution_tracker.execution_errors[0])
 
+            return dict(out_data=execution_tracker.output_datasets,
+                        num_jobs=len(execution_tracker.successful_jobs),
+                        job_errors=execution_tracker.execution_errors,
+                        jobs=execution_tracker.successful_jobs,
+                        output_collections=execution_tracker.output_collections,
+                        implicit_collections=execution_tracker.implicit_collections)
+
     def handle_single_execution(self, trans, rerun_remap_job_id, params, history, mapping_over_collection, execution_cache=None):
         """
         Return a pair with whether execution is successful as well as either
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index e6d37538110..6e217e81215 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -24,12 +24,16 @@ class PartialJobExecution(Exception):
         self.jobs = jobs
 
 
-def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None):
+MappingParameters = collections.namedtuple("MappingParameters", ["param_template", "param_combinations"])
+
+
+def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None):
     """
     Execute a tool and return object containing summary (output data, number of
     failures, etc...).
     """
     all_jobs_timer = ExecutionTimer()
+    param_combinations = mapping_params.param_combinations
     execution_tracker = ToolExecutionTracker(tool, param_combinations, collection_info)
     app = trans.app
     execution_cache = ToolExecutionCache(trans)
@@ -120,12 +124,8 @@ def execute(trans, tool, param_combinations, history, rerun_remap_job_id=None, c
     log.debug("Executed %d job(s) for tool %s request: %s" % (job_count, tool.id, all_jobs_timer))
     if collection_info:
         history = history or tool.get_default_history_by_trans(trans)
-        if len(param_combinations) == 0:
-            template = "Attempting to map over an empty collection, this is not yet implemented. collection_info is [%s]"
-            message = template % collection_info
-            log.warning(message)
-            raise Exception(message)
-        params = param_combinations[0]
+        # TODO: this perhaps should always just be the param_template. Going to try to be safe first. -John
+        params = param_combinations[0] if param_combinations else mapping_params.param_template
         execution_tracker.create_output_collections(trans, history, params)
 
     return execution_tracker
@@ -196,13 +196,13 @@ class ToolExecutionTracker(object):
         collections = {}
 
         implicit_inputs = list(self.collection_info.collections.items())
-        for output_name, outputs in self.outputs_by_output_name.items():
+        for output_name, output in self.tool.outputs.items():
+            outputs = self.outputs_by_output_name[output_name]
             if not len(structure) == len(outputs):
                 # Output does not have the same structure, if all jobs were
                 # successfully submitted this shouldn't have happened.
                 log.warning("Problem matching up datasets while attempting to create implicit dataset collections")
                 continue
-            output = self.tool.outputs[output_name]
 
             element_identifiers = None
             if hasattr(output, "default_identifier_source"):
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 7abc55636a5..0ad4609b915 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -21,7 +21,7 @@ from galaxy.tools import (
     DefaultToolState,
     ToolInputsNotReadyException
 )
-from galaxy.tools.execute import execute, PartialJobExecution
+from galaxy.tools.execute import execute, MappingParameters, PartialJobExecution
 from galaxy.tools.parameters import (
     check_param,
     params_to_incoming,
@@ -875,10 +875,11 @@ class ToolModule(WorkflowModule):
         # workflow should be delayed.
         partial_jobs = None
         try:
+            mapping_params = MappingParameters(tool_state.inputs, param_combinations)
             execution_tracker = execute(
                 trans=self.trans,
                 tool=tool,
-                param_combinations=param_combinations,
+                mapping_params=mapping_params,
                 history=invocation.history,
                 collection_info=collection_info,
                 workflow_invocation_uuid=invocation.uuid.hex,
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index e11ce93c8be..c3e37ff74f3 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -681,6 +681,24 @@ class ToolsTestCase(api.ApiTestCase):
         }
         self._run_and_check_simple_collection_mapping(history_id, inputs)
 
+    @skip_without_tool("cat1")
+    def test_map_over_empty_collection(self):
+        with self.dataset_populator.test_history() as history_id:
+            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[]).json()['id']
+            inputs = {
+                "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            }
+            create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
+            outputs = create['outputs']
+            jobs = create['jobs']
+            implicit_collections = create['implicit_collections']
+            self.assertEquals(len(jobs), 0)
+            self.assertEquals(len(outputs), 0)
+            self.assertEquals(len(implicit_collections), 1)
+
+            empty_output = implicit_collections[0]
+            assert empty_output["name"] == "Concatenate datasets on collection 1", empty_output
+
     @skip_without_tool("output_action_change_format")
     def test_map_over_with_output_format_actions(self):
         for use_action in ["do", "dont"]:
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 47d9820887a..876fc167269 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1272,6 +1272,86 @@ test_data:
 """, history_id=history_id, wait=True)
             self.assertEqual("chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
 
+    @skip_without_tool("empty_list")
+    @skip_without_tool("count_list")
+    @skip_without_tool("random_lines1")
+    def test_empty_list_mapping(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+outputs:
+  - id: count_list
+    source: count_list#out_file1
+steps:
+  - tool_id: empty_list
+    label: empty_list
+    state:
+      input1:
+        $link: input1
+  - tool_id: random_lines1
+    label: random_lines
+    state:
+      num_lines: 2
+      input:
+        $link: empty_list#output
+      seed_source:
+        seed_source_selector: set_seed
+        seed: asdf
+  - tool_id: count_list
+    label: count_list
+    state:
+      input1:
+        $link: random_lines#out_file1
+
+test_data:
+  input1:
+    value: 1.bed
+    type: File
+""", history_id=history_id, wait=True)
+            self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id))
+
+    @skip_without_tool("empty_list")
+    @skip_without_tool("count_multi_file")
+    @skip_without_tool("random_lines1")
+    def test_empty_list_reduction(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+outputs:
+  - id: count_multi_file
+    source: count_multi_file#out_file1
+steps:
+  - tool_id: empty_list
+    label: empty_list
+    state:
+      input1:
+        $link: input1
+  - tool_id: random_lines1
+    label: random_lines
+    state:
+      num_lines: 2
+      input:
+        $link: empty_list#output
+      seed_source:
+        seed_source_selector: set_seed
+        seed: asdf
+  - tool_id: count_multi_file
+    label: count_multi_file
+    state:
+      input1:
+        $link: random_lines#out_file1
+
+test_data:
+  input1:
+    value: 1.bed
+    type: File
+""", history_id=history_id, wait=True)
+            self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id))
+
     @skip_without_tool("cat")
     def test_cancel_new_workflow_when_history_deleted(self):
         with self.dataset_populator.test_history() as history_id:
diff --git a/test/base/populators.py b/test/base/populators.py
index b64b57ff526..45b3d1a13ec 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -615,7 +615,7 @@ class BaseDatasetCollectionPopulator(object):
         return element_identifiers
 
     def list_identifiers(self, history_id, contents=None):
-        count = 3 if not contents else len(contents)
+        count = 3 if contents is None else len(contents)
         # Contents can be a list of strings (with name auto-assigned here) or a list of
         # 2-tuples of form (name, dataset_content).
         if contents and isinstance(contents[0], tuple):
diff --git a/test/functional/tools/for_workflows/count_list.xml b/test/functional/tools/for_workflows/count_list.xml
new file mode 100644
index 00000000000..abb56f955c3
--- /dev/null
+++ b/test/functional/tools/for_workflows/count_list.xml
@@ -0,0 +1,16 @@
+<tool id="count_list" name="count_list">
+    <description>count the number of items in a list</description>
+    <command><![CDATA[
+        echo '${len($input1.keys())}' > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data_collection" label="Concatenate Dataset" collection_type="list" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/for_workflows/count_multi_file.xml b/test/functional/tools/for_workflows/count_multi_file.xml
new file mode 100644
index 00000000000..c7a2c8ce124
--- /dev/null
+++ b/test/functional/tools/for_workflows/count_multi_file.xml
@@ -0,0 +1,16 @@
+<tool id="count_multi_file" name="count_multi_file">
+    <description>count the number of datasets in a multiple file input</description>
+    <command><![CDATA[
+        echo '${len($input1)}' > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset" multiple="true" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/for_workflows/empty_list.xml b/test/functional/tools/for_workflows/empty_list.xml
new file mode 100644
index 00000000000..df251d5db0e
--- /dev/null
+++ b/test/functional/tools/for_workflows/empty_list.xml
@@ -0,0 +1,22 @@
+<tool id="empty_list" name="empty_list" version="0.1.0">
+  <description>always produce an empty list</description>
+  <command detect_errors="exit_code">
+      mkdir outputs;
+      cd outputs;
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="txt" label="Input Text" />
+  </inputs>
+  <outputs>
+    <collection name="output" type="list" label="lines">
+      <discover_datasets pattern="__name__" directory="outputs" />
+    </collection>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="simple_lines_both.txt" />
+      <output_collection name="output" type="list" count="0">
+      </output_collection>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 88ecc25f816..a469930b9c3 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -140,6 +140,9 @@
   <tool file="for_workflows/mapper.xml" />
   <tool file="for_workflows/mapper2.xml" />
   <tool file="for_workflows/split.xml" />
+  <tool file="for_workflows/empty_list.xml" />
+  <tool file="for_workflows/count_list.xml" />
+  <tool file="for_workflows/count_multi_file.xml" />
   <tool file="for_workflows/create_input_collection.xml" />
 
   <section id="filter" name="For Tours">

From 53cba4aa74b0d2543445824a7636f92249baa150 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 5 Oct 2017 14:39:53 -0400
Subject: [PATCH 11/22] Refactor collection manager into smaller, more focused
 methods.

Stronger assertions to verify arguments are correct.
---
 lib/galaxy/managers/collections.py | 50 +++++++++++++++++++-----------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 0e6420a43c3..c0e57fc9e51 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -105,37 +105,29 @@ class DatasetCollectionManager(object):
             message = "Internal logic error - create called with unknown parent type %s" % type(parent)
             log.exception(message)
             raise MessageException(message)
-        tags = tags or {}
-        if implicit_collection_info:
-            for _, v in implicit_collection_info.get('implicit_inputs', []):
-                for tag in [t for t in v.tags if t.user_tname == 'name']:
-                    tags[tag.value] = tag
-        for _, tag in tags.items():
-            dataset_collection_instance.tags.append(tag.copy(cls=model.HistoryDatasetCollectionTagAssociation))
 
+        implicit_inputs = []
+        if implicit_collection_info:
+            implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
+        tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
         return self.__persist(dataset_collection_instance)
 
     def create_dataset_collection(self, trans, collection_type, element_identifiers=None, elements=None,
                                   hide_source_items=None):
+        # Make sure at least one of these is None.
+        assert element_identifiers is None or elements is None
+
         if element_identifiers is None and elements is None:
             raise RequestParameterInvalidException(ERROR_INVALID_ELEMENTS_SPECIFICATION)
         if not collection_type:
             raise RequestParameterInvalidException(ERROR_NO_COLLECTION_TYPE)
+
         collection_type_description = self.collection_type_descriptions.for_collection_type(collection_type)
+
         # If we have elements, this is an internal request, don't need to load
         # objects from identifiers.
         if elements is None:
-            if collection_type_description.has_subcollections():
-                # Nested collection - recursively create collections and update identifiers.
-                self.__recursively_create_collections(trans, element_identifiers)
-            new_collection = False
-            for element_identifier in element_identifiers:
-                if element_identifier.get("src") == "new_collection" and element_identifier.get('collection_type') == '':
-                    new_collection = True
-                    elements = self.__load_elements(trans, element_identifier['element_identifiers'])
-            if not new_collection:
-                elements = self.__load_elements(trans, element_identifiers)
-
+            elements = self._element_identifiers_to_elements(trans, collection_type_description, element_identifiers)
         # else if elements is set, it better be an ordered dict!
 
         if elements is not self.ELEMENTS_UNINITIALIZED:
@@ -150,6 +142,28 @@ class DatasetCollectionManager(object):
         dataset_collection.collection_type = collection_type
         return dataset_collection
 
+    def _element_identifiers_to_elements(self, trans, collection_type_description, element_identifiers):
+        if collection_type_description.has_subcollections():
+            # Nested collection - recursively create collections and update identifiers.
+            self.__recursively_create_collections(trans, element_identifiers)
+        new_collection = False
+        for element_identifier in element_identifiers:
+            if element_identifier.get("src") == "new_collection" and element_identifier.get('collection_type') == '':
+                new_collection = True
+                elements = self.__load_elements(trans, element_identifier['element_identifiers'])
+        if not new_collection:
+            elements = self.__load_elements(trans, element_identifiers)
+        return elements
+
+    def _append_tags(self, dataset_collection_instance, implicit_inputs=None, tags=None):
+        tags = tags or {}
+        implicit_inputs = implicit_inputs or []
+        for _, v in implicit_inputs:
+            for tag in [t for t in v.tags if t.user_tname == 'name']:
+                tags[tag.value] = tag
+        for _, tag in tags.items():
+            dataset_collection_instance.tags.append(tag.copy(cls=model.HistoryDatasetCollectionTagAssociation))
+
     def set_collection_elements(self, dataset_collection, dataset_instances):
         if dataset_collection.populated:
             raise Exception("Cannot reset elements of an already populated dataset collection.")

From 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 4 Oct 2017 14:01:51 -0400
Subject: [PATCH 12/22] Pre-build collections during mapping to be more
 recoverable.

Create mapped over collections ahead of time instead of at the end only if they are valid.

- This way if there is a problem that problem can be reported in the state of the mapped collection.
- This way datasets can just be hidden instead of displayed and then hidden (fixes #1790).
- I think this should improve performance and prevent locks because we no longer have conflicting threads trying to write dataset state.
- We populate the collection as we go so we can recover and continue scheduling the mapped step (needed for #3883)
---
 lib/galaxy/dataset_collections/matching.py    |   8 +-
 lib/galaxy/dataset_collections/structure.py   |  88 +++-
 .../dataset_collections/type_description.py   |   1 +
 lib/galaxy/managers/collections.py            |  65 ++-
 lib/galaxy/managers/collections_util.py       |  16 +-
 lib/galaxy/model/__init__.py                  |  21 +-
 lib/galaxy/tools/__init__.py                  |  15 +-
 lib/galaxy/tools/actions/__init__.py          |  21 +-
 lib/galaxy/tools/actions/model_operations.py  |   4 +-
 lib/galaxy/tools/execute.py                   | 416 ++++++++++++------
 lib/galaxy/tools/parser/output_objects.py     |   5 +-
 lib/galaxy/workflow/modules.py                |  32 +-
 lib/galaxy/workflow/run.py                    |  29 +-
 test/api/test_tools.py                        |   2 +-
 test/api/test_workflow_extraction.py          |   2 +-
 test/api/test_workflows.py                    |   8 +-
 test/base/populators.py                       |  17 +
 .../unit/dataset_collections/test_matching.py |   1 +
 18 files changed, 516 insertions(+), 235 deletions(-)

diff --git a/lib/galaxy/dataset_collections/matching.py b/lib/galaxy/dataset_collections/matching.py
index 94b4f2d5d66..aa62b626a9f 100644
--- a/lib/galaxy/dataset_collections/matching.py
+++ b/lib/galaxy/dataset_collections/matching.py
@@ -44,23 +44,29 @@ class MatchingCollections(object):
         self.linked_structure = None
         self.unlinked_structures = []
         self.collections = {}
+        self.subcollection_types = {}
 
     def __attempt_add_to_linked_match(self, input_name, hdca, collection_type_description, subcollection_type):
         structure = get_structure(hdca, collection_type_description, leaf_subcollection_type=subcollection_type)
         if not self.linked_structure:
             self.linked_structure = structure
             self.collections[input_name] = hdca
+            self.subcollection_types[input_name] = subcollection_type
         else:
             if not self.linked_structure.can_match(structure):
                 raise exceptions.MessageException(CANNOT_MATCH_ERROR_MESSAGE)
             self.collections[input_name] = hdca
+            self.subcollection_types[input_name] = subcollection_type
 
     def slice_collections(self):
         return self.linked_structure.walk_collections(self.collections)
 
+    def subcollection_mapping_type(self, input_name):
+        return self.subcollection_types[input_name]
+
     @property
     def structure(self):
-        """Yield cross product of all unlinked datasets to linked dataset."""
+        """Yield cross product of all unlinked collections structures to linked collection structure."""
         effective_structure = leaf
         for unlinked_structure in self.unlinked_structures:
             effective_structure = effective_structure.multiply(unlinked_structure)
diff --git a/lib/galaxy/dataset_collections/structure.py b/lib/galaxy/dataset_collections/structure.py
index 3278dd65e40..19058b15b42 100644
--- a/lib/galaxy/dataset_collections/structure.py
+++ b/lib/galaxy/dataset_collections/structure.py
@@ -1,12 +1,17 @@
 """ Module for reasoning about structure of and matching hierarchical collections of data.
 """
 import logging
-log = logging.getLogger(__name__)
+
+import six
 
 from .type_description import map_over_collection_type
 
+log = logging.getLogger(__name__)
 
+
+@six.python_2_unicode_compatible
 class Leaf(object):
+    children_known = True
 
     def __len__(self):
         return 1
@@ -18,18 +23,60 @@ class Leaf(object):
     def clone(self):
         return self
 
-    def multiply(self, other_structure):
-        return other_structure.clone()
+    def multiply(self, other_structure, uninitialized=False):
+        if not uninitialized:
+            return other_structure.clone()
+        else:
+            return UnitializedTree(other_structure.collection_type_description)
+
+    def sliced_collection_type(self, collection):
+        return input
+
+    def __str__(self):
+        return "Leaf[]"
 
 
 leaf = Leaf()
 
 
-class Tree(object):
+class BaseTree(object):
+
+    def __init__(self, collection_type_description):
+        self.collection_type_description = collection_type_description
+
+
+@six.python_2_unicode_compatible
+class UnitializedTree(BaseTree):
+    children_known = False
+
+    def clone(self):
+        return self
+
+    @property
+    def is_leaf(self):
+        return False
+
+    def __len__(self):
+        raise Exception("Unknown length")
+
+    def multiply(self, other_structure, uninitialized=False):
+        if other_structure.is_leaf:
+            return self.clone()
+
+        new_collection_type = self.collection_type_description.multiply(other_structure.collection_type_description)
+        return UnitializedTree(new_collection_type)
+
+    def __str__(self):
+        return "UnitializedTree[collection_type=%s]" % self.collection_type_description
+
+
+@six.python_2_unicode_compatible
+class Tree(BaseTree):
+    children_known = True
 
     def __init__(self, children, collection_type_description):
+        super(Tree, self).__init__(collection_type_description)
         self.children = children
-        self.collection_type_description = collection_type_description
 
     @staticmethod
     def for_dataset_collection(dataset_collection, collection_type_description):
@@ -107,14 +154,14 @@ class Tree(object):
             element_identifiers=element_identifiers,
         )
 
-    def multiply(self, other_structure):
+    def multiply(self, other_structure, uninitialized=False):
         if other_structure.is_leaf:
             return self.clone()
 
         new_collection_type = self.collection_type_description.multiply(other_structure.collection_type_description)
         new_children = []
         for (identifier, structure) in self.children:
-            new_children.append((identifier, structure.multiply(other_structure)))
+            new_children.append((identifier, structure.multiply(other_structure, uninitialized=uninitialized)))
 
         return Tree(new_children, new_collection_type)
 
@@ -122,6 +169,30 @@ class Tree(object):
         cloned_children = [(_[0], _[1].clone()) for _ in self.children]
         return Tree(cloned_children, self.collection_type_description)
 
+    def __str__(self):
+        return "Tree[collection_type=%s,children=%s]" % (self.collection_type_description, ",".join(map(lambda identifier_and_element: "%s=%s" % (identifier_and_element[0], identifier_and_element[1]), self.children)))
+
+
+def tool_output_to_structure(get_sliced_input_collection_type, tool_output, collections_manager):
+    if not tool_output.collection:
+        tree = leaf
+    else:
+        collection_type_descriptions = collections_manager.collection_type_descriptions
+        # Okay this is ToolCollectionOutputStructure not a Structure - different
+        # concepts of structure.
+        if tool_output.dynamic_structure:
+            # Two cases collection_type_source and collection_type right?
+            tree = UnitializedTree(collection_type_descriptions.for_type_description("list"))  # list is obviously wrong...
+        else:
+            structured_like = tool_output.structure.structured_like
+            if structured_like:
+                collection_type = get_sliced_input_collection_type(structured_like)
+            else:
+                collection_type = tool_output.structure.collection_type
+            tree = UnitializedTree(collection_type)
+
+    return tree
+
 
 def dict_map(func, input_dict):
     return dict((k, func(v)) for k, v in input_dict.items())
@@ -131,4 +202,5 @@ def get_structure(dataset_collection_instance, collection_type_description, leaf
     if leaf_subcollection_type:
         collection_type_description = collection_type_description.effective_collection_type_description(leaf_subcollection_type)
 
-    return Tree.for_dataset_collection(dataset_collection_instance.collection, collection_type_description)
+    collection = dataset_collection_instance.collection
+    return Tree.for_dataset_collection(collection, collection_type_description)
diff --git a/lib/galaxy/dataset_collections/type_description.py b/lib/galaxy/dataset_collections/type_description.py
index f7b8bed1eb7..ee76a4609b5 100644
--- a/lib/galaxy/dataset_collections/type_description.py
+++ b/lib/galaxy/dataset_collections/type_description.py
@@ -8,6 +8,7 @@ class CollectionTypeDescriptionFactory(object):
         self.type_registry = type_registry
 
     def for_collection_type(self, collection_type):
+        assert collection_type is not None
         return CollectionTypeDescription(collection_type, self)
 
 
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index c0e57fc9e51..8939eae80a8 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -46,6 +46,37 @@ class DatasetCollectionManager(object):
         self.tag_manager = tags.GalaxyTagManager(app.model.context)
         self.ldda_manager = lddas.LDDAManager(app)
 
+    def precreate_dataset_collection_instance(self, trans, parent, name, implicit_inputs, implicit_output_name, structure):
+        dataset_collection = self.precreate_dataset_collection(structure)
+        return self._create_instance_for_collection(
+            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name,
+        )
+
+    def precreate_dataset_collection(self, structure):
+        if structure.is_leaf or not structure.children_known:
+            return model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
+        else:
+            collection_type_description = structure.collection_type_description
+            dataset_collection = model.DatasetCollection(populated=False)
+            dataset_collection.collection_type = collection_type_description.collection_type
+            elements = []
+            for index, (identifier, substructure) in enumerate(structure.children):
+                # TODO: Open question - populate these now or later?
+                if substructure.is_leaf:
+                    element = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
+                else:
+                    element = self.precreate_dataset_collection(substructure)
+
+                element = model.DatasetCollectionElement(
+                    element=element,
+                    element_identifier=identifier,
+                    element_index=index,
+                )
+                elements.append(element)
+            dataset_collection.elements = elements
+
+            return dataset_collection
+
     def create(self, trans, parent, name, collection_type, element_identifiers=None,
                elements=None, implicit_collection_info=None, trusted_identifiers=None,
                hide_source_items=False, tags=None):
@@ -68,27 +99,30 @@ class DatasetCollectionManager(object):
             hide_source_items=hide_source_items,
         )
 
+        implicit_inputs = []
+        if implicit_collection_info:
+            implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
+
+        implicit_output_name = None
+        if implicit_collection_info:
+            implicit_output_name = implicit_collection_info["implicit_output_name"]
+
+        return self._create_instance_for_collection(
+            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags
+        )
+
+    def _create_instance_for_collection(self, trans, parent, name, dataset_collection, implicit_output_name=None, implicit_inputs=None, tags=None):
         if isinstance(parent, model.History):
             dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
                 collection=dataset_collection,
                 name=name,
             )
-            if implicit_collection_info:
-                for input_name, input_collection in implicit_collection_info["implicit_inputs"]:
+            if implicit_inputs:
+                for input_name, input_collection in implicit_inputs:
                     dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
-                for output_dataset in implicit_collection_info.get("outputs"):
-                    if output_dataset not in trans.sa_session:
-                        output_dataset = trans.sa_session.query(type(output_dataset)).get(output_dataset.id)
-                    if isinstance(output_dataset, model.HistoryDatasetAssociation):
-                        output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
-                    elif isinstance(output_dataset, model.HistoryDatasetCollectionAssociation):
-                        dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
-                    else:
-                        # dataset collection, don't need to do anything...
-                        pass
-                    trans.sa_session.add(output_dataset)
 
-                dataset_collection_instance.implicit_output_name = implicit_collection_info["implicit_output_name"]
+            if implicit_output_name:
+                dataset_collection_instance.implicit_output_name = implicit_output_name
 
             log.debug("Created collection with %d elements" % (len(dataset_collection_instance.collection.elements)))
             # Handle setting hid
@@ -106,9 +140,6 @@ class DatasetCollectionManager(object):
             log.exception(message)
             raise MessageException(message)
 
-        implicit_inputs = []
-        if implicit_collection_info:
-            implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
         tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
         return self.__persist(dataset_collection_instance)
 
diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py
index 831a7b8cdb7..190cbd2b929 100644
--- a/lib/galaxy/managers/collections_util.py
+++ b/lib/galaxy/managers/collections_util.py
@@ -122,12 +122,16 @@ def dictify_dataset_collection_instance(dataset_collection_instance, parent, sec
 
 def dictify_element(element):
     dictified = element.to_dict(view="element")
-    object_detials = element.element_object.to_dict()
-    if element.child_collection:
-        # Recursively yield elements for each nested collection...
-        child_collection = element.child_collection
-        object_detials["elements"] = [dictify_element(_) for _ in child_collection.elements]
-        object_detials["populated"] = child_collection.populated
+    element_object = element.element_object
+    if element_object is not None:
+        object_detials = element.element_object.to_dict()
+        if element.child_collection:
+            # Recursively yield elements for each nested collection...
+            child_collection = element.child_collection
+            object_detials["elements"] = [dictify_element(_) for _ in child_collection.elements]
+            object_detials["populated"] = child_collection.populated
+    else:
+        object_detials = None
 
     dictified["object"] = object_detials
     return dictified
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 707f96cbdbf..019dcae1530 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3218,6 +3218,15 @@ class DatasetCollection(object, Dictifiable, UsesAnnotations):
         self.populated_state = DatasetCollection.populated_states.FAILED
         self.populated_state_message = message
 
+    def finalize(self):
+        # All jobs have written out their elements - everything should be populated
+        # but might not be - check that second case! (TODO)
+        self.mark_as_populated()
+        if self.has_subcollections:
+            # THIS IS WRONG - SHOULD ONLY BE TO THE DEPTH OF THE MAP OVER.
+            for element in self.elements:
+                element.child_collection.finalize()
+
     @property
     def dataset_instances(self):
         instances = []
@@ -3485,6 +3494,8 @@ class DatasetCollectionElement(object, Dictifiable):
     dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
     dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
 
+    UNINITIALIZED_ELEMENT = object()
+
     def __init__(
         self,
         id=None,
@@ -3499,7 +3510,7 @@ class DatasetCollectionElement(object, Dictifiable):
             self.ldda = element
         elif isinstance(element, DatasetCollection):
             self.child_collection = element
-        else:
+        elif element != self.UNINITIALIZED_ELEMENT:
             raise AttributeError('Unknown element type provided: %s' % type(element))
 
         self.id = id
@@ -3517,7 +3528,7 @@ class DatasetCollectionElement(object, Dictifiable):
             # TOOD: Rename element_type to element_type.
             return "dataset_collection"
         else:
-            raise Exception("Unknown element instance type")
+            return None
 
     @property
     def is_collection(self):
@@ -3532,7 +3543,7 @@ class DatasetCollectionElement(object, Dictifiable):
         elif self.child_collection:
             return self.child_collection
         else:
-            raise Exception("Unknown element instance type")
+            return None
 
     @property
     def dataset_instance(self):
@@ -4194,6 +4205,10 @@ class WorkflowInvocationStep(object, Dictifiable):
     def update(self):
         self.workflow_invocation.update()
 
+    @property
+    def is_new(self):
+        return self.state == self.states.NEW
+
     def add_output(self, output_name, output_object):
         if output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationStepOutputDatasetAssociation()
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 9731214c194..4d872d4fc60 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1314,13 +1314,20 @@ class Tool(object, Dictifiable):
                         output_collections=execution_tracker.output_collections,
                         implicit_collections=execution_tracker.implicit_collections)
 
-    def handle_single_execution(self, trans, rerun_remap_job_id, params, history, mapping_over_collection, execution_cache=None):
+    def handle_single_execution(self, trans, rerun_remap_job_id, execution_slice, history, execution_cache=None):
         """
         Return a pair with whether execution is successful as well as either
         resulting output data or an error message indicating the problem.
         """
         try:
-            job, out_data = self.execute(trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id, mapping_over_collection=mapping_over_collection, execution_cache=execution_cache)
+            job, out_data = self.execute(
+                trans,
+                incoming=execution_slice.param_combination,
+                history=history,
+                rerun_remap_job_id=rerun_remap_job_id,
+                execution_cache=execution_cache,
+                dataset_collection_elements=execution_slice.dataset_collection_elements,
+            )
         except httpexceptions.HTTPFound as e:
             # if it's a paste redirect exception, pass it up the stack
             raise e
@@ -2263,7 +2270,7 @@ class DatabaseOperationTool(Tool):
     def check_inputs_ready(self, input_datasets, input_dataset_collections):
         def check_dataset_instance(input_dataset):
             if input_dataset.is_pending:
-                raise ToolInputsNotReadyException()
+                raise ToolInputsNotReadyException("An input dataset is pending.")
 
             if self.require_dataset_ok:
                 if input_dataset.state != input_dataset.dataset.states.OK:
@@ -2275,7 +2282,7 @@ class DatabaseOperationTool(Tool):
         for input_dataset_collection_pairs in input_dataset_collections.values():
             for input_dataset_collection, is_mapped in input_dataset_collection_pairs:
                 if not input_dataset_collection.collection.populated:
-                    raise ToolInputsNotReadyException()
+                    raise ToolInputsNotReadyException("An input collection is not populated.")
 
             map(check_dataset_instance, input_dataset_collection.dataset_instances)
 
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 66bbac2c78a..14bd8f54452 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -195,7 +195,7 @@ class DefaultToolAction(object):
 
         return history, inp_data, inp_dataset_collections
 
-    def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, mapping_over_collection=False, execution_cache=None):
+    def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, execution_cache=None, dataset_collection_elements=None):
         """
         Executes a tool, creating job and tool outputs, associating them, and
         submitting the job to the job queue. If history is not specified, use
@@ -267,7 +267,7 @@ class DefaultToolAction(object):
             tool=tool,
             tool_action=self,
             input_collections=input_collections,
-            mapping_over_collection=mapping_over_collection,
+            dataset_collection_elements=dataset_collection_elements,
             on_text=on_text,
             incoming=incoming,
             params=wrapped_params.params,
@@ -304,8 +304,12 @@ class DefaultToolAction(object):
                 data = app.model.HistoryDatasetAssociation(extension=ext, create_dataset=True, flush=False)
                 if hidden is None:
                     hidden = output.hidden
+                if not hidden and dataset_collection_elements is not None:  # Mapping over a collection - hide datasets
+                    hidden = True
                 if hidden:
                     data.visible = False
+                if dataset_collection_elements is not None and name in dataset_collection_elements:
+                    dataset_collection_elements[name].hda = data
                 trans.sa_session.add(data)
                 trans.app.security_agent.set_all_dataset_permissions(data.dataset, output_permissions, new=True)
             for _, tag in preserved_tags.items():
@@ -351,6 +355,7 @@ class DefaultToolAction(object):
 
         for name, output in tool.outputs.items():
             if not filter_output(output, incoming):
+                handle_output_timer = ExecutionTimer()
                 if output.collection:
                     collections_manager = app.dataset_collections_service
                     element_identifiers = []
@@ -402,15 +407,14 @@ class DefaultToolAction(object):
                         element_kwds = dict(elements=collections_manager.ELEMENTS_UNINITIALIZED)
                     else:
                         element_kwds = dict(element_identifiers=element_identifiers)
-
                     output_collections.create_collection(
                         output=output,
                         name=name,
                         tags=preserved_tags,
                         **element_kwds
                     )
+                    log.info("Handled collection output named %s for tool %s %s" % (name, tool.id, handle_output_timer))
                 else:
-                    handle_output_timer = ExecutionTimer()
                     handle_output(name, output)
                     log.info("Handled output named %s for tool %s %s" % (name, tool.id, handle_output_timer))
 
@@ -670,13 +674,13 @@ class OutputCollections(object):
     parameter).
     """
 
-    def __init__(self, trans, history, tool, tool_action, input_collections, mapping_over_collection, on_text, incoming, params, job_params):
+    def __init__(self, trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params):
         self.trans = trans
         self.history = history
         self.tool = tool
         self.tool_action = tool_action
         self.input_collections = input_collections
-        self.mapping_over_collection = mapping_over_collection
+        self.dataset_collection_elements = dataset_collection_elements
         self.on_text = on_text
         self.incoming = incoming
         self.params = params
@@ -710,12 +714,15 @@ class OutputCollections(object):
                         for dataset in value.dataset_instances:
                             assert dataset.history is not None
 
-        if self.mapping_over_collection:
+        if self.dataset_collection_elements is not None:
             dc = collections_manager.create_dataset_collection(
                 self.trans,
                 collection_type=collection_type,
                 **element_kwds
             )
+            if name in self.dataset_collection_elements:
+                self.dataset_collection_elements[name].child_collection = dc
+                # self.trans.sa_session.add(self.dataset_collection_elements[name])
             self.out_collections[name] = dc
         else:
             hdca_name = self.tool_action.get_output_name(
diff --git a/lib/galaxy/tools/actions/model_operations.py b/lib/galaxy/tools/actions/model_operations.py
index 4edcd6ce141..842a3c085d5 100644
--- a/lib/galaxy/tools/actions/model_operations.py
+++ b/lib/galaxy/tools/actions/model_operations.py
@@ -21,7 +21,7 @@ class ModelOperationToolAction(DefaultToolAction):
 
         tool.check_inputs_ready(inp_data, inp_dataset_collections)
 
-    def execute(self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, mapping_over_collection=False, execution_cache=None, **kwargs):
+    def execute(self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, execution_cache=None, **kwargs):
         if execution_cache is None:
             execution_cache = ToolExecutionCache(trans)
 
@@ -42,7 +42,7 @@ class ModelOperationToolAction(DefaultToolAction):
             tool=tool,
             tool_action=self,
             input_collections=input_collections,
-            mapping_over_collection=mapping_over_collection,
+            dataset_collection_elements=kwargs.get("dataset_collection_elements", None),
             on_text=on_text,
             incoming=incoming,
             params=wrapped_params.params,
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 6e217e81215..34794d6d338 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -4,12 +4,15 @@ from various states, tracking results, and building implicit dataset
 collections from matched collections.
 """
 import collections
+import itertools
 import logging
 from threading import Thread
 
 from six.moves.queue import Queue
 
-from galaxy.tools.actions import on_text_for_names, ToolExecutionCache
+from galaxy import model
+from galaxy.dataset_collections.structure import tool_output_to_structure
+from galaxy.tools.actions import filter_output, on_text_for_names, ToolExecutionCache
 from galaxy.tools.parser import ToolOutputCollectionPart
 from galaxy.util import ExecutionTimer
 
@@ -20,47 +23,49 @@ EXECUTION_SUCCESS_MESSAGE = "Tool [%s] created job [%s] %s"
 
 class PartialJobExecution(Exception):
 
-    def __init__(self, jobs):
-        self.jobs = jobs
+    def __init__(self):
+        pass
 
 
 MappingParameters = collections.namedtuple("MappingParameters", ["param_template", "param_combinations"])
 
 
-def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None):
+def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None, job_callback=None):
     """
     Execute a tool and return object containing summary (output data, number of
     failures, etc...).
     """
+    if max_num_jobs:
+        assert invocation_step is not None
+    if rerun_remap_job_id:
+        assert invocation_step is None
+
     all_jobs_timer = ExecutionTimer()
-    param_combinations = mapping_params.param_combinations
-    execution_tracker = ToolExecutionTracker(tool, param_combinations, collection_info)
+    if invocation_step is None:
+        execution_tracker = ToolExecutionTracker(tool, mapping_params, collection_info)
+    else:
+        execution_tracker = WorkflowStepExecutionTracker(tool, mapping_params, collection_info, invocation_step, job_callback=job_callback)
     app = trans.app
     execution_cache = ToolExecutionCache(trans)
 
-    new_jobs = []
-
-    def execute_single_job(params):
+    def execute_single_job(execution_slice):
         job_timer = ExecutionTimer()
+        params = execution_slice.param_combination
         if workflow_invocation_uuid:
             params['__workflow_invocation_uuid__'] = workflow_invocation_uuid
         elif '__workflow_invocation_uuid__' in params:
             # Only workflow invocation code gets to set this, ignore user supplied
             # values or rerun parameters.
             del params['__workflow_invocation_uuid__']
-        job, result = tool.handle_single_execution(trans, rerun_remap_job_id, params, history, collection_info, execution_cache)
+
+        job, result = tool.handle_single_execution(trans, rerun_remap_job_id, execution_slice, history, execution_cache)
         if job:
             message = EXECUTION_SUCCESS_MESSAGE % (tool.id, job.id, job_timer)
             log.debug(message)
-            execution_tracker.record_success(job, result)
-            new_jobs.append(job)
+            execution_tracker.record_success(execution_slice, job, result)
         else:
             execution_tracker.record_error(result)
 
-    config = app.config
-    burst_at = getattr(config, 'tool_submission_burst_at', 10)
-    burst_threads = getattr(config, 'tool_submission_burst_threads', 1)
-
     tool_action = tool.tool_action
     if hasattr(tool_action, "check_inputs_ready"):
         for params in execution_tracker.param_combinations:
@@ -72,24 +77,23 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
                 history
             )
 
-    if invocation_step:
-        execution_tracker.recover_successful_jobs(invocation_step)
+    execution_tracker.ensure_implicit_collections_populated(trans, history, mapping_params.param_template)
+    config = app.config
+    burst_at = getattr(config, 'tool_submission_burst_at', 10)
+    burst_threads = getattr(config, 'tool_submission_burst_threads', 1)
 
-    previously_executed_jobs_count = len(execution_tracker.successful_jobs)
     job_count = len(execution_tracker.param_combinations)
 
     jobs_executed = 0
     has_remaining_jobs = False
 
     if (job_count < burst_at or burst_threads < 2):
-        for index, params in enumerate(execution_tracker.param_combinations):
-            if index < previously_executed_jobs_count:
-                continue
-            elif max_num_jobs and jobs_executed >= max_num_jobs:
+        for execution_slice in execution_tracker.new_execution_slices():
+            if max_num_jobs and jobs_executed >= max_num_jobs:
                 has_remaining_jobs = True
                 break
             else:
-                execute_single_job(params)
+                execute_single_job(execution_slice)
                 jobs_executed += 1
     else:
         # TODO: re-record success...
@@ -106,59 +110,240 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
             t.daemon = True
             t.start()
 
-        for index, params in enumerate(execution_tracker.param_combinations):
-            if index < previously_executed_jobs_count:
-                continue
-            elif max_num_jobs and jobs_executed >= max_num_jobs:
+        for execution_slice in execution_tracker.new_execution_slices():
+            if max_num_jobs and jobs_executed >= max_num_jobs:
                 has_remaining_jobs = True
                 break
             else:
-                q.put(params)
+                q.put(execution_slice)
                 jobs_executed += 1
 
         q.join()
 
     if has_remaining_jobs:
-        raise PartialJobExecution(new_jobs)
+        raise PartialJobExecution()
+    else:
+        execution_tracker.finalize_dataset_collections(trans)
 
     log.debug("Executed %d job(s) for tool %s request: %s" % (job_count, tool.id, all_jobs_timer))
-    if collection_info:
-        history = history or tool.get_default_history_by_trans(trans)
-        # TODO: this perhaps should always just be the param_template. Going to try to be safe first. -John
-        params = param_combinations[0] if param_combinations else mapping_params.param_template
-        execution_tracker.create_output_collections(trans, history, params)
-
     return execution_tracker
 
 
-class ToolExecutionTracker(object):
+class ExecutionSlice(object):
 
-    def __init__(self, tool, param_combinations, collection_info):
+    def __init__(self, job_index, param_combination, dataset_collection_elements=None):
+        self.job_index = job_index
+        self.param_combination = param_combination
+        self.dataset_collection_elements = dataset_collection_elements
+
+
+class ExecutionTracker(object):
+
+    def __init__(self, tool, mapping_params, collection_info):
+        # Known ahead of time...
         self.tool = tool
-        self.param_combinations = param_combinations
+        self.mapping_params = mapping_params
         self.collection_info = collection_info
-        self.successful_jobs = []
+
+        self._on_text = None
+
+        # Populated as we go...
         self.failed_jobs = 0
         self.execution_errors = []
+
+        self.successful_jobs = []
         self.output_datasets = []
         self.output_collections = []
-        self.outputs_by_output_name = collections.defaultdict(list)
+
         self.implicit_collections = {}
 
-    def recover_successful_jobs(self, invocation_step):
-        # TODO: Optimize away the need to do this - we should just be dealing with IDs
-        # and such and we shouldn't fetch them until the very end when we need them to create
-        # collections.
-        for job_assoc in invocation_step.jobs:
-            job = job_assoc.job
-            for job_output in job.output_datasets:
-                self.outputs_by_output_name[job_output.name].append(job_output.dataset)
-            for job_output in job.output_dataset_collections:
-                self.outputs_by_output_name[job_output.name].append(job_output.dataset_collection)
+    @property
+    def param_combinations(self):
+        return self.mapping_params.param_combinations
 
-    def record_success(self, job, outputs):
+    @property
+    def example_params(self):
+        if self.mapping_params.param_combinations:
+            return self.mapping_params.param_combinations[0]
+        else:
+            # TODO: This isn't quite right - what we want is something like param_template wrapped,
+            # need a test case with an output filter applied to an empty list, still this is
+            # an improvement over not allowing mapping of empty lists.
+            return self.mapping_params.param_template
+
+    @property
+    def job_count(self):
+        return len(self.param_combinations)
+
+    def record_error(self, error):
+        self.failed_jobs += 1
+        message = "There was a failure executing a job for tool [%s] - %s"
+        log.warning(message, self.tool.id, error)
+        self.execution_errors.append(error)
+
+    @property
+    def on_text(self):
+        if self._on_text is None:
+            collection_names = ["collection %d" % c.hid for c in self.collection_info.collections.values()]
+            self._on_text = on_text_for_names(collection_names)
+
+        return self._on_text
+
+    def output_name(self, trans, history, params, output):
+        on_text = self.on_text
+
+        try:
+            output_collection_name = self.tool.tool_action.get_output_name(
+                output,
+                dataset=None,
+                tool=self.tool,
+                on_text=on_text,
+                trans=trans,
+                history=history,
+                params=params,
+                incoming=None,
+                job_params=None,
+            )
+        except Exception:
+            output_collection_name = "%s across %s" % (self.tool.name, on_text)
+
+        return output_collection_name
+
+    def sliced_input_collection_type(self, input_name):
+        if self.is_implicit_input(input_name):
+            subcollection_mapping_type = self.collection_info.subcollection_mapping_type(input_name)
+            return subcollection_mapping_type
+            # return self.collection_info.structure.sliced_input_collection_type(self.implicit_inputs[input_name])
+        else:
+            return self.mapping_params.param_template[input_name].collection.collection_type
+
+    def _structure_for_output(self, trans, tool_output):
+        structure = self.collection_info.structure
+        if hasattr(tool_output, "default_identifier_source"):
+            # Switch the structure for outputs if the output specified a default_identifier_source
+            collection_type_descriptions = trans.app.dataset_collections_service.collection_type_descriptions
+
+            source_collection = self.collection_info.collections.get(tool_output.default_identifier_source)
+            if source_collection:
+                collection_type_description = collection_type_descriptions.for_collection_type(source_collection.collection.collection_type)
+                _structure = structure.for_dataset_collection(source_collection.collection, collection_type_description=collection_type_description)
+                if structure.can_match(_structure):
+                    structure = _structure
+
+        return structure
+
+    def _element_identifiers_for_output(self, trans, tool_output, outputs):
+        output_structure = self._structure_for_output(trans, tool_output)
+        element_identifiers = output_structure.element_identifiers_for_outputs(trans, outputs)
+        return element_identifiers
+
+    def _mapped_output_structure(self, trans, tool_output):
+        collections_manager = trans.app.dataset_collections_service
+        output_structure = tool_output_to_structure(self.sliced_input_collection_type, tool_output, collections_manager)
+        mapping_structure = self._structure_for_output(trans, tool_output)
+        # Output structure may not be known, but input structure must be,
+        # otherwise this step of the workflow shouldn't have been scheduled
+        # or the tool should not have been executable on this input.
+        mapped_output_structure = mapping_structure.multiply(output_structure, uninitialized=True)
+        return mapped_output_structure
+
+    def ensure_implicit_collections_populated(self, trans, history, params):
+        if not self.collection_info:
+            return
+
+        history = history or self.tool.get_default_history_by_trans(trans)
+        # params = param_combinations[0] if param_combinations else mapping_params.param_template
+        self.precreate_output_collections(trans, history, params)
+
+    def precreate_output_collections(self, trans, history, params):
+        # params is just one sample tool param execution with parallelized
+        # collection replaced with a specific dataset. Need to replace this
+        # with the collection and wrap everything up so can evaluate output
+        # label.
+        params.update(self.collection_info.collections)  # Replace datasets with source collections for labelling outputs.
+
+        collection_instances = {}
+        implicit_inputs = self.implicit_inputs
+        for output_name, output in self.tool.outputs.items():
+            if filter_output(output, self.example_params):
+                continue
+            output_collection_name = self.output_name(trans, history, params, output)
+            effective_structure = self._mapped_output_structure(trans, output)
+            collection_instance = trans.app.dataset_collections_service.precreate_dataset_collection_instance(
+                trans=trans,
+                parent=history,
+                name=output_collection_name,
+                implicit_inputs=implicit_inputs,
+                implicit_output_name=output_name,
+                structure=effective_structure,
+            )
+            collection_instances[output_name] = collection_instance
+            trans.sa_session.add(collection_instance)
+        # Needed to flush the association created just above with
+        # job.add_output_dataset_collection.
+        trans.sa_session.flush()
+        self.implicit_collections = collection_instances
+
+    def finalize_dataset_collections(self, trans):
+        # TODO: this probably needs to be reworked some, we should have the collection methods
+        # return a list of changed objects to add to the session and flush and we should only
+        # be finalizing collections to a depth of self.collection_info.structure. So for instance
+        # if you are mapping a list over a tool that dynamically generates lists - we won't actually
+        # know the structure of the inner list until after its job is complete.
+        if self.failed_jobs > 0:
+            for implicit_collection in self.implicit_collections.values():
+                implicit_collection.collection.handle_population_failed("One or more jobs failed during dataset initialization.")
+                trans.sa_session.add(implicit_collection.collection)
+        else:
+            for implicit_collection in self.implicit_collections.values():
+                implicit_collection.collection.finalize()
+                trans.sa_session.add(implicit_collection.collection)
+        trans.sa_session.flush()
+
+    @property
+    def implicit_inputs(self):
+        implicit_inputs = list(self.collection_info.collections.items())
+        return implicit_inputs
+
+    def is_implicit_input(self, input_name):
+        return input_name in self.collection_info.collections
+
+    def walk_implicit_collections(self):
+        return self.collection_info.structure.walk_collections(self.implicit_collections)
+
+    def new_execution_slices(self):
+        if self.collection_info is None:
+            for job_index, param_combination in enumerate(self.param_combinations):
+                yield ExecutionSlice(job_index, param_combination)
+        else:
+            for execution_slice in self.new_collection_execution_slices():
+                yield execution_slice
+
+    def record_success(self, execution_slice, job, outputs):
+        # TODO: successful_jobs need to be inserted in the correct place...
         self.successful_jobs.append(job)
         self.output_datasets.extend(outputs)
+        for job_output in job.output_dataset_collection_instances:
+            self.output_collections.append((job_output.name, job_output.dataset_collection_instance))
+        if self.implicit_collections:
+            for output_name, collection_instance in self.implicit_collections.items():
+                job.add_output_dataset_collection(output_name, collection_instance)
+
+
+# Seperate these because workflows need to track their jobs belong to the invocation
+# in the database immediately and they can be recovered.
+class ToolExecutionTracker(ExecutionTracker):
+
+    def __init__(self, tool, mapping_params, collection_info):
+        super(ToolExecutionTracker, self).__init__(tool, mapping_params, collection_info)
+
+        # New to track these things for tool output API response in the tool case,
+        # in the workflow case we just write stuff to the database and forget about
+        # it.
+        self.outputs_by_output_name = collections.defaultdict(list)
+
+    def record_success(self, execution_slice, job, outputs):
+        super(ToolExecutionTracker, self).record_success(execution_slice, job, outputs)
         for output_name, output_dataset in outputs:
             if ToolOutputCollectionPart.is_named_collection_part_name(output_name):
                 # Skip known collection outputs, these will be covered by
@@ -167,101 +352,58 @@ class ToolExecutionTracker(object):
             self.outputs_by_output_name[output_name].append(output_dataset)
         for job_output in job.output_dataset_collections:
             self.outputs_by_output_name[job_output.name].append(job_output.dataset_collection)
-        for job_output in job.output_dataset_collection_instances:
-            self.output_collections.append((job_output.name, job_output.dataset_collection_instance))
 
-    def record_error(self, error):
-        self.failed_jobs += 1
-        message = "There was a failure executing a job for tool [%s] - %s"
-        log.warning(message, self.tool.id, error)
-        self.execution_errors.append(error)
+    def new_collection_execution_slices(self):
+        for job_index, (param_combination, dataset_collection_elements) in enumerate(itertools.izip(self.param_combinations, self.walk_implicit_collections())):
+            for dataset_collection_element in dataset_collection_elements.values():
+                assert dataset_collection_element.element_object is None
 
-    def create_output_collections(self, trans, history, params):
-        # TODO: Move this function - it doesn't belong here but it does need
-        # the information in this class and potential extensions.
-        if self.failed_jobs > 0:
-            return []
+            yield ExecutionSlice(job_index, param_combination, dataset_collection_elements)
 
-        structure = self.collection_info.structure
 
-        # params is just one sample tool param execution with parallelized
-        # collection replaced with a specific dataset. Need to replace this
-        # with the collection and wrap everything up so can evaluate output
-        # label.
-        params.update(self.collection_info.collections)  # Replace datasets with source collections for labelling outputs.
+class WorkflowStepExecutionTracker(ExecutionTracker):
 
-        collection_names = ["collection %d" % c.hid for c in self.collection_info.collections.values()]
-        on_text = on_text_for_names(collection_names)
+    def __init__(self, tool, mapping_params, collection_info, invocation_step, job_callback):
+        super(WorkflowStepExecutionTracker, self).__init__(tool, mapping_params, collection_info)
+        self.invocation_step = invocation_step
+        self.job_callback = job_callback
 
-        collections = {}
+    def record_success(self, execution_slice, job, outputs):
+        super(WorkflowStepExecutionTracker, self).record_success(execution_slice, job, outputs)
+        job_assoc = model.WorkflowInvocationStepJobAssociation()
+        job_assoc.index = execution_slice.job_index
+        job_assoc.workflow_invocation_step = self.invocation_step
+        job_assoc.job_id = job.id
+        self.job_callback(job)
 
-        implicit_inputs = list(self.collection_info.collections.items())
-        for output_name, output in self.tool.outputs.items():
-            outputs = self.outputs_by_output_name[output_name]
-            if not len(structure) == len(outputs):
-                # Output does not have the same structure, if all jobs were
-                # successfully submitted this shouldn't have happened.
-                log.warning("Problem matching up datasets while attempting to create implicit dataset collections")
+    def new_collection_execution_slices(self):
+        for job_index, (param_combination, dataset_collection_elements) in enumerate(itertools.izip(self.param_combinations, self.walk_implicit_collections())):
+            # Two options here - check if the element has been populated or check if the
+            # a WorkflowInvocationStepJobAssociation exists. Not sure which is better but
+            # for now I have the first so lets check.
+            found_result = False
+            for dataset_collection_element in dataset_collection_elements.values():
+                if dataset_collection_element.element_object is not None:
+                    found_result = True
+                    break
+            if found_result:
                 continue
+            yield ExecutionSlice(job_index, param_combination, dataset_collection_elements)
 
-            element_identifiers = None
-            if hasattr(output, "default_identifier_source"):
-                # Switch the structure for outputs if the output specified a default_identifier_source
-                collection_type_descriptions = trans.app.dataset_collections_service.collection_type_descriptions
+    def ensure_implicit_collections_populated(self, trans, history, params):
+        if not self. collection_info:
+            return
 
-                source_collection = self.collection_info.collections.get(output.default_identifier_source)
-                if source_collection:
-                    collection_type_description = collection_type_descriptions.for_collection_type(source_collection.collection.collection_type)
-                    _structure = structure.for_dataset_collection(source_collection.collection, collection_type_description=collection_type_description)
-                    if structure.can_match(_structure):
-                        element_identifiers = _structure.element_identifiers_for_outputs(trans, outputs)
-
-            if not element_identifiers:
-                element_identifiers = structure.element_identifiers_for_outputs(trans, outputs)
-
-            implicit_collection_info = dict(
-                implicit_inputs=implicit_inputs,
-                implicit_output_name=output_name,
-                outputs=outputs
-            )
-            try:
-                output_collection_name = self.tool.tool_action.get_output_name(
-                    output,
-                    dataset=None,
-                    tool=self.tool,
-                    on_text=on_text,
-                    trans=trans,
-                    history=history,
-                    params=params,
-                    incoming=None,
-                    job_params=None,
-                )
-            except Exception:
-                output_collection_name = "%s across %s" % (self.tool.name, on_text)
-
-            child_element_identifiers = element_identifiers["element_identifiers"]
-            collection_type = element_identifiers["collection_type"]
-            collection = trans.app.dataset_collections_service.create(
-                trans=trans,
-                parent=history,
-                name=output_collection_name,
-                element_identifiers=child_element_identifiers,
-                collection_type=collection_type,
-                implicit_collection_info=implicit_collection_info,
-            )
-            for job in self.successful_jobs:
-                # TODO: Think through this, may only want this for output
-                # collections - or we may be already recording data in some
-                # other way.
-                if job not in trans.sa_session:
-                    job = trans.sa_session.query(trans.app.model.Job).get(job.id)
-                job.add_output_dataset_collection(output_name, collection)
-            collections[output_name] = collection
-
-        # Needed to flush the association created just above with
-        # job.add_output_dataset_collection.
-        trans.sa_session.flush()
-        self.implicit_collections = collections
+        history = history or self.tool.get_default_history_by_trans(trans)
+        if self.invocation_step.is_new:
+            self.precreate_output_collections(trans, history, params)
+        else:
+            collections = {}
+            for output_assoc in self.invocation_step.output_dataset_collections:
+                implicit_collection = output_assoc.dataset_collection
+                assert hasattr(implicit_collection, "history_content_type")  # make sure it is an HDCA and not a DC
+                collections[output_assoc.output_name] = output_assoc.dataset_collection
+            self.implicit_collections = collections
 
 
 __all__ = ('execute', )
diff --git a/lib/galaxy/tools/parser/output_objects.py b/lib/galaxy/tools/parser/output_objects.py
index 3dd543a3744..e680c6717be 100644
--- a/lib/galaxy/tools/parser/output_objects.py
+++ b/lib/galaxy/tools/parser/output_objects.py
@@ -195,7 +195,10 @@ class ToolOutputCollectionStructure(object):
         if self.structured_like:
             collection_prototype = inputs[self.structured_like].collection
         else:
-            collection_prototype = type_registry.prototype(self.collection_type)
+            collection_type = self.collection_type
+            assert collection_type
+            collection_prototype = type_registry.prototype(collection_type)
+            collection_prototype.collection_type = collection_type
         return collection_prototype
 
 
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 0ad4609b915..ba44feeb5e6 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -220,8 +220,9 @@ class WorkflowModule(object):
         Use the supplied workflow progress object to track outputs, find
         inputs, etc....
 
-        Return jobs created and a boolean indicating if there are additional
-        jobs to create on subsequent workflow scheduling tests.
+        Return a False if there is additional processing required to
+        on subsequent workflow scheduling runs, None or True means the workflow
+        step executed properly.
         """
         raise TypeError("Abstract method")
 
@@ -871,9 +872,7 @@ class ToolModule(WorkflowModule):
 
             param_combinations.append(execution_state.inputs)
 
-        # Will be set if only a subset of required jobs have been scheduled and the
-        # workflow should be delayed.
-        partial_jobs = None
+        complete = False
         try:
             mapping_params = MappingParameters(tool_state.inputs, param_combinations)
             execution_tracker = execute(
@@ -884,36 +883,29 @@ class ToolModule(WorkflowModule):
                 collection_info=collection_info,
                 workflow_invocation_uuid=invocation.uuid.hex,
                 invocation_step=invocation_step,
+                job_callback=lambda job: self._handle_post_job_actions(step, job, invocation.replacement_dict),
             )
-        except PartialJobExecution as p:
-            partial_jobs = p.jobs
+            complete = True
+        except PartialJobExecution:
+            pass
+
         except ToolInputsNotReadyException:
             delayed_why = "tool [%s] inputs are not ready, this special tool requires inputs to be ready" % tool.id
             raise DelayedWorkflowEvaluation(why=delayed_why)
 
-        if partial_jobs is None:
+        if invocation_step.is_new:
             if collection_info:
                 step_outputs = dict(execution_tracker.implicit_collections)
             else:
                 step_outputs = dict(execution_tracker.output_datasets)
                 step_outputs.update(execution_tracker.output_collections)
             progress.set_step_outputs(invocation_step, step_outputs)
-            jobs = execution_tracker.successful_jobs
-        else:
-            jobs = partial_jobs
-
-        for job in jobs:
-            self._handle_post_job_actions(step, job, invocation.replacement_dict)
 
         if execution_tracker.execution_errors:
-            failed_count = len(execution_tracker.execution_errors)
-            success_count = len(execution_tracker.successful_jobs)
-            all_count = failed_count + success_count
-            message = "Failed to create %d out of %s job(s) for workflow step." % (failed_count, all_count)
+            message = "Failed to create one or more job(s) for workflow step."
             raise Exception(message)
 
-        complete = partial_jobs is None
-        return jobs, complete
+        return complete
 
     def recover_mapping(self, invocation_step, progress):
         outputs = {}
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 75222d5a46d..9a3c409243c 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -1,7 +1,7 @@
 import logging
 import uuid
 
-from galaxy import model, util
+from galaxy import model
 from galaxy.util import ExecutionTimer
 from galaxy.util.odict import odict
 from galaxy.workflow import modules
@@ -165,7 +165,6 @@ class WorkflowInvoker(object):
         for (step, workflow_invocation_step) in remaining_steps:
             step_delayed = False
             step_timer = ExecutionTimer()
-            jobs = None
             try:
                 self.__check_implicitly_dependent_steps(step)
 
@@ -174,29 +173,11 @@ class WorkflowInvoker(object):
                     workflow_invocation_step.workflow_invocation = workflow_invocation
                     workflow_invocation_step.workflow_step = step
                     workflow_invocation_step.state = 'new'
-                    previously_executed_jobs_count = 0
 
                     workflow_invocation.steps.append(workflow_invocation_step)
-                else:
-                    previously_executed_jobs_count = len(workflow_invocation_step.jobs)
 
-                jobs_or_none = self._invoke_step(workflow_invocation_step)
-                if jobs_or_none:
-                    jobs, complete = jobs_or_none
-                else:
-                    jobs, complete = [], True
-
-                for job in (util.listify(jobs) or []):
-                    job_assoc = model.WorkflowInvocationStepJobAssociation()
-                    job_assoc.index = previously_executed_jobs_count
-                    job_assoc.workflow_invocation_step = workflow_invocation_step
-                    # Job may not be generated in this thread if bursting is enabled
-                    # https://github.com/galaxyproject/galaxy/issues/2259
-                    job_assoc.job_id = job.id
-
-                    previously_executed_jobs_count += 1
-
-                if not complete:
+                incomplete_or_none = self._invoke_step(workflow_invocation_step)
+                if incomplete_or_none is False:
                     step_delayed = delayed_steps = True
                     workflow_invocation_step.state = 'ready'
                     self.progress.mark_step_outputs_delayed(step, why="Not all jobs scheduled for state.")
@@ -268,8 +249,8 @@ class WorkflowInvoker(object):
                 pass
 
     def _invoke_step(self, invocation_step):
-        jobs_or_none = invocation_step.workflow_step.module.execute(self.trans, self.progress, invocation_step)
-        return jobs_or_none
+        incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans, self.progress, invocation_step)
+        return incomplete_or_none
 
 
 STEP_OUTPUT_DELAYED = object()
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index c3e37ff74f3..49a819909d6 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -1001,7 +1001,7 @@ class ToolsTestCase(api.ApiTestCase):
         self.assertEquals(len(jobs), 2)
         self.assertEquals(len(implicit_collections), 1)
         implicit_collection = implicit_collections[0]
-        assert implicit_collection["collection_type"] == "list:paired", implicit_collection
+        assert implicit_collection["collection_type"] == "list:paired", implicit_collection["collection_type"]
         outer_elements = implicit_collection["elements"]
         assert len(outer_elements) == 2
 
diff --git a/test/api/test_workflow_extraction.py b/test/api/test_workflow_extraction.py
index 57008511576..d2cc98378c8 100644
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -467,7 +467,7 @@ test_data:
                     disconnected_inputs.append(value)
 
         if disconnected_inputs:
-            template = "%d step(s_ disconnected in extracted workflow - disconnectect steps are %s - workflow is %s"
+            template = "%d steps disconnected in extracted workflow - disconnectect steps are %s - workflow is %s"
             message = template % (len(disconnected_inputs), disconnected_inputs, workflow)
             raise AssertionError(message)
 
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 876fc167269..ff03293ebb5 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -768,7 +768,9 @@ steps:
             }
             invocation_id = self.__invoke_workflow(history_id, workflow_id, inputs)
             self.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
-            content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
+            collection_details = self.dataset_populator.get_history_collection_details(history_id, hid=7)
+            assert collection_details["populated_state"] == "ok"
+            content = self.dataset_populator.get_history_dataset_content(history_id, hid=11)
             self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0")
 
     @skip_without_tool("collection_split_on_column")
@@ -1621,7 +1623,7 @@ test_data:
     def wait_for_invocation_and_jobs(self, history_id, workflow_id, invocation_id, assert_ok=True):
         self.workflow_populator.wait_for_invocation(workflow_id, invocation_id)
         time.sleep(.5)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok)
+        self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=assert_ok)
         time.sleep(.5)
 
     def test_cannot_run_inaccessible_workflow(self):
@@ -1740,7 +1742,7 @@ test_data:
         value: 1.fastq
         type: File
 """, history_id=history_id)
-        content = self.dataset_populator.get_history_dataset_details(history_id, hid=3, wait=True, assert_ok=True)
+        content = self.dataset_populator.get_history_dataset_details(history_id, hid=4, wait=True, assert_ok=True)
         name = content["name"]
         assert name == "my new name", name
 
diff --git a/test/base/populators.py b/test/base/populators.py
index 45b3d1a13ec..ae98d60d15e 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -163,6 +163,23 @@ class BaseDatasetPopulator(object):
             self._summarize_history(history_id)
             raise
 
+    def wait_for_history_jobs(self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+        query_params = {"history_id": history_id}
+
+        def has_active_jobs():
+            jobs_response = self._get("jobs", query_params)
+            assert jobs_response.status_code == 200
+            active_jobs = [j for j in jobs_response.json() if j["state"] in ["new", "upload", "waiting", "queued", "running"]]
+
+            if len(active_jobs) == 0:
+                return True
+            else:
+                return None
+
+        wait_on(has_active_jobs, "active jobs", timeout=timeout)
+        if assert_ok:
+            return self.wait_for_history(history_id, assert_ok=True, timeout=timeout)
+
     def wait_for_job(self, job_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
         return wait_on_state(lambda: self.get_job_details(job_id), assert_ok=assert_ok, timeout=timeout)
 
diff --git a/test/unit/dataset_collections/test_matching.py b/test/unit/dataset_collections/test_matching.py
index c27056abeb3..b3aa022479d 100644
--- a/test/unit/dataset_collections/test_matching.py
+++ b/test/unit/dataset_collections/test_matching.py
@@ -117,6 +117,7 @@ class MockCollection(object):
     def __init__(self, collection_type, elements):
         self.collection_type = collection_type
         self.elements = elements
+        self.populated = True
 
 
 class MockCollectionElement(object):

From 40fd72a1980bd2df5ea116aae1016c8bad6c3ca1 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 Oct 2017 22:15:33 -0400
Subject: [PATCH 13/22] Allow rescheduling of single workflow steps.

Implement maximum_workflow_jobs_per_scheduling_iteration to test this and mitigate memory issues associated with scheduling large workflow steps (maybe).

Fixes #3883.
---
 config/galaxy.ini.sample                      |  8 ++
 lib/galaxy/config.py                          |  1 +
 lib/galaxy/tools/execute.py                   |  6 +-
 lib/galaxy/workflow/modules.py                | 20 ++--
 lib/galaxy/workflow/run.py                    | 25 +++--
 ...st_maximum_worklfow_invocation_duration.py | 48 ----------
 .../test_workflow_scheduling_options.py       | 92 +++++++++++++++++++
 7 files changed, 134 insertions(+), 66 deletions(-)
 delete mode 100644 test/integration/test_maximum_worklfow_invocation_duration.py
 create mode 100644 test/integration/test_workflow_scheduling_options.py

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 11d457d892c..1d14bbb025a 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -1131,6 +1131,14 @@ use_interactive = True
 # invocation to schedule indefinitely. The default corresponds to 1 month.
 #maximum_workflow_invocation_duration = 2678400
 
+# Specify a maximum number of jobs that any given workflow scheduling iteration can create.
+# Set this to a positive integer to prevent large collection jobs in a workflow from
+# preventing other jobs from executing. This may also mitigate memory issues associated with
+# scheduling workflows at the expense of increased total DB traffic because model objects
+# are expunged from the SQL alchemy session between workflow invocation scheduling iterations.
+# Set to -1 to disable any such maximum (the default).
+#maximum_workflow_jobs_per_scheduling_iteration = -1
+
 # Force serial scheduling of workflows within the context of a particular history
 #history_local_serial_workflow_scheduling=False
 
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index af2a9aa0142..72fbd663208 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -388,6 +388,7 @@ class Configuration(object):
         self.history_local_serial_workflow_scheduling = string_as_bool(kwargs.get('history_local_serial_workflow_scheduling', 'False'))
         self.parallelize_workflow_scheduling_within_histories = string_as_bool(kwargs.get('parallelize_workflow_scheduling_within_histories', 'False'))
         self.maximum_workflow_invocation_duration = int(kwargs.get("maximum_workflow_invocation_duration", 2678400))
+        self.maximum_workflow_jobs_per_scheduling_iteration = int(kwargs.get("maximum_workflow_jobs_per_scheduling_iteration", -1))
 
         self.cache_user_job_count = string_as_bool(kwargs.get('cache_user_job_count', False))
         self.pbs_application_server = kwargs.get('pbs_application_server', "")
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 34794d6d338..7e96ce8c914 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -23,8 +23,8 @@ EXECUTION_SUCCESS_MESSAGE = "Tool [%s] created job [%s] %s"
 
 class PartialJobExecution(Exception):
 
-    def __init__(self):
-        pass
+    def __init__(self, execution_tracker):
+        self.execution_tracker = execution_tracker
 
 
 MappingParameters = collections.namedtuple("MappingParameters", ["param_template", "param_combinations"])
@@ -121,7 +121,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
         q.join()
 
     if has_remaining_jobs:
-        raise PartialJobExecution()
+        raise PartialJobExecution(execution_tracker)
     else:
         execution_tracker.finalize_dataset_collections(trans)
 
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index ba44feeb5e6..80cec0cbd97 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -875,6 +875,7 @@ class ToolModule(WorkflowModule):
         complete = False
         try:
             mapping_params = MappingParameters(tool_state.inputs, param_combinations)
+            max_num_jobs = progress.maximum_jobs_to_schedule_or_none
             execution_tracker = execute(
                 trans=self.trans,
                 tool=tool,
@@ -883,23 +884,24 @@ class ToolModule(WorkflowModule):
                 collection_info=collection_info,
                 workflow_invocation_uuid=invocation.uuid.hex,
                 invocation_step=invocation_step,
+                max_num_jobs=max_num_jobs,
                 job_callback=lambda job: self._handle_post_job_actions(step, job, invocation.replacement_dict),
             )
             complete = True
-        except PartialJobExecution:
-            pass
+        except PartialJobExecution as pje:
+            execution_tracker = pje.execution_tracker
 
         except ToolInputsNotReadyException:
             delayed_why = "tool [%s] inputs are not ready, this special tool requires inputs to be ready" % tool.id
             raise DelayedWorkflowEvaluation(why=delayed_why)
 
-        if invocation_step.is_new:
-            if collection_info:
-                step_outputs = dict(execution_tracker.implicit_collections)
-            else:
-                step_outputs = dict(execution_tracker.output_datasets)
-                step_outputs.update(execution_tracker.output_collections)
-            progress.set_step_outputs(invocation_step, step_outputs)
+        progress.record_executed_job_count(len(execution_tracker.successful_jobs))
+        if collection_info:
+            step_outputs = dict(execution_tracker.implicit_collections)
+        else:
+            step_outputs = dict(execution_tracker.output_datasets)
+            step_outputs.update(execution_tracker.output_collections)
+        progress.set_step_outputs(invocation_step, step_outputs, already_persisted=not invocation_step.is_new)
 
         if execution_tracker.execution_errors:
             message = "Failed to create one or more job(s) for workflow step."
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 9a3c409243c..a1c76b2bf80 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -140,12 +140,18 @@ class WorkflowInvoker(object):
 
         module_injector = modules.WorkflowModuleInjector(trans)
         if progress is None:
-            progress = WorkflowProgress(self.workflow_invocation, workflow_run_config.inputs, module_injector)
+            progress = WorkflowProgress(
+                self.workflow_invocation,
+                workflow_run_config.inputs,
+                module_injector,
+                jobs_per_scheduling_iteration=getattr(trans.app.config, "maximum_workflow_jobs_per_scheduling_iteration", -1),
+            )
         self.progress = progress
 
     def invoke(self):
         workflow_invocation = self.workflow_invocation
-        maximum_duration = getattr(self.trans.app.config, "maximum_workflow_invocation_duration", -1)
+        config = self.trans.app.config
+        maximum_duration = getattr(config, "maximum_workflow_invocation_duration", -1)
         if maximum_duration > 0 and workflow_invocation.seconds_since_created > maximum_duration:
             log.debug("Workflow invocation [%s] exceeded maximum number of seconds allowed for scheduling [%s], failing." % (workflow_invocation.id, maximum_duration))
             workflow_invocation.state = model.WorkflowInvocation.states.FAILED
@@ -258,16 +264,23 @@ STEP_OUTPUT_DELAYED = object()
 
 class WorkflowProgress(object):
 
-    def __init__(self, workflow_invocation, inputs_by_step_id, module_injector):
+    def __init__(self, workflow_invocation, inputs_by_step_id, module_injector, jobs_per_scheduling_iteration=-1):
         self.outputs = odict()
         self.module_injector = module_injector
         self.workflow_invocation = workflow_invocation
         self.inputs_by_step_id = inputs_by_step_id
-        self.jobs_per_scheduling_iteration = 1
+        self.jobs_per_scheduling_iteration = jobs_per_scheduling_iteration
+        self.jobs_scheduled_this_iteration = 0
 
     @property
-    def maximum_jobs_to_schedule(self):
-        return 1
+    def maximum_jobs_to_schedule_or_none(self):
+        if self.jobs_per_scheduling_iteration > 0:
+            return self.jobs_per_scheduling_iteration - self.jobs_scheduled_this_iteration
+        else:
+            return None
+
+    def record_executed_job_count(self, job_count):
+        self.jobs_scheduled_this_iteration += job_count
 
     def remaining_steps(self):
         # Previously computed and persisted step states.
diff --git a/test/integration/test_maximum_worklfow_invocation_duration.py b/test/integration/test_maximum_worklfow_invocation_duration.py
deleted file mode 100644
index b06661b4448..00000000000
--- a/test/integration/test_maximum_worklfow_invocation_duration.py
+++ /dev/null
@@ -1,48 +0,0 @@
-"""Integration tests for maximum workflow invocation duration configuration option."""
-
-import time
-
-from json import dumps
-
-from base import integration_util
-from base.populators import (
-    DatasetPopulator,
-    WorkflowPopulator,
-)
-
-
-class MaximumWorkflowInvocationDurationTestCase(integration_util.IntegrationTestCase):
-    """Start a Pulsar job."""
-
-    framework_tool_and_types = True
-
-    def setUp(self):
-        super(MaximumWorkflowInvocationDurationTestCase, self).setUp()
-        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
-        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
-
-    @classmethod
-    def handle_galaxy_config_kwds(cls, config):
-        config["maximum_workflow_invocation_duration"] = 20
-
-    def do_test(self):
-        workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
-        workflow_id = self.workflow_populator.create_workflow(workflow)
-        history_id = self.dataset_populator.new_history()
-        hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
-        index_map = {
-            '0': dict(src="hda", id=hda1["id"])
-        }
-        request = {}
-        request["history"] = "hist_id=%s" % history_id
-        request["inputs"] = dumps(index_map)
-        request["inputs_by"] = 'step_index'
-        url = "workflows/%s/invocations" % (workflow_id)
-        invocation_response = self._post(url, data=request)
-        invocation_url = url + "/" + invocation_response.json()["id"]
-        time.sleep(5)
-        state = self._get(invocation_url).json()["state"]
-        assert state != "failed", state
-        time.sleep(35)
-        state = self._get(invocation_url).json()["state"]
-        assert state == "failed", state
diff --git a/test/integration/test_workflow_scheduling_options.py b/test/integration/test_workflow_scheduling_options.py
new file mode 100644
index 00000000000..e1df0ba3417
--- /dev/null
+++ b/test/integration/test_workflow_scheduling_options.py
@@ -0,0 +1,92 @@
+"""Integration tests for workflow scheduling configuration option."""
+
+import time
+
+from json import dumps
+
+from base import integration_util
+from base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    WorkflowPopulator,
+)
+
+
+class MaximumWorkflowInvocationDurationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super(MaximumWorkflowInvocationDurationTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["maximum_workflow_invocation_duration"] = 20
+
+    def do_test(self):
+        workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
+        workflow_id = self.workflow_populator.create_workflow(workflow)
+        history_id = self.dataset_populator.new_history()
+        hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+        index_map = {
+            '0': dict(src="hda", id=hda1["id"])
+        }
+        request = {}
+        request["history"] = "hist_id=%s" % history_id
+        request["inputs"] = dumps(index_map)
+        request["inputs_by"] = 'step_index'
+        url = "workflows/%s/invocations" % (workflow_id)
+        invocation_response = self._post(url, data=request)
+        invocation_url = url + "/" + invocation_response.json()["id"]
+        time.sleep(5)
+        state = self._get(invocation_url).json()["state"]
+        assert state != "failed", state
+        time.sleep(35)
+        state = self._get(invocation_url).json()["state"]
+        assert state == "failed", state
+
+
+class MaximumWorkflowJobsPerSchedulingIterationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super(MaximumWorkflowJobsPerSchedulingIterationTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
+
+    def do_test(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
+class: GalaxyWorkflow
+steps:
+  - type: input_collection
+  - tool_id: collection_creates_pair
+    state:
+      input1:
+        $link: 0
+  - tool_id: collection_paired_test
+    state:
+      f1:
+        $link: 1#paired_output
+  - tool_id: cat_list
+    state:
+      input1:
+        $link: 2#out1
+""")
+        with self.dataset_populator.test_history() as history_id:
+            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            inputs = {
+                '0': {"src": "hdca", "id": hdca1["id"]},
+            }
+            invocation_id = self.workflow_populator.invoke_workflow(history_id, workflow_id, inputs)
+            self.workflow_populator.wait_for_workflow(history_id, workflow_id, invocation_id)
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            self.assertEqual("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0))

From d69962e7f4de38963401a032ada5131e6190b5e5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 15 Nov 2017 08:56:10 -0500
Subject: [PATCH 14/22] Implement model abstraction for
 ``ImplicitCollectionJobs``.

These aggregate all the jobs contributing to an implicitly created HistoryDatasetCollectionAssociation.

- Model enhancements that allow this.
- API endpoint for jobs summary of history content (somewhat uniform across HDAs and HDCAs just for consistency).
- Test cases.
- Rework history contents API a bit to eliminate more costly state summary checks by default.
---
 lib/galaxy/managers/collections.py            | 15 +++--
 lib/galaxy/managers/hdcas.py                  | 21 +++---
 lib/galaxy/managers/jobs.py                   | 50 +++++++++++++-
 lib/galaxy/model/__init__.py                  | 43 ++++++++++++
 lib/galaxy/model/mapping.py                   | 54 ++++++++++++++-
 .../versions/0136_record_workflow_outputs.py  | 43 +++++++++++-
 lib/galaxy/tools/actions/__init__.py          |  1 +
 lib/galaxy/tools/execute.py                   | 66 ++++++++++++-------
 .../webapps/galaxy/api/history_contents.py    | 34 ++++++++++
 lib/galaxy/webapps/galaxy/buildapp.py         |  4 ++
 scripts/db_shell.py                           |  1 +
 test/api/test_history_contents.py             | 37 ++++++++++-
 test/api/test_tools.py                        | 23 +++----
 test/base/populators.py                       |  7 ++
 14 files changed, 343 insertions(+), 56 deletions(-)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 8939eae80a8..356729593a9 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -47,10 +47,12 @@ class DatasetCollectionManager(object):
         self.ldda_manager = lddas.LDDAManager(app)
 
     def precreate_dataset_collection_instance(self, trans, parent, name, implicit_inputs, implicit_output_name, structure):
+        # TODO: prebuild all required HIDs and send them in so no need to flush in between.
         dataset_collection = self.precreate_dataset_collection(structure)
-        return self._create_instance_for_collection(
-            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name,
+        instance = self._create_instance_for_collection(
+            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, flush=False
         )
+        return instance
 
     def precreate_dataset_collection(self, structure):
         if structure.is_leaf or not structure.children_known:
@@ -111,7 +113,7 @@ class DatasetCollectionManager(object):
             trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags
         )
 
-    def _create_instance_for_collection(self, trans, parent, name, dataset_collection, implicit_output_name=None, implicit_inputs=None, tags=None):
+    def _create_instance_for_collection(self, trans, parent, name, dataset_collection, implicit_output_name=None, implicit_inputs=None, tags=None, flush=True):
         if isinstance(parent, model.History):
             dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
                 collection=dataset_collection,
@@ -141,7 +143,7 @@ class DatasetCollectionManager(object):
             raise MessageException(message)
 
         tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
-        return self.__persist(dataset_collection_instance)
+        return self.__persist(dataset_collection_instance, flush=flush)
 
     def create_dataset_collection(self, trans, collection_type, element_identifiers=None, elements=None,
                                   hide_source_items=None):
@@ -285,10 +287,11 @@ class DatasetCollectionManager(object):
         collections = list(filter(query.direct_match, collections))
         return collections
 
-    def __persist(self, dataset_collection_instance):
+    def __persist(self, dataset_collection_instance, flush=True):
         context = self.model.context
         context.add(dataset_collection_instance)
-        context.flush()
+        if flush:
+            context.flush()
         return dataset_collection_instance
 
     def __recursively_create_collections(self, trans, element_identifiers):
diff --git a/lib/galaxy/managers/hdcas.py b/lib/galaxy/managers/hdcas.py
index e6591c61f4d..877c27390ab 100644
--- a/lib/galaxy/managers/hdcas.py
+++ b/lib/galaxy/managers/hdcas.py
@@ -117,12 +117,12 @@ class DCSerializer(base.ModelSerializer):
             'create_time',
             'update_time',
             'collection_type',
-            'populated',
             'populated_state',
             'populated_state_message',
         ])
         self.add_view('detailed', [
-            'elements'
+            'populated',
+            'elements',
         ], include_keys_from='summary')
 
     def add_serializers(self):
@@ -130,7 +130,7 @@ class DCSerializer(base.ModelSerializer):
         self.serializers.update({
             'model_class'   : lambda *a, **c: 'DatasetCollection',
             'elements'      : self.serialize_elements,
-            'element_count' : self.serialize_element_count
+            'element_count' : self.serialize_element_count,
         })
 
     def serialize_elements(self, item, key, **context):
@@ -163,12 +163,12 @@ class DCASerializer(base.ModelSerializer):
             'id',
             'create_time', 'update_time',
             'collection_type',
-            'populated',
             'populated_state',
             'populated_state_message',
         ])
         self.add_view('detailed', [
-            'elements'
+            'populated',
+            'elements',
         ], include_keys_from='summary')
 
     def add_serializers(self):
@@ -184,7 +184,7 @@ class DCASerializer(base.ModelSerializer):
             'populated_state',
             'populated_state_message',
             'elements',
-            'element_count'
+            'element_count',
         ]
         for key in collection_keys:
             self.serializers[key] = self._proxy_to_dataset_collection(key=key)
@@ -221,15 +221,14 @@ class HDCASerializer(
             'history_content_type',
 
             'collection_type',
-            'populated',
             'populated_state',
             'populated_state_message',
 
+            'job_source_id',
+            'job_source_type',
+
             'name',
             'type_id',
-            'history_id',
-            'hid',
-            'history_content_type',
             'deleted',
             # 'purged',
             'visible',
@@ -238,6 +237,7 @@ class HDCASerializer(
             'tags',  # TODO: detail view only (maybe)
         ])
         self.add_view('detailed', [
+            'populated',
             'elements'
         ], include_keys_from='summary')
 
@@ -254,6 +254,7 @@ class HDCASerializer(
             'history_id'                : self.serialize_id,
             'history_content_type'      : lambda *a, **c: self.hdca_manager.model_class.content_type,
             'type_id'                   : self.serialize_type_id,
+            'job_source_id'             : self.serialize_id,
 
             'url'   : lambda i, k, **c: self.url_for('history_content_typed',
                                                      history_id=self.app.security.encode_id(i.history_id),
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index a291d377b23..b967f897c9e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -3,8 +3,9 @@ import logging
 
 from boltons.iterutils import remap
 from six import string_types
-from sqlalchemy import and_, false, or_
+from sqlalchemy import and_, false, func, or_
 from sqlalchemy.orm import aliased
+from sqlalchemy.sql import select
 
 from galaxy import model
 from galaxy.managers.collections import DatasetCollectionManager
@@ -243,3 +244,50 @@ class JobSearch(object):
                 log.info("Searching jobs finished %s", search_timer)
                 return job
         return None
+
+
+def summarize_jobs_to_dict(sa_session, jobs_source):
+    """Proudce a summary of jobs for job summary endpoints.
+
+    :type   jobs_source: a Job or ImplicitCollectionJobs or None
+    :param  jobs_source: the object to summarize
+
+    :rtype:     dict
+    :returns:   dictionary containing job summary information
+    """
+    rval = None
+    if jobs_source is None:
+        pass
+    elif isinstance(jobs_source, model.Job):
+        rval = {
+            "populated_state": "ok",
+            "states": {jobs_source.state: 1},
+            "model": "Job",
+            "id": jobs_source.id,
+        }
+    else:
+        populated_state = jobs_source.populated_state
+        rval = {
+            "id": jobs_source.id,
+            "populated_state": populated_state,
+            "model": "ImplicitCollectionJobs",
+        }
+        if populated_state == "ok":
+            # produce state summary...
+            states = {}
+            join = model.ImplicitCollectionJobs.table.join(
+                model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
+            )
+            statement = select(
+                [model.Job.state, func.count("*")]
+            ).select_from(
+                join
+            ).where(
+                model.ImplicitCollectionJobs.id == jobs_source.id
+            ).group_by(
+                model.Job.state
+            )
+            for row in sa_session.execute(statement):
+                states[row[0]] = row[1]
+            rval["states"] = states
+    return rval
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 019dcae1530..a495bb65a75 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1054,6 +1054,29 @@ class ImplicitlyCreatedDatasetCollectionInput(object):
         self.input_dataset_collection = input_dataset_collection
 
 
+class ImplicitCollectionJobs(object):
+
+    populated_states = Bunch(
+        NEW='new',  # New implicit jobs object, unpopulated job associations
+        OK='ok',  # Job associations are set and fixed.
+        FAILED='failed',  # There were issues populating job associations, object is in error.
+    )
+
+    def __init__(
+        self,
+        id=None,
+        populated_state=None,
+    ):
+        self.id = id
+        self.populated_state = populated_state or ImplicitCollectionJobs.populated_states.NEW
+
+
+class ImplicitCollectionJobsJobAssociation(object):
+
+    def __init__(self):
+        pass
+
+
 class PostJobAction(object):
     def __init__(self, action_type, workflow_step, output_name=None, action_arguments=None):
         self.action_type = action_type
@@ -3402,6 +3425,19 @@ class HistoryDatasetCollectionAssociation(DatasetCollectionInstance,
         return ((type_coerce(cls.content_type, types.Unicode) + u'-' +
                  type_coerce(cls.id, types.Unicode)).label('type_id'))
 
+    @property
+    def job_source_type(self):
+        if self.implicit_collection_jobs_id:
+            return "ImplicitCollectionJobs"
+        elif self.job_id:
+            return "Job"
+        else:
+            return None
+
+    @property
+    def job_source_id(self):
+        return self.implicit_collection_jobs_id or self.job_id
+
     def to_hda_representative(self, multiple=False):
         rval = []
         for dataset in self.collection.dataset_elements:
@@ -3419,6 +3455,8 @@ class HistoryDatasetCollectionAssociation(DatasetCollectionInstance,
             history_content_type=self.history_content_type,
             visible=self.visible,
             deleted=self.deleted,
+            job_source_id=self.job_source_id,
+            job_source_type=self.job_source_type,
             **self._base_to_dict(view=view)
         )
 
@@ -3450,6 +3488,11 @@ class HistoryDatasetCollectionAssociation(DatasetCollectionInstance,
             name=self.name,
             copied_from_history_dataset_collection_association=self,
         )
+        if self.implicit_collection_jobs_id:
+            hdca.implicit_collection_jobs_id = self.implicit_collection_jobs_id
+        elif self.job_id:
+            hdca.job_id = self.job_id
+
         collection_copy = self.collection.copy(
             destination=hdca,
             element_destination=element_destination,
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 49d6d4ed206..f53799db844 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -557,6 +557,20 @@ model.ImplicitlyCreatedDatasetCollectionInput.table = Table(
         ForeignKey("history_dataset_collection_association.id"), index=True),
     Column("name", Unicode(255)))
 
+model.ImplicitCollectionJobs.table = Table(
+    "implicit_collection_jobs", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("populated_state", TrimmedString(64), default='new', nullable=False),
+)
+
+model.ImplicitCollectionJobsJobAssociation.table = Table(
+    "implicit_collection_jobs_job_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),  # Consider making this nullable...
+    Column("order_index", Integer, nullable=False),
+)
+
 model.JobExternalOutputMetadata.table = Table(
     "job_external_output_metadata", metadata,
     Column("id", Integer, primary_key=True),
@@ -716,7 +730,10 @@ model.HistoryDatasetCollectionAssociation.table = Table(
     Column("deleted", Boolean, default=False),
     Column("copied_from_history_dataset_collection_association_id", Integer,
         ForeignKey("history_dataset_collection_association.id"), nullable=True),
-    Column("implicit_output_name", Unicode(255), nullable=True))
+    Column("implicit_output_name", Unicode(255), nullable=True),
+    Column("job_id", ForeignKey("job.id"), index=True, nullable=True),
+    Column("implicit_collection_jobs_id", ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
+)
 
 model.LibraryDatasetCollectionAssociation.table = Table(
     "library_dataset_collection_association", metadata,
@@ -2111,6 +2128,31 @@ simple_mapping(model.ImplicitlyCreatedDatasetCollectionInput,
     ),
 )
 
+simple_mapping(model.ImplicitCollectionJobs)
+
+# simple_mapping(
+#     model.ImplicitCollectionJobsHistoryDatasetCollectionAssociation,
+#     history_dataset_collection_associations=relation(
+#         model.HistoryDatasetCollectionAssociation,
+#         backref=backref("implicit_collection_jobs_association", uselist=False),
+#         uselist=True,
+#     ),
+# )
+
+simple_mapping(
+    model.ImplicitCollectionJobsJobAssociation,
+    implicit_collection_jobs=relation(
+        model.ImplicitCollectionJobs,
+        backref=backref("jobs", uselist=True),
+        uselist=False,
+    ),
+    job=relation(
+        model.Job,
+        backref=backref("implicit_collection_jobs_association", uselist=False),
+        uselist=False,
+    ),
+)
+
 mapper(model.JobParameter, model.JobParameter.table)
 
 mapper(model.JobExternalOutputMetadata, model.JobExternalOutputMetadata.table, properties=dict(
@@ -2202,6 +2244,16 @@ simple_mapping(model.HistoryDatasetCollectionAssociation,
                       model.ImplicitlyCreatedDatasetCollectionInput.table.c.dataset_collection_id)),
         backref="dataset_collection",
     ),
+    implicit_collection_jobs=relation(
+        model.ImplicitCollectionJobs,
+        backref=backref("history_dataset_collection_associations", uselist=True),
+        uselist=False,
+    ),
+    job=relation(
+        model.Job,
+        backref=backref("history_dataset_collection_associations", uselist=True),
+        uselist=False,
+    ),
     tags=relation(model.HistoryDatasetCollectionTagAssociation,
         order_by=model.HistoryDatasetCollectionTagAssociation.table.c.id,
         backref='dataset_collections'),
diff --git a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
index 1b83a49aa31..ead24344502 100644
--- a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
+++ b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
@@ -1,5 +1,5 @@
 """
-Migration script for workflow request tables.
+Migration script for collections and workflows connections.
 """
 from __future__ import print_function
 
@@ -79,6 +79,26 @@ def get_new_tables():
         Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
     )
 
+    implicit_collection_jobs_table = Table(
+        "implicit_collection_jobs", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("populated_state", TrimmedString(64), default='new', nullable=False),
+    )
+
+    # implicit_collection_jobs_history_dataset_collection_association_table = Table(
+    #    "implicit_collection_jobs_dataset_collection_association", metadata,
+    #    Column("id", Integer, primary_key=True),
+    #    Column("history_dataset_collection_association_id", Integer, ForeignKey("history_dataset_collection_association_id.id"), index=True, nullable=False),
+    # )
+
+    implicit_collection_jobs_job_association_table = Table(
+        "implicit_collection_jobs_job_association", metadata,
+        Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
+        Column("id", Integer, primary_key=True),
+        Column("job_id", Integer, ForeignKey("job.id"), index=True),  # Consider making this nullable...
+        Column("order_index", Integer, nullable=False),
+    )
+
     tables = OrderedDict()
     tables["workflow_invocation_step"] = workflow_invocation_step_table
     tables["workflow_invocation_output_dataset_association"] = workflow_invocation_output_dataset_association_table
@@ -86,6 +106,9 @@ def get_new_tables():
     tables["workflow_invocation_step_output_dataset_association"] = workflow_invocation_step_output_dataset_association_table
     tables["workflow_invocation_step_output_dataset_collection_association"] = workflow_invocation_step_output_dataset_collection_association_table
     tables["workflow_invocation_step_job_association"] = workflow_invocation_step_job_association_table
+    tables["implicit_collection_jobs"] = implicit_collection_jobs_table
+    # tables["implicit_collection_jobs_history_dataset_collection_association"] = implicit_collection_jobs_history_dataset_collection_association_table
+    tables["implicit_collection_jobs_job_association"] = implicit_collection_jobs_job_association_table
 
     return tables
 
@@ -157,6 +180,24 @@ def upgrade(migrate_engine):
         "WHERE job_id is not NULL "
     migrate_engine.execute(cmd)
 
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
+        job_id_column = Column("job_id", Integer, ForeignKey("job.id"), nullable=True)
+    else:
+        implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, nullable=True)
+        job_id_column = Column("job_id", Integer, nullable=True)
+    __add_column(implicit_collection_jobs_id_column, "history_dataset_collection_association", metadata)
+    __add_column(job_id_column, "history_dataset_collection_association", metadata)
+    # TODO: matching drop... steal from 0131
+
+
+def __add_column(column, table_name, metadata, **kwds):
+    try:
+        table = Table(table_name, metadata, autoload=True)
+        column.create(table, **kwds)
+    except Exception:
+        log.exception("Adding column %s failed.", column)
+
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 14bd8f54452..bfc467fb727 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -598,6 +598,7 @@ class DefaultToolAction(object):
             job.add_implicit_output_dataset_collection(name, dataset_collection)
         for name, dataset_collection_instance in out_collection_instances.items():
             job.add_output_dataset_collection(name, dataset_collection_instance)
+            dataset_collection_instance.job = job
 
     def _check_input_data_access(self, trans, job, inp_data, current_user_roles):
         access_timer = ExecutionTimer()
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 7e96ce8c914..ce04b02670c 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -42,9 +42,9 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
 
     all_jobs_timer = ExecutionTimer()
     if invocation_step is None:
-        execution_tracker = ToolExecutionTracker(tool, mapping_params, collection_info)
+        execution_tracker = ToolExecutionTracker(trans, tool, mapping_params, collection_info)
     else:
-        execution_tracker = WorkflowStepExecutionTracker(tool, mapping_params, collection_info, invocation_step, job_callback=job_callback)
+        execution_tracker = WorkflowStepExecutionTracker(trans, tool, mapping_params, collection_info, invocation_step, job_callback=job_callback)
     app = trans.app
     execution_cache = ToolExecutionCache(trans)
 
@@ -77,7 +77,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
                 history
             )
 
-    execution_tracker.ensure_implicit_collections_populated(trans, history, mapping_params.param_template)
+    execution_tracker.ensure_implicit_collections_populated(history, mapping_params.param_template)
     config = app.config
     burst_at = getattr(config, 'tool_submission_burst_at', 10)
     burst_threads = getattr(config, 'tool_submission_burst_threads', 1)
@@ -139,8 +139,9 @@ class ExecutionSlice(object):
 
 class ExecutionTracker(object):
 
-    def __init__(self, tool, mapping_params, collection_info):
+    def __init__(self, trans, tool, mapping_params, collection_info):
         # Known ahead of time...
+        self.trans = trans
         self.tool = tool
         self.mapping_params = mapping_params
         self.collection_info = collection_info
@@ -247,23 +248,26 @@ class ExecutionTracker(object):
         mapped_output_structure = mapping_structure.multiply(output_structure, uninitialized=True)
         return mapped_output_structure
 
-    def ensure_implicit_collections_populated(self, trans, history, params):
+    def ensure_implicit_collections_populated(self, history, params):
         if not self.collection_info:
             return
 
-        history = history or self.tool.get_default_history_by_trans(trans)
+        history = history or self.tool.get_default_history_by_trans(self.trans)
         # params = param_combinations[0] if param_combinations else mapping_params.param_template
-        self.precreate_output_collections(trans, history, params)
+        self.precreate_output_collections(history, params)
 
-    def precreate_output_collections(self, trans, history, params):
+    def precreate_output_collections(self, history, params):
         # params is just one sample tool param execution with parallelized
         # collection replaced with a specific dataset. Need to replace this
         # with the collection and wrap everything up so can evaluate output
         # label.
+        trans = self.trans
         params.update(self.collection_info.collections)  # Replace datasets with source collections for labelling outputs.
 
         collection_instances = {}
         implicit_inputs = self.implicit_inputs
+
+        implicit_collection_jobs = model.ImplicitCollectionJobs()
         for output_name, output in self.tool.outputs.items():
             if filter_output(output, self.example_params):
                 continue
@@ -277,6 +281,7 @@ class ExecutionTracker(object):
                 implicit_output_name=output_name,
                 structure=effective_structure,
             )
+            collection_instance.implicit_collection_jobs = implicit_collection_jobs
             collection_instances[output_name] = collection_instance
             trans.sa_session.add(collection_instance)
         # Needed to flush the association created just above with
@@ -291,11 +296,19 @@ class ExecutionTracker(object):
         # if you are mapping a list over a tool that dynamically generates lists - we won't actually
         # know the structure of the inner list until after its job is complete.
         if self.failed_jobs > 0:
-            for implicit_collection in self.implicit_collections.values():
+            for i, implicit_collection in enumerate(self.implicit_collections.values()):
+                if i == 0:
+                    implicit_collection_jobs = implicit_collection.implicit_collection_jobs
+                    implicit_collection_jobs.populated_state = "failed"
+                    trans.sa_session.add(implicit_collection_jobs)
                 implicit_collection.collection.handle_population_failed("One or more jobs failed during dataset initialization.")
                 trans.sa_session.add(implicit_collection.collection)
         else:
-            for implicit_collection in self.implicit_collections.values():
+            for i, implicit_collection in enumerate(self.implicit_collections.values()):
+                if i == 0:
+                    implicit_collection_jobs = implicit_collection.implicit_collection_jobs
+                    implicit_collection_jobs.populated_state = "ok"
+                    trans.sa_session.add(implicit_collection_jobs)
                 implicit_collection.collection.finalize()
                 trans.sa_session.add(implicit_collection.collection)
         trans.sa_session.flush()
@@ -326,16 +339,25 @@ class ExecutionTracker(object):
         for job_output in job.output_dataset_collection_instances:
             self.output_collections.append((job_output.name, job_output.dataset_collection_instance))
         if self.implicit_collections:
+            implicit_collection_jobs = None
             for output_name, collection_instance in self.implicit_collections.items():
                 job.add_output_dataset_collection(output_name, collection_instance)
+                if implicit_collection_jobs is None:
+                    implicit_collection_jobs = collection_instance.implicit_collection_jobs
+
+            job_assoc = model.ImplicitCollectionJobsJobAssociation()
+            job_assoc.order_index = execution_slice.job_index
+            job_assoc.implicit_collection_jobs = implicit_collection_jobs
+            job_assoc.job_id = job.id
+            self.trans.sa_session.add(job_assoc)
 
 
 # Seperate these because workflows need to track their jobs belong to the invocation
 # in the database immediately and they can be recovered.
 class ToolExecutionTracker(ExecutionTracker):
 
-    def __init__(self, tool, mapping_params, collection_info):
-        super(ToolExecutionTracker, self).__init__(tool, mapping_params, collection_info)
+    def __init__(self, trans, tool, mapping_params, collection_info):
+        super(ToolExecutionTracker, self).__init__(trans, tool, mapping_params, collection_info)
 
         # New to track these things for tool output API response in the tool case,
         # in the workflow case we just write stuff to the database and forget about
@@ -363,17 +385,17 @@ class ToolExecutionTracker(ExecutionTracker):
 
 class WorkflowStepExecutionTracker(ExecutionTracker):
 
-    def __init__(self, tool, mapping_params, collection_info, invocation_step, job_callback):
-        super(WorkflowStepExecutionTracker, self).__init__(tool, mapping_params, collection_info)
+    def __init__(self, trans, tool, mapping_params, collection_info, invocation_step, job_callback):
+        super(WorkflowStepExecutionTracker, self).__init__(trans, tool, mapping_params, collection_info)
         self.invocation_step = invocation_step
         self.job_callback = job_callback
 
     def record_success(self, execution_slice, job, outputs):
         super(WorkflowStepExecutionTracker, self).record_success(execution_slice, job, outputs)
-        job_assoc = model.WorkflowInvocationStepJobAssociation()
-        job_assoc.index = execution_slice.job_index
-        job_assoc.workflow_invocation_step = self.invocation_step
-        job_assoc.job_id = job.id
+        # job_assoc = model.WorkflowInvocationStepJobAssociation()
+        # job_assoc.index = execution_slice.job_index
+        # job_assoc.workflow_invocation_step = self.invocation_step
+        # job_assoc.job_id = job.id
         self.job_callback(job)
 
     def new_collection_execution_slices(self):
@@ -390,13 +412,13 @@ class WorkflowStepExecutionTracker(ExecutionTracker):
                 continue
             yield ExecutionSlice(job_index, param_combination, dataset_collection_elements)
 
-    def ensure_implicit_collections_populated(self, trans, history, params):
-        if not self. collection_info:
+    def ensure_implicit_collections_populated(self, history, params):
+        if not self.collection_info:
             return
 
-        history = history or self.tool.get_default_history_by_trans(trans)
+        history = history or self.tool.get_default_history_by_trans(self.trans)
         if self.invocation_step.is_new:
-            self.precreate_output_collections(trans, history, params)
+            self.precreate_output_collections(history, params)
         else:
             collections = {}
             for output_assoc in self.invocation_step.output_dataset_collections:
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 87954ef4542..f6fc932b5a0 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -21,6 +21,7 @@ from galaxy.managers.collections_util import (
     dictify_dataset_collection_instance,
     get_hda_and_element_identifiers
 )
+from galaxy.managers.jobs import summarize_jobs_to_dict
 from galaxy.util.json import safe_dumps
 from galaxy.util.streamball import StreamBall
 from galaxy.web import (
@@ -154,6 +155,39 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         elif contents_type == 'dataset_collection':
             return self.__show_dataset_collection(trans, id, history_id, **kwd)
 
+    @expose_api_anonymous
+    def show_jobs_summary(self, trans, id, history_id, **kwd):
+        """
+        * GET /api/histories/{history_id}/contents/{type}/{id}/jobs_summary
+            return detailed information about an HDA or HDCAs jobs
+        .. note:: Anonymous users are allowed to get their current history contents
+
+        :type   id:         str
+        :param  id:         the encoded id of the HDA to return
+        :type   history_id: str
+        :param  history_id: encoded id string of the HDA's or the HDCA's History
+
+        :rtype:     dict
+        :returns:   dictionary containing
+        """
+        contents_type = self.__get_contents_type(trans, kwd)
+        # At most one of job or implicit_collection_jobs should be found.
+        job = None
+        implicit_collection_jobs = None
+        if contents_type == 'dataset':
+            hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
+            job = hda.creating_job
+        elif contents_type == 'dataset_collection':
+            dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
+            job_source_type = dataset_collection_instance.job_source_type
+            if job_source_type == "Job":
+                job = dataset_collection_instance.job
+            elif job_source_type == "ImplicitCollectionJobs":
+                implicit_collection_jobs = dataset_collection_instance.implicit_collection_jobs
+
+        assert job is None or implicit_collection_jobs is None
+        return self.encode_all_ids(trans, summarize_jobs_to_dict(trans.sa_session, job or implicit_collection_jobs))
+
     def __get_contents_type(self, trans, kwd):
         contents_type = kwd.get('type', 'dataset')
         if contents_type not in ['dataset', 'dataset_collection']:
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 5b8aadb97c0..cab77e6cfb4 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -363,6 +363,10 @@ def populate_api_routes(webapp, app):
                           action='download_dataset_collection',
                           conditions=dict(method=["GET"]))
 
+    webapp.mapper.connect("/api/histories/{history_id}/contents/{type:%s}s/{id}/jobs_summary" % "|".join(valid_history_contents_types),
+                          action="show_jobs_summary",
+                          controller='history_contents',
+                          conditions=dict(method=["GET"]))
     # ---- visualizations registry ---- generic template renderer
     # @deprecated: this route should be considered deprecated
     webapp.add_route('/visualization/show/{visualization_name}', controller='visualization', action='render', visualization_name=None)
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index f7e10d61086..c896ec04af6 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -23,6 +23,7 @@ from six import string_types
 from sqlalchemy import *  # noqa
 from sqlalchemy.orm import *  # noqa
 from sqlalchemy.exc import *  # noqa
+from sqlalchemy.sql import label  # noqa
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
diff --git a/test/api/test_history_contents.py b/test/api/test_history_contents.py
index 5cb2822556b..1d9d77da2f2 100644
--- a/test/api/test_history_contents.py
+++ b/test/api/test_history_contents.py
@@ -6,9 +6,11 @@ from requests import delete, put
 
 from base import api  # noqa: I100
 from base.populators import (  # noqa: I100
+    DatasetPopulator,
     DatasetCollectionPopulator,
     LibraryPopulator,
-    TestsDatasets
+    skip_without_tool,
+    TestsDatasets,
 )
 
 
@@ -18,6 +20,7 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
     def setUp(self):
         super(HistoryContentsApiTestCase, self).setUp()
         self.history_id = self._new_history()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
         self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
         self.library_populator = LibraryPopulator(self)
 
@@ -177,6 +180,38 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
         dataset_collection = show_response.json()
         assert dataset_collection["deleted"]
 
+    @skip_without_tool("collection_creates_list")
+    def test_jobs_summary_simple_hdca(self):
+        create_response = self.dataset_collection_populator.create_list_in_history(self.history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
+        hdca_id = create_response.json()["id"]
+        run = self.dataset_populator.run_collection_creates_list(self.history_id, hdca_id)
+        collections = run['output_collections']
+        collection = collections[0]
+        jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % (self.history_id, collection["id"])
+        jobs_summary_response = self._get(jobs_summary_url)
+        self._assert_status_code_is(jobs_summary_response, 200)
+        jobs_summary = jobs_summary_response.json()
+        self._assert_has_keys(jobs_summary, "populated_state", "states")
+
+    @skip_without_tool("cat1")
+    def test_jobs_summary_implicit_hdca(self):
+        create_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, contents=["123", "456"])
+        hdca_id = create_response.json()["id"]
+        inputs = {
+            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+        }
+        run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=self.history_id)
+        self.dataset_populator.wait_for_history_jobs(self.history_id)
+        collections = run['implicit_collections']
+        collection = collections[0]
+        jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % (self.history_id, collection["id"])
+        jobs_summary_response = self._get(jobs_summary_url)
+        self._assert_status_code_is(jobs_summary_response, 200)
+        jobs_summary = jobs_summary_response.json()
+        self._assert_has_keys(jobs_summary, "populated_state", "states")
+        states = jobs_summary["states"]
+        assert states.get("ok") == 2, states
+
     def test_dataset_collection_hide_originals(self):
         payload = self.dataset_collection_populator.create_pair_payload(
             self.history_id,
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 49a819909d6..264cd0d64f7 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -433,20 +433,15 @@ class ToolsTestCase(api.ApiTestCase):
 
     @skip_without_tool("collection_creates_list")
     def test_list_collection_output(self):
-        history_id = self.dataset_populator.new_history()
-        create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
-        hdca_id = create_response.json()["id"]
-        inputs = {
-            "input1": {"src": "hdca", "id": hdca_id},
-        }
-        # TODO: real problem here - shouldn't have to have this wait.
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        create = self._run("collection_creates_list", history_id, inputs, assert_ok=True)
-        output_collection = self._assert_one_job_one_collection_run(create)
-        element0, element1 = self._assert_elements_are(output_collection, "data1", "data2")
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        self._verify_element(history_id, element0, contents="identifier is data1\n", file_ext="txt")
-        self._verify_element(history_id, element1, contents="identifier is data2\n", file_ext="txt")
+        with self.dataset_populator.test_history() as history_id:
+            create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
+            hdca_id = create_response.json()["id"]
+            create = self.dataset_populator.run_collection_creates_list(history_id, hdca_id)
+            output_collection = self._assert_one_job_one_collection_run(create)
+            element0, element1 = self._assert_elements_are(output_collection, "data1", "data2")
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            self._verify_element(history_id, element0, contents="identifier is data1\n", file_ext="txt")
+            self._verify_element(history_id, element1, contents="identifier is data2\n", file_ext="txt")
 
     @skip_without_tool("collection_creates_list_2")
     def test_list_collection_output_format_source(self):
diff --git a/test/base/populators.py b/test/base/populators.py
index ae98d60d15e..16bccfcbd9e 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -291,6 +291,13 @@ class BaseDatasetPopulator(object):
         assert details_response.status_code == 200, details_response.content
         return details_response.json()
 
+    def run_collection_creates_list(self, history_id, hdca_id):
+        inputs = {
+            "input1": {"src": "hdca", "id": hdca_id},
+        }
+        self.wait_for_history(history_id, assert_ok=True)
+        return self.run_tool("collection_creates_list", inputs, history_id)
+
     def __history_content_id(self, history_id, wait=True, **kwds):
         if wait:
             assert_ok = kwds.get("assert_ok", True)

From e82012bde154c456f24743f3b61c0ed9ffc7eca2 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 25 Oct 2017 09:05:32 -0400
Subject: [PATCH 15/22] Undo splitting WorkflowInvocationStep...

... this concept of ImplicitCollectionJobs makes more sense for tracking collections of implicitly created jobs.
---
 lib/galaxy/jobs/actions/post.py               |  12 +-
 lib/galaxy/model/__init__.py                  |  22 +-
 lib/galaxy/model/mapping.py                   |  24 +-
 .../versions/0136_record_workflow_outputs.py  | 236 ++++++++----------
 lib/galaxy/tools/execute.py                   |  18 +-
 5 files changed, 143 insertions(+), 169 deletions(-)

diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py
index 138d4b8005b..267a765e66f 100644
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -269,10 +269,10 @@ class DeleteIntermediatesAction(DefaultJobAction):
         # concurrently, sometimes non-terminal steps won't be cleaned up
         # because of the lag in job state updates.
         sa_session.flush()
-        if not job.workflow_invocation_step_assoc.workflow_invocation_step:
+        if not job.workflow_invocation_step:
             log.debug("This job is not part of a workflow invocation, delete intermediates aborted.")
             return
-        wfi = job.workflow_invocation_step_assoc.workflow_invocation_step.workflow_invocation
+        wfi = job.workflow_invocation_step.workflow_invocation
         sa_session.refresh(wfi)
         if wfi.active:
             log.debug("Workflow still scheduling so new jobs may appear, skipping deletion of intermediate files.")
@@ -285,9 +285,9 @@ class DeleteIntermediatesAction(DefaultJobAction):
             jobs_to_check = []
             for wfi_step in wfi_steps:
                 sa_session.refresh(wfi_step)
-                wfi_step_job_assocs = wfi_step.jobs
-                if wfi_step_job_assocs:
-                    jobs_to_check.extend(map(lambda j: j.job, wfi_step_job_assocs))
+                wfi_step_job = wfi_step.job
+                if wfi_step_job:
+                    jobs_to_check.append(wfi_step_job)
                 else:
                     log.debug("No job found yet for wfi_step %s, (step %s)" % (wfi_step, wfi_step.workflow_step))
             for j2c in jobs_to_check:
@@ -302,7 +302,7 @@ class DeleteIntermediatesAction(DefaultJobAction):
                 for (input_dataset, creating_job) in creating_jobs:
                     sa_session.refresh(creating_job)
                     sa_session.refresh(input_dataset)
-                for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step_assoc and creating_job.workflow_invocation_step_assoc.workflow_invocation_step.workflow_invocation == wfi]:
+                for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
                     # note that the above input_dataset is a reference to a
                     # job.input_dataset.dataset at this point
                     safe_to_delete = True
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index a495bb65a75..98679c442be 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -803,9 +803,8 @@ class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable):
 
     def set_final_state(self, final_state):
         self.set_state(final_state)
-        workflow_invocation_step_assoc = self.workflow_invocation_step_assoc
-        if workflow_invocation_step_assoc:
-            workflow_invocation_step_assoc.workflow_invocation_step.update()
+        if self.workflow_invocation_step:
+            self.workflow_invocation_step.update()
 
     def get_destination_configuration(self, config, key, default=None):
         """ Get a destination parameter that can be defaulted back
@@ -1070,6 +1069,10 @@ class ImplicitCollectionJobs(object):
         self.id = id
         self.populated_state = populated_state or ImplicitCollectionJobs.populated_states.NEW
 
+    @property
+    def job_list(self):
+        return [icjja.job for icjja in self.jobs]
+
 
 class ImplicitCollectionJobsJobAssociation(object):
 
@@ -4159,12 +4162,12 @@ class WorkflowInvocation(object, UsesCreateAndUpdateTime, Dictifiable):
             inputs = {}
             for step in self.steps:
                 if step.workflow_step.type == 'tool':
-                    for step_job_assoc in step.jobs:
+                    for job in step.jobs:
                         for step_input in step.workflow_step.input_connections:
                             output_step_type = step_input.output_step.type
                             if output_step_type in ['data_input', 'data_collection_input']:
                                 src = "hda" if output_step_type == 'data_input' else 'hdca'
-                                for job_input in step_job_assoc.job.input_datasets:
+                                for job_input in job.input_datasets:
                                     if job_input.name == step_input.input_name:
                                         inputs[str(step_input.output_step.order_index)] = {
                                             "id": job_input.dataset_id, "src": src,
@@ -4268,6 +4271,15 @@ class WorkflowInvocationStep(object, Dictifiable):
         else:
             raise Exception("Uknown output type encountered")
 
+    @property
+    def jobs(self):
+        if self.job:
+            return [self.job]
+        elif self.implicit_collection_jobs:
+            return self.implicit_collection_jobs.job_list
+        else:
+            return []
+
     def to_dict(self, view='collection', value_mapper=None):
         rval = super(WorkflowInvocationStep, self).to_dict(view=view, value_mapper=value_mapper)
         rval['order_index'] = self.workflow_step.order_index
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index f53799db844..895da39a79b 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -919,18 +919,10 @@ model.WorkflowInvocationStep.table = Table(
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
     Column("state", TrimmedString(64), index=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
+    Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
     Column("action", JSONType, nullable=True))
 
-
-model.WorkflowInvocationStepJobAssociation.table = Table(
-    "workflow_invocation_step_job_association", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
-    Column("order_index", Integer, nullable=True),  # recovering partially complete WorkflowInvocationSteps requires knowing which jobs have been scheduled
-    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
-)
-
-
 model.WorkflowInvocationOutputDatasetAssociation.table = Table(
     "workflow_invocation_output_dataset_association", metadata,
     Column("id", Integer, primary_key=True),
@@ -2420,16 +2412,10 @@ mapper(model.WorkflowInvocationToSubworkflowInvocationAssociation, model.Workflo
     workflow_step=relation(model.WorkflowStep),
 ))
 
-
-simple_mapping(model.WorkflowInvocationStepJobAssociation,
-    workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="jobs"),
-    job=relation(model.Job,
-        backref=backref('workflow_invocation_step_assoc',
-            uselist=False)))
-
-
 simple_mapping(model.WorkflowInvocationStep,
-    workflow_step=relation(model.WorkflowStep))
+    workflow_step=relation(model.WorkflowStep),
+    job=relation(model.Job, backref=backref('workflow_invocation_step', uselist=False), uselist=False),
+    implicit_collection_jobs=relation(model.ImplicitCollectionJobs, backref=backref('workflow_invocation_step', uselist=False), uselist=False),)
 
 
 simple_mapping(model.WorkflowRequestInputParameter,
diff --git a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
index ead24344502..1c23ed1c56c 100644
--- a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
+++ b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
@@ -8,10 +8,9 @@ import logging
 
 from collections import OrderedDict
 
-from migrate.changeset.constraint import ForeignKeyConstraint
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table
+from sqlalchemy import Column, ForeignKey, Integer, MetaData, String, Table
 
-from galaxy.model.custom_types import JSONType, TrimmedString
+from galaxy.model.custom_types import TrimmedString
 
 
 now = datetime.datetime.utcnow
@@ -20,92 +19,93 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 
+workflow_invocation_output_dataset_association_table = Table(
+    "workflow_invocation_output_dataset_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
+)
+
+workflow_invocation_output_dataset_collection_association_table = Table(
+    "workflow_invocation_output_dataset_collection_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
+)
+
+workflow_invocation_step_output_dataset_association_table = Table(
+    "workflow_invocation_step_output_dataset_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("output_name", String(255), nullable=True),
+)
+
+workflow_invocation_step_output_dataset_collection_association_table = Table(
+    "workflow_invocation_step_output_dataset_collection_association", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("output_name", String(255), nullable=True),
+)
+
+# workflow_invocation_step_table = Table(
+#     "workflow_invocation_step", metadata,
+#     Column("id", Integer, primary_key=True),
+#     Column("create_time", DateTime, default=now),
+#     Column("update_time", DateTime, default=now, onupdate=now),
+#     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
+#     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+#     Column("action", JSONType, nullable=True),
+#     Column("state", TrimmedString(64), default="new"),
+# )
+
+# workflow_invocation_step_job_association_table = Table(
+#     "workflow_invocation_step_job_association", metadata,
+#     Column("id", Integer, primary_key=True),
+#     Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
+#     Column("order_index", Integer, nullable=True),
+#     Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+# )
+
+implicit_collection_jobs_table = Table(
+    "implicit_collection_jobs", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("populated_state", TrimmedString(64), default='new', nullable=False),
+)
+
+# implicit_collection_jobs_history_dataset_collection_association_table = Table(
+#    "implicit_collection_jobs_dataset_collection_association", metadata,
+#    Column("id", Integer, primary_key=True),
+#    Column("history_dataset_collection_association_id", Integer, ForeignKey("history_dataset_collection_association_id.id"), index=True, nullable=False),
+# )
+
+implicit_collection_jobs_job_association_table = Table(
+    "implicit_collection_jobs_job_association", metadata,
+    Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),  # Consider making this nullable...
+    Column("order_index", Integer, nullable=False),
+)
+
+
 def get_new_tables():
     # Normally we define this globally in the file, but we need to delay the
     # reading of existing tables because an existing workflow_invocation_step
     # table exists that we want to recreate.
 
-    workflow_invocation_output_dataset_association_table = Table(
-        "workflow_invocation_output_dataset_association", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
-        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
-        Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-        Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
-    )
-
-    workflow_invocation_output_dataset_collection_association_table = Table(
-        "workflow_invocation_output_dataset_collection_association", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
-        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
-        Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-        Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
-    )
-
-    workflow_invocation_step_output_dataset_association_table = Table(
-        "workflow_invocation_step_output_dataset_association", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
-        Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-        Column("output_name", String(255), nullable=True),
-    )
-
-    workflow_invocation_step_output_dataset_collection_association_table = Table(
-        "workflow_invocation_step_output_dataset_collection_association", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
-        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
-        Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-        Column("output_name", String(255), nullable=True),
-    )
-
-    workflow_invocation_step_table = Table(
-        "workflow_invocation_step", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("create_time", DateTime, default=now),
-        Column("update_time", DateTime, default=now, onupdate=now),
-        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
-        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-        Column("action", JSONType, nullable=True),
-        Column("state", TrimmedString(64), default="new"),
-    )
-
-    workflow_invocation_step_job_association_table = Table(
-        "workflow_invocation_step_job_association", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
-        Column("order_index", Integer, nullable=True),
-        Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
-    )
-
-    implicit_collection_jobs_table = Table(
-        "implicit_collection_jobs", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("populated_state", TrimmedString(64), default='new', nullable=False),
-    )
-
-    # implicit_collection_jobs_history_dataset_collection_association_table = Table(
-    #    "implicit_collection_jobs_dataset_collection_association", metadata,
-    #    Column("id", Integer, primary_key=True),
-    #    Column("history_dataset_collection_association_id", Integer, ForeignKey("history_dataset_collection_association_id.id"), index=True, nullable=False),
-    # )
-
-    implicit_collection_jobs_job_association_table = Table(
-        "implicit_collection_jobs_job_association", metadata,
-        Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
-        Column("id", Integer, primary_key=True),
-        Column("job_id", Integer, ForeignKey("job.id"), index=True),  # Consider making this nullable...
-        Column("order_index", Integer, nullable=False),
-    )
-
     tables = OrderedDict()
-    tables["workflow_invocation_step"] = workflow_invocation_step_table
+    # tables["workflow_invocation_step"] = workflow_invocation_step_table
     tables["workflow_invocation_output_dataset_association"] = workflow_invocation_output_dataset_association_table
     tables["workflow_invocation_output_dataset_collection_association"] = workflow_invocation_output_dataset_collection_association_table
     tables["workflow_invocation_step_output_dataset_association"] = workflow_invocation_step_output_dataset_association_table
     tables["workflow_invocation_step_output_dataset_collection_association"] = workflow_invocation_step_output_dataset_collection_association_table
-    tables["workflow_invocation_step_job_association"] = workflow_invocation_step_job_association_table
+    # tables["workflow_invocation_step_job_association"] = workflow_invocation_step_job_association_table
     tables["implicit_collection_jobs"] = implicit_collection_jobs_table
     # tables["implicit_collection_jobs_history_dataset_collection_association"] = implicit_collection_jobs_history_dataset_collection_association_table
     tables["implicit_collection_jobs_job_association"] = implicit_collection_jobs_job_association_table
@@ -117,21 +117,6 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     print(__doc__)
 
-    LegacyWorkflowInvocationStep_table = Table("workflow_invocation_step", metadata, autoload=True)
-    ExistingWorkflowInvocation_table = Table("workflow_invocation", metadata, autoload=True)
-
-    cons = ForeignKeyConstraint([LegacyWorkflowInvocationStep_table.c.workflow_invocation_id], [ExistingWorkflowInvocation_table.c.id])
-    cons.drop()
-
-    for index in LegacyWorkflowInvocationStep_table.indexes:
-        index.drop()
-
-    LegacyWorkflowInvocationStep_table.rename("workflow_invocation_step_premigrate135")
-    # Try to deregister that workflow_invocation_step to work around some caching problems
-    # it seems.
-    LegacyWorkflowInvocationStep_table.deregister()
-    metadata._remove_table("workflow_invocation_step", metadata.schema)
-
     metadata.reflect()
     tables = get_new_tables()
     for table in tables.values():
@@ -145,41 +130,8 @@ def upgrade(migrate_engine):
         else:
             raise Exception("Unhandled database type")
 
-    # Skips action - since I can't aggregate (sql needs a RANDOM(col)) that and it is only used by optional
-    # beta extensions.
-    cmd = \
-        "INSERT INTO workflow_invocation_step " + \
-        "(id, create_time, update_time, workflow_invocation_id, workflow_step_id, action, state)" + \
-        "SELECT " + \
-        nextval('workflow_invocation_step') + " AS id, " \
-        "MIN(create_time) AS create_time, " + \
-        "MAX(update_time) AS update_time, " + \
-        "workflow_invocation_step_premigrate135.workflow_invocation_id AS workflow_invocation_id, " +\
-        "workflow_invocation_step_premigrate135.workflow_step_id AS workflow_step_id, " + \
-        "NULL AS action, " + \
-        "'scheduled' AS state " + \
-        "FROM workflow_invocation_step_premigrate135 " + \
-        "WHERE workflow_invocation_step_premigrate135.workflow_step_id IS NOT NULL AND workflow_invocation_step_premigrate135.workflow_invocation_id IS NOT NULL " +\
-        "GROUP BY workflow_invocation_step_premigrate135.workflow_invocation_id, workflow_invocation_step_premigrate135.workflow_step_id " + \
-        ""
-    migrate_engine.execute(cmd)
-
-    cmd = \
-        "INSERT INTO workflow_invocation_step_job_association " + \
-        "(id, workflow_invocation_step_id, order_index, job_id) " + \
-        "SELECT " + \
-        nextval('workflow_invocation_step_job_association') + " AS id, " \
-        "workflow_invocation_step.id AS workflow_invocation_step_id, " + \
-        "NULL AS order_index, " + \
-        "job_id AS job_id " + \
-        "FROM workflow_invocation_step_premigrate135 " + \
-        "LEFT JOIN workflow_invocation_step on (" + \
-        "  workflow_invocation_step.workflow_invocation_id = workflow_invocation_step_premigrate135.workflow_invocation_id " + \
-        "  AND workflow_invocation_step.workflow_step_id = workflow_invocation_step_premigrate135.workflow_step_id" + \
-        ") " + \
-        "WHERE job_id is not NULL "
-    migrate_engine.execute(cmd)
-
+    # Set default for creation to scheduled, actual mapping has new as default.
+    workflow_invocation_step_state_column = Column("state", TrimmedString(64), default="scheduled")
     if migrate_engine.name in ['postgres', 'postgresql']:
         implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
         job_id_column = Column("job_id", Integer, ForeignKey("job.id"), nullable=True)
@@ -188,6 +140,11 @@ def upgrade(migrate_engine):
         job_id_column = Column("job_id", Integer, nullable=True)
     __add_column(implicit_collection_jobs_id_column, "history_dataset_collection_association", metadata)
     __add_column(job_id_column, "history_dataset_collection_association", metadata)
+
+    implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
+    __add_column(implicit_collection_jobs_id_column, "workflow_invocation_step", metadata)
+    __add_column(workflow_invocation_step_state_column, "workflow_invocation_step", metadata)
+
     # TODO: matching drop... steal from 0131
 
 
@@ -199,17 +156,26 @@ def __add_column(column, table_name, metadata, **kwds):
         log.exception("Adding column %s failed.", column)
 
 
+def __drop_column(column_name, table_name, metadata):
+    try:
+        table = Table(table_name, metadata, autoload=True)
+        getattr(table.c, column_name).drop()
+    except Exception:
+        log.exception("Dropping column %s failed.", column_name)
+
+
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    tables = get_new_tables()
-    for table in tables.values():
-        __drop(table)
+    __drop_column("implicit_collection_jobs_id", "history_dataset_collection_association", metadata)
+    __drop_column("job_id", "history_dataset_collection_association", metadata)
+    __drop_column("implicit_collection_jobs_id", "workflow_invocation_step", metadata)
+    __drop_column("state", "workflow_invocation_step", metadata)
 
-    # Drop new workflow invocation step and job association table and restore legacy data.
-    LegacyWorkflowInvocationStep_table = Table("workflow_invocation_step_premigrate135", metadata, autoload=True)
-    LegacyWorkflowInvocationStep_table.rename("workflow_invocation_step")
+    tables = get_new_tables()
+    for table in reversed(tables.values()):
+        __drop(table)
 
 
 def __create(table):
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index ce04b02670c..80130a51b1d 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -8,6 +8,8 @@ import itertools
 import logging
 from threading import Thread
 
+import six
+
 from six.moves.queue import Queue
 
 from galaxy import model
@@ -289,6 +291,14 @@ class ExecutionTracker(object):
         trans.sa_session.flush()
         self.implicit_collections = collection_instances
 
+    @property
+    def implicit_collection_jobs(self):
+        # TODO: refactor to track this properly maybe?
+        if self.implicit_collections:
+            return six.next(six.itervalues(self.implicit_collections)).implicit_collection_jobs
+        else:
+            return None
+
     def finalize_dataset_collections(self, trans):
         # TODO: this probably needs to be reworked some, we should have the collection methods
         # return a list of changed objects to add to the session and flush and we should only
@@ -392,10 +402,10 @@ class WorkflowStepExecutionTracker(ExecutionTracker):
 
     def record_success(self, execution_slice, job, outputs):
         super(WorkflowStepExecutionTracker, self).record_success(execution_slice, job, outputs)
-        # job_assoc = model.WorkflowInvocationStepJobAssociation()
-        # job_assoc.index = execution_slice.job_index
-        # job_assoc.workflow_invocation_step = self.invocation_step
-        # job_assoc.job_id = job.id
+        if self.collection_info:
+            self.invocation_step.implicit_collection_jobs = self.implicit_collection_jobs
+        else:
+            self.invocation_step.job = job
         self.job_callback(job)
 
     def new_collection_execution_slices(self):

From 0dceb5a553d589324d4a9a97ec5f7629bc379b48 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Nov 2017 08:44:56 -0500
Subject: [PATCH 16/22] Add element count to DatasetCollection objects.

There are no places where this count is not set atomically in one thread so this should not have any performance downsides versus the older approach of calculating it on the fly (which was very expensive).
---
 lib/galaxy/dataset_collections/builder.py     |  1 +
 lib/galaxy/managers/collections.py            |  1 +
 lib/galaxy/managers/collections_util.py       |  1 +
 lib/galaxy/managers/hdcas.py                  | 12 ++----
 lib/galaxy/model/__init__.py                  |  1 +
 lib/galaxy/model/mapping.py                   |  1 +
 .../versions/0136_record_workflow_outputs.py  | 38 +++++--------------
 test/api/test_dataset_collections.py          |  4 +-
 8 files changed, 19 insertions(+), 40 deletions(-)

diff --git a/lib/galaxy/dataset_collections/builder.py b/lib/galaxy/dataset_collections/builder.py
index b32b26ae312..bdb21e75cbf 100644
--- a/lib/galaxy/dataset_collections/builder.py
+++ b/lib/galaxy/dataset_collections/builder.py
@@ -24,6 +24,7 @@ def set_collection_elements(dataset_collection, type, dataset_instances):
         element_index += 1
 
     dataset_collection.elements = elements
+    dataset_collection.element_count = element_index
     return dataset_collection
 
 
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 356729593a9..e823b0f44ca 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -76,6 +76,7 @@ class DatasetCollectionManager(object):
                 )
                 elements.append(element)
             dataset_collection.elements = elements
+            dataset_collection.element_count = len(elements)
 
             return dataset_collection
 
diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py
index 190cbd2b929..65101597d77 100644
--- a/lib/galaxy/managers/collections_util.py
+++ b/lib/galaxy/managers/collections_util.py
@@ -130,6 +130,7 @@ def dictify_element(element):
             child_collection = element.child_collection
             object_detials["elements"] = [dictify_element(_) for _ in child_collection.elements]
             object_detials["populated"] = child_collection.populated
+            object_detials["element_count"] = child_collection.element_count
     else:
         object_detials = None
 
diff --git a/lib/galaxy/managers/hdcas.py b/lib/galaxy/managers/hdcas.py
index 877c27390ab..ea3cdb1706c 100644
--- a/lib/galaxy/managers/hdcas.py
+++ b/lib/galaxy/managers/hdcas.py
@@ -119,6 +119,7 @@ class DCSerializer(base.ModelSerializer):
             'collection_type',
             'populated_state',
             'populated_state_message',
+            'element_count',
         ])
         self.add_view('detailed', [
             'populated',
@@ -130,7 +131,6 @@ class DCSerializer(base.ModelSerializer):
         self.serializers.update({
             'model_class'   : lambda *a, **c: 'DatasetCollection',
             'elements'      : self.serialize_elements,
-            'element_count' : self.serialize_element_count,
         })
 
     def serialize_elements(self, item, key, **context):
@@ -140,14 +140,6 @@ class DCSerializer(base.ModelSerializer):
             returned.append(serialized)
         return returned
 
-    def serialize_element_count(self, item, key, **context):
-        """Return the count of elements for this collection."""
-        # TODO: app.model.context -> session
-        # TODO: to the container interface (dataset_collection_contents)
-        return (self.app.model.context.query(model.DatasetCollectionElement)
-            .filter(model.DatasetCollectionElement.dataset_collection_id == item.id)
-            .count())
-
 
 class DCASerializer(base.ModelSerializer):
     """
@@ -165,6 +157,7 @@ class DCASerializer(base.ModelSerializer):
             'collection_type',
             'populated_state',
             'populated_state_message',
+            'element_count',
         ])
         self.add_view('detailed', [
             'populated',
@@ -223,6 +216,7 @@ class HDCASerializer(
             'collection_type',
             'populated_state',
             'populated_state_message',
+            'element_count',
 
             'job_source_id',
             'job_source_type',
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 98679c442be..e968423a6a7 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3353,6 +3353,7 @@ class DatasetCollectionInstance(object, HasName):
             populated=self.populated,
             populated_state=self.collection.populated_state,
             populated_state_message=self.collection.populated_state_message,
+            element_count=self.collection.element_count,
             type="collection",  # contents type (distinguished from file or folder (in case of library))
         )
 
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 895da39a79b..ad4aec98d3b 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -716,6 +716,7 @@ model.DatasetCollection.table = Table(
     Column("collection_type", Unicode(255), nullable=False),
     Column("populated_state", TrimmedString(64), default='ok', nullable=False),
     Column("populated_state_message", TEXT),
+    Column("element_count", Integer, nullable=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now))
 
diff --git a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
index 1c23ed1c56c..4f739a2e7c3 100644
--- a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
+++ b/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
@@ -54,37 +54,12 @@ workflow_invocation_step_output_dataset_collection_association_table = Table(
     Column("output_name", String(255), nullable=True),
 )
 
-# workflow_invocation_step_table = Table(
-#     "workflow_invocation_step", metadata,
-#     Column("id", Integer, primary_key=True),
-#     Column("create_time", DateTime, default=now),
-#     Column("update_time", DateTime, default=now, onupdate=now),
-#     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
-#     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-#     Column("action", JSONType, nullable=True),
-#     Column("state", TrimmedString(64), default="new"),
-# )
-
-# workflow_invocation_step_job_association_table = Table(
-#     "workflow_invocation_step_job_association", metadata,
-#     Column("id", Integer, primary_key=True),
-#     Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True, nullable=False),
-#     Column("order_index", Integer, nullable=True),
-#     Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
-# )
-
 implicit_collection_jobs_table = Table(
     "implicit_collection_jobs", metadata,
     Column("id", Integer, primary_key=True),
     Column("populated_state", TrimmedString(64), default='new', nullable=False),
 )
 
-# implicit_collection_jobs_history_dataset_collection_association_table = Table(
-#    "implicit_collection_jobs_dataset_collection_association", metadata,
-#    Column("id", Integer, primary_key=True),
-#    Column("history_dataset_collection_association_id", Integer, ForeignKey("history_dataset_collection_association_id.id"), index=True, nullable=False),
-# )
-
 implicit_collection_jobs_job_association_table = Table(
     "implicit_collection_jobs_job_association", metadata,
     Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
@@ -100,14 +75,11 @@ def get_new_tables():
     # table exists that we want to recreate.
 
     tables = OrderedDict()
-    # tables["workflow_invocation_step"] = workflow_invocation_step_table
     tables["workflow_invocation_output_dataset_association"] = workflow_invocation_output_dataset_association_table
     tables["workflow_invocation_output_dataset_collection_association"] = workflow_invocation_output_dataset_collection_association_table
     tables["workflow_invocation_step_output_dataset_association"] = workflow_invocation_step_output_dataset_association_table
     tables["workflow_invocation_step_output_dataset_collection_association"] = workflow_invocation_step_output_dataset_collection_association_table
-    # tables["workflow_invocation_step_job_association"] = workflow_invocation_step_job_association_table
     tables["implicit_collection_jobs"] = implicit_collection_jobs_table
-    # tables["implicit_collection_jobs_history_dataset_collection_association"] = implicit_collection_jobs_history_dataset_collection_association_table
     tables["implicit_collection_jobs_job_association"] = implicit_collection_jobs_job_association_table
 
     return tables
@@ -138,14 +110,21 @@ def upgrade(migrate_engine):
     else:
         implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, nullable=True)
         job_id_column = Column("job_id", Integer, nullable=True)
+    dataset_collection_element_count_column = Column("element_count", Integer, nullable=True)
+
     __add_column(implicit_collection_jobs_id_column, "history_dataset_collection_association", metadata)
     __add_column(job_id_column, "history_dataset_collection_association", metadata)
+    __add_column(dataset_collection_element_count_column, "dataset_collection", metadata)
 
     implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
     __add_column(implicit_collection_jobs_id_column, "workflow_invocation_step", metadata)
     __add_column(workflow_invocation_step_state_column, "workflow_invocation_step", metadata)
 
-    # TODO: matching drop... steal from 0131
+    cmd = \
+        "UPDATE dataset_collection SET element_count = " + \
+        "(SELECT (CASE WHEN count(*) > 0 THEN count(*) ELSE 0 END) FROM dataset_collection_element WHERE " + \
+        "dataset_collection_element.dataset_collection_id = dataset_collection.id)"
+    migrate_engine.execute(cmd)
 
 
 def __add_column(column, table_name, metadata, **kwds):
@@ -172,6 +151,7 @@ def downgrade(migrate_engine):
     __drop_column("job_id", "history_dataset_collection_association", metadata)
     __drop_column("implicit_collection_jobs_id", "workflow_invocation_step", metadata)
     __drop_column("state", "workflow_invocation_step", metadata)
+    __drop_column("element_count", "dataset_collection", metadata)
 
     tables = get_new_tables()
     for table in reversed(tables.values()):
diff --git a/test/api/test_dataset_collections.py b/test/api/test_dataset_collections.py
index f8db6028570..69bdbbdc8ff 100644
--- a/test/api/test_dataset_collections.py
+++ b/test/api/test_dataset_collections.py
@@ -87,7 +87,7 @@ class DatasetCollectionApiTestCase(api.ApiTestCase):
         pair_1_element = returned_collections[0]
         self._assert_has_keys(pair_1_element, "element_index")
         pair_1_object = pair_1_element["object"]
-        self._assert_has_keys(pair_1_object, "collection_type", "elements")
+        self._assert_has_keys(pair_1_object, "collection_type", "elements", "element_count")
         self.assertEquals(pair_1_object["collection_type"], "paired")
         self.assertEquals(pair_1_object["populated"], True)
         pair_elements = pair_1_object["elements"]
@@ -195,7 +195,7 @@ class DatasetCollectionApiTestCase(api.ApiTestCase):
     def _check_create_response(self, create_response):
         self._assert_status_code_is(create_response, 200)
         dataset_collection = create_response.json()
-        self._assert_has_keys(dataset_collection, "elements", "url", "name", "collection_type")
+        self._assert_has_keys(dataset_collection, "elements", "url", "name", "collection_type", "element_count")
         return dataset_collection
 
     def _download_dataset_collection(self, history_id, hdca_id):

From ca09e803aeaf856556433e69bf5a48f8bab60c5d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Nov 2017 14:11:55 -0500
Subject: [PATCH 17/22] Dataset collection state UX test case.

---
 test/api/test_tools.py                        |  6 +-
 test/base/populators.py                       |  8 ++
 .../collection_creates_dynamic_nested.xml     |  8 +-
 ...collection_creates_dynamic_nested_fail.xml |  2 +-
 test/galaxy_selenium/navigates_galaxy.py      |  3 +
 test/galaxy_selenium/navigation.yml           | 21 ++++
 test/selenium_tests/framework.py              | 17 +++-
 .../test_history_copy_elements.py             | 40 ++++++++
 .../selenium_tests/test_history_multi_view.py | 24 +++++
 .../test_history_panel_collections.py         | 99 +++++++++++++++++++
 10 files changed, 218 insertions(+), 10 deletions(-)
 create mode 100644 test/selenium_tests/test_history_copy_elements.py
 create mode 100644 test/selenium_tests/test_history_multi_view.py
 create mode 100644 test/selenium_tests/test_history_panel_collections.py

diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 264cd0d64f7..a1ea61d38fb 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -206,11 +206,7 @@ class ToolsTestCase(api.ApiTestCase):
         with self.dataset_populator.test_history() as history_id:
             history_id = self.dataset_populator.new_history()
             ok_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()["id"]
-            exit_code_inputs = {
-                "input": {'batch': True, 'values': [{"src": "hdca", "id": ok_hdca_id}]},
-            }
-            response = self._run("exit_code_from_file", history_id, exit_code_inputs, assert_ok=False).json()
-            self.dataset_populator.wait_for_history(history_id, assert_ok=False)
+            response = self.dataset_populator.run_exit_code_from_file(history_id, ok_hdca_id)
 
             mixed_implicit_collections = response["implicit_collections"]
             self.assertEquals(len(mixed_implicit_collections), 1)
diff --git a/test/base/populators.py b/test/base/populators.py
index 16bccfcbd9e..9ff96bb4bb4 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -298,6 +298,14 @@ class BaseDatasetPopulator(object):
         self.wait_for_history(history_id, assert_ok=True)
         return self.run_tool("collection_creates_list", inputs, history_id)
 
+    def run_exit_code_from_file(self, history_id, hdca_id):
+        exit_code_inputs = {
+            "input": {'batch': True, 'values': [{"src": "hdca", "id": hdca_id}]},
+        }
+        response = self.run_tool("exit_code_from_file", exit_code_inputs, history_id, assert_ok=False).json()
+        self.wait_for_history(history_id, assert_ok=False)
+        return response
+
     def __history_content_id(self, history_id, wait=True, **kwds):
         if wait:
             assert_ok = kwds.get("assert_ok", True)
diff --git a/test/functional/tools/collection_creates_dynamic_nested.xml b/test/functional/tools/collection_creates_dynamic_nested.xml
index 68edc0cc34b..40a3f50247c 100644
--- a/test/functional/tools/collection_creates_dynamic_nested.xml
+++ b/test/functional/tools/collection_creates_dynamic_nested.xml
@@ -1,14 +1,16 @@
 <tool id="collection_creates_dynamic_nested" name="collection_creates_dynamic_nested" version="0.1.0">
-  <command>
+  <command><![CDATA[
     echo "A" > oe1_ie1.fq ;
     echo "B" > oe1_ie2.fq ;
     echo "C" > oe2_ie1.fq ;
     echo "D" > oe2_ie2.fq ;
     echo "E" > oe3_ie1.fq ;
-    echo "F" > oe3_ie2.fq
-  </command>
+    echo "F" > oe3_ie2.fq ;
+    sleep '$sleep_time';    
+  ]]></command>
   <inputs>
     <param name="foo" type="text" label="Dummy Parameter" />
+    <param name="sleep_time" type="integer" label="Sleep Time" value="0" />
   </inputs>
   <outputs>
     <collection name="list_output" type="list:list" label="Duplicate List">
diff --git a/test/functional/tools/collection_creates_dynamic_nested_fail.xml b/test/functional/tools/collection_creates_dynamic_nested_fail.xml
index 370e85f19b6..68a44bef693 100644
--- a/test/functional/tools/collection_creates_dynamic_nested_fail.xml
+++ b/test/functional/tools/collection_creates_dynamic_nested_fail.xml
@@ -12,7 +12,7 @@
     <param name="foo" type="text" label="Dummy Parameter" />
   </inputs>
   <outputs>
-    <collection name="list_output" type="list:list" label="Duplicate List">
+    <collection name="list_output" type="list:list" label="Failed List">
       <!-- Use named regex group to grab pattern
            <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
            identifier of the outer list and identifier_1 is the list identifier
diff --git a/test/galaxy_selenium/navigates_galaxy.py b/test/galaxy_selenium/navigates_galaxy.py
index 810cf87efcc..1152543ac4f 100644
--- a/test/galaxy_selenium/navigates_galaxy.py
+++ b/test/galaxy_selenium/navigates_galaxy.py
@@ -843,6 +843,9 @@ class NavigatesGalaxy(HasDriver):
         menu_selection_element = self.wait_for_sizzle_selector_clickable(menu_item_sizzle_selector)
         menu_selection_element.click()
 
+    def history_panel_click_copy_elements(self):
+        self.click_history_option("Copy Datasets")
+
     @retry_during_transitions
     def histories_click_advanced_search(self):
         search_selector = '#standard-search .advanced-search-toggle'
diff --git a/test/galaxy_selenium/navigation.yml b/test/galaxy_selenium/navigation.yml
index 2490d5a0c84..1fed9f43b64 100644
--- a/test/galaxy_selenium/navigation.yml
+++ b/test/galaxy_selenium/navigation.yml
@@ -126,12 +126,33 @@ history_panel:
     options_button: '#history-options-button'
     options_button_icon: '#history-options-button span.fa-cog'
     options_menu: '#history-options-button-menu'
+    multi_view_button: '#history-view-multi-button'
 
   text:
     tooltip_name: 'Click to rename history'
     new_name: 'Unnamed history'
     new_size: '(empty)'
 
+multi_history_view:
+
+  selectors:
+    _: '.multi-panel-history'
+    current_label: '.current-label'
+    create_new_button: '.create-new'
+    drag_drop_help: '.history-drop-target-help'
+
+history_copy_elements:
+
+  selectors:
+    # Following two don't really work as CSS would only work as jQuery/sizzle I think
+    # since the page is dynamically generated.
+    # https://stackoverflow.com/questions/10645552/is-it-possible-to-use-an-input-value-attribute-as-a-css-selector
+    dataset_checkbox: "input[id='dataset|${id}']"
+    collection_checkbox: 'input[id="dataset_collection|${id}"]'
+    new_history_name: '#new_history_name'
+    copy_button: "input[type='submit']"
+    done_link: '.donemessage a'
+
 collection_builders:
 
   selectors:
diff --git a/test/selenium_tests/framework.py b/test/selenium_tests/framework.py
index a2574bbe7f1..0db3b5e9fc8 100644
--- a/test/selenium_tests/framework.py
+++ b/test/selenium_tests/framework.py
@@ -339,6 +339,14 @@ class SeleniumTestCase(FunctionalTestCase, NavigatesGalaxy, UsesApiTestCaseMixin
         with self.main_panel():
             self.assert_no_error_message()
 
+    @property
+    def dataset_populator(self):
+        return SeleniumSessionDatasetPopulator(self)
+
+    @property
+    def dataset_collection_populator(self):
+        return SeleniumSessionDatasetCollectionPopulator(self)
+
     @property
     def workflow_populator(self):
         return SeleniumSessionWorkflowPopulator(self)
@@ -465,13 +473,20 @@ class SeleniumSessionGetPostMixin:
     """Mixin for adapting Galaxy testing populators helpers to Selenium session backed bioblend."""
 
     def _get(self, route):
-        return self.selenium_test_case.api_get(route)
+        full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
+        response = requests.get(full_url, cookies=self.selenium_test_case.selenium_to_requests_cookies())
+        return response
 
     def _post(self, route, data={}):
         full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
         response = requests.post(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
         return response
 
+    def _delete(self, route, data={}):
+        full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
+        response = requests.delete(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
+        return response
+
     def __url(self, route):
         return self._gi.url + "/" + route
 
diff --git a/test/selenium_tests/test_history_copy_elements.py b/test/selenium_tests/test_history_copy_elements.py
new file mode 100644
index 00000000000..43f1be123e3
--- /dev/null
+++ b/test/selenium_tests/test_history_copy_elements.py
@@ -0,0 +1,40 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class HistoryCopyElementsTestCase(SeleniumTestCase):
+
+    ensure_registered = True
+
+    @selenium_test
+    def test_copy_hdca(self):
+        history_id = self.current_history_id()
+        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_hid = input_collection["hid"]
+
+        failed_response = self.dataset_populator.run_exit_code_from_file(history_id, input_collection["id"])
+        failed_collection = failed_response["implicit_collections"][0]
+        failed_hid = failed_collection["hid"]
+
+        self.home()
+
+        self.history_panel_wait_for_hid_state(input_hid, "ok")
+        self.history_panel_wait_for_hid_state(failed_hid, "error")
+        self.history_panel_click_copy_elements()
+
+        with self.main_panel():
+            self.components.history_copy_elements.collection_checkbox(id=input_collection["id"]).wait_for_and_click()
+            self.components.history_copy_elements.collection_checkbox(id=failed_collection["id"]).wait_for_and_click()
+
+            text_element = self.components.history_copy_elements.new_history_name.wait_for_and_click()
+            text_element.send_keys("newhistfor_copy_hdca")
+            self.components.history_copy_elements.copy_button.wait_for_and_click()
+            self.sleep_for(self.wait_types.UX_TRANSITION)
+            self.components.history_copy_elements.done_link.wait_for_and_click()
+
+        # Okay copied first
+        self.history_panel_wait_for_hid_state(5, "ok")
+        # Then 4 datasets and then the failed collection (this was six when coming from the original history)
+        self.history_panel_wait_for_hid_state(10, "error")
diff --git a/test/selenium_tests/test_history_multi_view.py b/test/selenium_tests/test_history_multi_view.py
new file mode 100644
index 00000000000..3160d1e9d2c
--- /dev/null
+++ b/test/selenium_tests/test_history_multi_view.py
@@ -0,0 +1,24 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class HistoryMultiViewTestCase(SeleniumTestCase):
+
+    ensure_registered = True
+
+    @selenium_test
+    def test_create_new_old_slides_next(self):
+        history_id = self.current_history_id()
+        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_hid = input_collection["hid"]
+
+        self.home()
+
+        hdca_selector = self.history_panel_wait_for_hid_state(input_hid, "ok")
+
+        self.components.history_panel.multi_view_button.wait_for_and_click()
+        self.components.multi_history_view.create_new_button.wait_for_and_click()
+        self.components.multi_history_view.drag_drop_help.wait_for_visible()
+        self.wait_for_visible(hdca_selector)
diff --git a/test/selenium_tests/test_history_panel_collections.py b/test/selenium_tests/test_history_panel_collections.py
new file mode 100644
index 00000000000..287345f7aea
--- /dev/null
+++ b/test/selenium_tests/test_history_panel_collections.py
@@ -0,0 +1,99 @@
+import time
+
+from base.api_asserts import assert_status_code_is
+
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class HistoryPanelCollectionsTestCase(SeleniumTestCase):
+
+    ensure_registered = True
+
+    @selenium_test
+    def test_mapping_collection_states(self):
+        history_id = self.current_history_id()
+        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_hid = input_collection["hid"]
+
+        # TODO: okay dataset...
+
+        failed_response = self.dataset_populator.run_exit_code_from_file(history_id, input_collection["id"])
+        failed_hid = failed_response["implicit_collections"][0]["hid"]
+
+        running_inputs = {
+            "input1": {'batch': True, 'values': [{"src": "hdca", "id": input_collection["id"]}]},
+            "sleep_time": 180,
+        }
+        running_response = self.dataset_populator.run_tool(
+            "cat_data_and_sleep",
+            running_inputs,
+            history_id,
+            assert_ok=False,
+        )
+        try:
+            assert_status_code_is(running_response, 200)
+            running_hid = running_response.json()["implicit_collections"][0]["hid"]
+
+            # sleep really shouldn't be needed :(
+            time.sleep(1)
+
+            self.home()
+
+            self.history_panel_wait_for_hid_state(input_hid, "ok")
+            self.history_panel_wait_for_hid_state(failed_hid, "error")
+            self.history_panel_wait_for_hid_state(running_hid, "running")
+            self.screenshot("history_panel_collections_state_mapping")
+        finally:
+            for job in running_response.json()["jobs"]:
+                self.dataset_populator.cancel_job(job["id"])
+
+    @selenium_test
+    def test_output_collection_states(self):
+        history_id = self.current_history_id()
+        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+
+        ok_inputs = {
+            "input1": {"src": "hdca", "id": input_collection["id"]}
+        }
+        ok_response = self.dataset_populator.run_tool(
+            "collection_creates_list",
+            ok_inputs,
+            history_id
+        )
+        ok_hid = ok_response["output_collections"][0]["hid"]
+
+        failed_response = self.dataset_populator.run_tool(
+            "collection_creates_dynamic_nested_fail",
+            {},
+            history_id,
+        )
+        failed_hid = failed_response["output_collections"][0]["hid"]
+
+        running_inputs = {
+            "sleep_time": 180,
+        }
+        running_response = self.dataset_populator.run_tool(
+            "collection_creates_dynamic_nested",
+            running_inputs,
+            history_id,
+            assert_ok=False,
+        )
+        try:
+            assert_status_code_is(running_response, 200)
+            running_hid = running_response.json()["output_collections"][0]["hid"]
+
+            # sleep really shouldn't be needed :(
+            time.sleep(1)
+
+            self.home()
+
+            self.history_panel_wait_for_hid_state(ok_hid, "ok")
+            self.history_panel_wait_for_hid_state(failed_hid, "error")
+            self.history_panel_wait_for_hid_state(running_hid, "running")
+            self.screenshot("history_panel_collections_state")
+        finally:
+            for job in running_response.json()["jobs"]:
+                self.dataset_populator.cancel_job(job["id"])

From 5a9f0dd11eb0ba0abfed29ae9da1d0a5a5a01360 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Nov 2017 16:33:37 -0400
Subject: [PATCH 18/22] Add job state tracking to the GUI.

- ``populated`` in the API response is gone - it was very expensive on the backend to calculate.
- Eliminate GUI "thread" fetching ``element_count`` for collections after the panel is loaded, this value is now available at load time thanks to recent state change optimizations on the backend.
- Track job state and implicit collection job states over time in a new "thread".
- New different colors of job states, add progress bar for multiple jobs.
---
 client/galaxy/scripts/mvc/history/hdca-li.js  | 102 ++++++++++-
 .../scripts/mvc/history/history-contents.js   |  60 +++++--
 .../scripts/mvc/history/history-model.js      |   7 +
 .../scripts/mvc/history/history-view.js       |  30 +---
 .../scripts/mvc/history/job-states-model.js   | 168 ++++++++++++++++++
 .../galaxy/scripts/mvc/history/multi-panel.js |  14 +-
 client/galaxy/style/less/base.less            |  31 ++++
 client/galaxy/style/less/list-item.less       |   7 +
 lib/galaxy/managers/jobs.py                   |  26 +++
 .../webapps/galaxy/api/history_contents.py    |  44 ++++-
 lib/galaxy/webapps/galaxy/buildapp.py         |   5 +
 11 files changed, 439 insertions(+), 55 deletions(-)
 create mode 100644 client/galaxy/scripts/mvc/history/job-states-model.js

diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js
index 7834ef9506b..ec3f6e443fb 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li.js
@@ -16,10 +16,14 @@ var HDCAListItemView = _super.extend(
         /** event listeners */
         _setUpListeners: function() {
             _super.prototype._setUpListeners.call(this);
+            var renderListen = (model, options) => {
+                this.render();
+            };
+            if (this.model.jobStatesSummary) {
+                this.listenTo(this.model.jobStatesSummary, "change", renderListen);
+            }
             this.listenTo(this.model, {
-                "change:tags change:populated change:visible": function(model, options) {
-                    this.render();
-                }
+                "change:tags change:visible change:state": renderListen
             });
         },
 
@@ -43,13 +47,95 @@ var HDCAListItemView = _super.extend(
         _swapNewRender: function($newRender) {
             _super.prototype._swapNewRender.call(this, $newRender);
             //TODO: model currently has no state
-            var state = !this.model.get("populated") ? STATES.RUNNING : STATES.OK;
-            //if( this.model.has( 'state' ) ){
+            var state;
+            var jobStatesSummary = this.model.jobStatesSummary;
+            if (jobStatesSummary) {
+                if (jobStatesSummary.new()) {
+                    state = "new";
+                } else if (jobStatesSummary.errored()) {
+                    state = "error";
+                } else if (jobStatesSummary.terminal()) {
+                    state = "ok";
+                } else if (jobStatesSummary.running()) {
+                    state = "running";
+                } else {
+                    state = "queued";
+                }
+            } else if (this.model.get("job_source_id")) {
+                // Initial rendering - polling will fill in more details in a bit.
+                state = STATES.NEW;
+            } else {
+                state = this.model.get("populated_state") ? STATES.OK : STATES.RUNNING;
+            }
             this.$el.addClass(`state-${state}`);
-            //}
+            var stateDescription = this.stateDescription();
+            this.$(".state-description").html(stateDescription);
             return this.$el;
         },
 
+        stateDescription: function() {
+            var collection = this.model;
+            var elementCount = collection.get("element_count");
+            var jobStateSource = collection.get("job_source_type");
+            var collectionType = this.model.get("collection_type");
+            var collectionTypeDescription;
+            if (collectionType == "list") {
+                collectionTypeDescription = "list";
+            } else if (collectionType == "paired") {
+                collectionTypeDescription = "dataset pair";
+            } else if (collectionType == "list:paired") {
+                collectionTypeDescription = "list of pairs";
+            } else {
+                collectionTypeDescription = "nested list";
+            }
+            var itemsDescription = "";
+            if (elementCount == 1) {
+                itemsDescription = ` with 1 item`;
+            } else if (elementCount) {
+                itemsDescription = ` with ${elementCount} items`;
+            }
+            var jobStatesSummary = collection.jobStatesSummary;
+            var simpleDescription = `${collectionTypeDescription}${itemsDescription}`;
+            if (!jobStateSource || jobStateSource == "Job") {
+                return `a ${simpleDescription}`;
+            } else if (!jobStatesSummary || !jobStatesSummary.hasDetails()) {
+                return `
+                    <div class="progress state-progress">
+                        <span class="note">Loading job data for ${collectionTypeDescription}...</span>
+                        <div class="progress-bar info" style="width:100%">
+                    </div>`;
+            } else {
+                var isNew = jobStatesSummary.new();
+                var jobCount = isNew ? null : jobStatesSummary.jobCount();
+                if (isNew) {
+                    return `
+                        <div class="progress state-progress">
+                            <span class="note">Creating jobs...</span>
+                            <div class="progress-bar info" style="width:100%">
+                        </div>`;
+                } else if (jobStatesSummary.errored()) {
+                    var errorCount = jobStatesSummary.numInError();
+                    return `a ${collectionTypeDescription} with ${errorCount} / ${jobCount} jobs in error`;
+                } else if (jobStatesSummary.terminal()) {
+                    return `a ${simpleDescription}`;
+                } else {
+                    var running = jobStatesSummary.states()["running"] || 0;
+                    var ok = jobStatesSummary.states()["ok"] || 0;
+                    var okPercent = ok / (jobCount * 1.0);
+                    var runningPercent = running / (jobCount * 1.0);
+                    var otherPercent = 1.0 - okPercent - runningPercent;
+                    var jobsStr = jobCount && jobCount > 1 ? `${jobCount} jobs` : `a job`;
+                    return `
+                        <div class="progress state-progress">
+                            <span class="note">${jobsStr} generating a ${collectionTypeDescription}</span>
+                            <div class="progress-bar ok" style="width:${okPercent * 100.0}%"></div>
+                            <div class="progress-bar running" style="width:${runningPercent * 100.0}%"></div>
+                            <div class="progress-bar new" style="width:${otherPercent * 100.0}%">
+                        </div>`;
+                }
+            }
+        },
+
         // ......................................................................... misc
         /** String representation */
         toString: function() {
@@ -69,7 +155,6 @@ HDCAListItemView.prototype.templates = (() => {
         }
     });
 
-    // could steal this from hda-base (or use mixed content)
     var titleBarTemplate = collection => `
         <div class="title-bar clear" tabindex="0">
             <span class="state-icon"></span>
@@ -77,7 +162,8 @@ HDCAListItemView.prototype.templates = (() => {
                 <span class="hid">${collection.hid}</span>
                 <span class="name">${_.escape(collection.name)}</span>
             </div>
-            <div class="subtitle"></div>
+            <div class="state-description">
+            </div>
             ${HISTORY_ITEM_LI.nametagTemplate(collection)}
         </div>
     `;
diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js
index 045745bf131..c175456fd9e 100644
--- a/client/galaxy/scripts/mvc/history/history-contents.js
+++ b/client/galaxy/scripts/mvc/history/history-contents.js
@@ -2,6 +2,7 @@ import CONTROLLED_FETCH_COLLECTION from "mvc/base/controlled-fetch-collection";
 import HDA_MODEL from "mvc/history/hda-model";
 import HDCA_MODEL from "mvc/history/hdca-model";
 import HISTORY_PREFS from "mvc/history/history-preferences";
+import JOB_STATES_MODEL from "mvc/history/job-states-model";
 import BASE_MVC from "mvc/base-mvc";
 import AJAX_QUEUE from "utils/ajax-queue";
 
@@ -37,6 +38,10 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
 
     /** Set up */
     initialize: function(models, options) {
+        this.on({
+            "sync add": this.trackJobStates
+        });
+
         options = options || {};
         _super.prototype.initialize.call(this, models, options);
 
@@ -53,6 +58,29 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         this.model.prototype.idAttribute = "type_id";
     },
 
+    trackJobStates: function() {
+        this.each(historyContent => {
+            if (historyContent.has("job_states_summary")) {
+                return;
+            }
+
+            if (historyContent.attributes.history_content_type === "dataset_collection") {
+                var jobSourceType = historyContent.attributes.job_source_type;
+                var jobSourceId = historyContent.attributes.job_source_id;
+                if (jobSourceType) {
+                    this.jobStateSummariesCollection.add({
+                        id: jobSourceId,
+                        model: jobSourceType,
+                        history_id: this.history_id,
+                        collection_id: historyContent.attributes.id
+                    });
+                    var jobStatesSummary = this.jobStateSummariesCollection.get(jobSourceId);
+                    historyContent.jobStatesSummary = jobStatesSummary;
+                }
+            }
+        });
+    },
+
     // ........................................................................ composite collection
     /** since history content is a mix, override model fn into a factory, creating based on history_content_type */
     model: function(attrs, options) {
@@ -82,17 +110,30 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         };
     },
 
+    stopPolling: function() {
+        if (this.jobStateSummariesCollection) {
+            this.jobStateSummariesCollection.active = false;
+            this.jobStateSummariesCollection.clearUpdateTimeout();
+        }
+    },
+
     setHistoryId: function(newId) {
+        this.stopPolling();
         this.historyId = newId;
-        this._setUpWebStorage();
+        if (newId) {
+            // If actually reflecting a history - setup storage and monitor jobs.
+
+            this._setUpWebStorage();
+
+            this.jobStateSummariesCollection = new JOB_STATES_MODEL.JobStatesSummaryCollection();
+            this.jobStateSummariesCollection.historyId = newId;
+            this.jobStateSummariesCollection.monitor();
+        }
     },
 
     /** Set up client side storage. Currently PersistanStorage keyed under 'history:<id>' */
     _setUpWebStorage: function(initialSettings) {
         // TODO: use initialSettings
-        if (!this.historyId) {
-            return;
-        }
         this.storage = new HISTORY_PREFS.HistoryPrefs({
             id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)
         });
@@ -303,17 +344,6 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         return this.fetch(options);
     },
 
-    /** specialty fetch method for retrieving the element_counts of all hdcas in the history */
-    fetchCollectionCounts: function(options) {
-        options = options || {};
-        options.keys = ["type_id", "element_count"].join(",");
-        options.filters = _.extend(options.filters || {}, {
-            history_content_type: "dataset_collection"
-        });
-        options.remove = false;
-        return this.fetch(options);
-    },
-
     // ............. quasi-batch ops
     // TODO: to batch
     /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */
diff --git a/client/galaxy/scripts/mvc/history/history-model.js b/client/galaxy/scripts/mvc/history/history-model.js
index 923b04672c5..48d3c5e6ca3 100644
--- a/client/galaxy/scripts/mvc/history/history-model.js
+++ b/client/galaxy/scripts/mvc/history/history-model.js
@@ -237,6 +237,13 @@ var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                 }
             },
 
+            stopPolling: function() {
+                this.clearUpdateTimeout();
+                if (this.contents) {
+                    this.contents.stopPolling();
+                }
+            },
+
             // ........................................................................ ajax
             /** override to use actual Dates objects for create/update times */
             parse: function(response, options) {
diff --git a/client/galaxy/scripts/mvc/history/history-view.js b/client/galaxy/scripts/mvc/history/history-view.js
index 140c2edb990..2cfa71fb99a 100644
--- a/client/galaxy/scripts/mvc/history/history-view.js
+++ b/client/galaxy/scripts/mvc/history/history-view.js
@@ -47,9 +47,6 @@ var HistoryView = _super.extend(
         /** string used for search placeholder */
         searchPlaceholder: _l("search datasets"),
 
-        /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */
-        FETCH_COLLECTION_COUNTS_DELAY: 2000,
-
         // ......................................................................... SET UP
         /** Set up the view, bind listeners.
          *  @param {Object} attributes optional settings for the panel
@@ -60,9 +57,6 @@ var HistoryView = _super.extend(
             // control contents/behavior based on where (and in what context) the panel is being used
             /** where should pages from links be displayed? (default to new tab/window) */
             this.linkTarget = attributes.linkTarget || "_blank";
-
-            /** timeout id for detailed fetch of collection counts, etc... */
-            this.detailedFetchTimeoutId = null;
         },
 
         /** create and return a collection for when none is initially passed */
@@ -77,20 +71,11 @@ var HistoryView = _super.extend(
         freeModel: function() {
             _super.prototype.freeModel.call(this);
             if (this.model) {
-                this.model.clearUpdateTimeout();
+                this.model.stopPolling();
             }
-            this._clearDetailedFetchTimeout();
             return this;
         },
 
-        /** clear the timeout and the cached timeout id */
-        _clearDetailedFetchTimeout: function() {
-            if (this.detailedFetchTimeoutId) {
-                clearTimeout(this.detailedFetchTimeoutId);
-                this.detailedFetchTimeoutId = null;
-            }
-        },
-
         /** create any event listeners for the panel
          *  @fires: rendered:initial    on the first render
          *  @fires: empty-history       when switching to a history with no contents or creating a new history
@@ -101,13 +86,6 @@ var HistoryView = _super.extend(
                 error: function(model, xhr, options, msg, details) {
                     this.errorHandler(model, xhr, options, msg, details);
                 },
-                "loading-done": () => {
-                    // after the initial load, decorate with more time consuming fields (like HDCA element_counts)
-                    this.detailedFetchTimeoutId = _.delay(() => {
-                        this.detailedFetchTimeoutId = null;
-                        this.model.contents.fetchCollectionCounts();
-                    }, this.FETCH_COLLECTION_COUNTS_DELAY);
-                },
                 "views:ready view:attached view:removed": function(view) {
                     this._renderSelectButton();
                 },
@@ -378,17 +356,17 @@ var HistoryView = _super.extend(
         }),
 
         _clickPrevPage: function(ev) {
-            this.model.clearUpdateTimeout();
+            this.model.stopPolling();
             this.model.contents.fetchPrevPage();
         },
 
         _clickNextPage: function(ev) {
-            this.model.clearUpdateTimeout();
+            this.model.stopPolling();
             this.model.contents.fetchNextPage();
         },
 
         _changePageSelect: function(ev) {
-            this.model.clearUpdateTimeout();
+            this.model.stopPolling();
             var page = $(ev.currentTarget).val();
             this.model.contents.fetchPage(page);
         },
diff --git a/client/galaxy/scripts/mvc/history/job-states-model.js b/client/galaxy/scripts/mvc/history/job-states-model.js
new file mode 100644
index 00000000000..fffee020ead
--- /dev/null
+++ b/client/galaxy/scripts/mvc/history/job-states-model.js
@@ -0,0 +1,168 @@
+import * as Backbone from "libs/backbone";
+import AJAX_QUEUE from "utils/ajax-queue";
+
+/** ms between fetches when checking running jobs/datasets for updates */
+var UPDATE_DELAY = 2000;
+var NON_TERMINAL_STATES = ["new", "queued", "running"];
+var ERROR_STATES = ["error", "deleted"];
+/** Fetch state on add or just wait for polling to start. */
+var FETCH_STATE_ON_ADD = false;
+var BATCH_FETCH_STATE = true;
+
+var JobStatesSummary = Backbone.Model.extend({
+    url: function() {
+        return `${Galaxy.root}api/histories/${this.attributes.history_id}/contents/dataset_collections/${
+            this.attributes.collection_id
+        }/jobs_summary`;
+    },
+
+    hasDetails: function() {
+        return this.has("populated_state");
+    },
+
+    new: function() {
+        return !this.hasDetails() || this.get("populated_state") == "new";
+    },
+
+    errored: function() {
+        return this.get("populated_state") === "error" || this.anyWithStates(ERROR_STATES);
+    },
+
+    states: function() {
+        return this.get("states") || {};
+    },
+
+    anyWithState: function(queryState) {
+        return (this.states()[queryState] || 0) > 0;
+    },
+
+    anyWithStates: function(queryStates) {
+        var states = this.states();
+        for (var index in queryStates) {
+            if ((states[queryStates[index]] || 0) > 0) {
+                return true;
+            }
+        }
+        return false;
+    },
+
+    numWithStates: function(queryStates) {
+        var states = this.states();
+        var count = 0;
+        for (var index in queryStates) {
+            count += states[queryStates[index]] || 0;
+        }
+        return count;
+    },
+
+    numInError: function() {
+        return this.numWithStates(ERROR_STATES);
+    },
+
+    running: function() {
+        return this.anyWithState("running");
+    },
+
+    terminal: function() {
+        if (this.new()) {
+            return false;
+        } else {
+            var anyNonTerminal = this.anyWithStates(NON_TERMINAL_STATES);
+            return !anyNonTerminal;
+        }
+    },
+
+    jobCount: function() {
+        var states = this.states();
+        var count = 0;
+        for (var index in states) {
+            count += states[index];
+        }
+        return count;
+    },
+
+    toString: function() {
+        return `JobStatesSummary(id=${this.get("id")})`;
+    }
+});
+
+var JobStatesSummaryCollection = Backbone.Collection.extend({
+    model: JobStatesSummary,
+
+    initialize: function() {
+        if (FETCH_STATE_ON_ADD) {
+            this.on({
+                add: model => model.fetch()
+            });
+        }
+
+        /** cached timeout id for the dataset updater */
+        this.updateTimeoutId = null;
+        // this.checkForUpdates();
+        this.active = true;
+    },
+
+    url: function() {
+        var nonTerminalModels = this.models.filter(model => {
+            return !model.terminal();
+        });
+        var ids = nonTerminalModels
+            .map(summary => {
+                return summary.get("id");
+            })
+            .join(",");
+        var types = nonTerminalModels
+            .map(summary => {
+                return summary.get("model");
+            })
+            .join(",");
+        return `${Galaxy.root}api/histories/${this.historyId}/jobs_summary?ids=${ids}&types=${types}`;
+    },
+
+    monitor: function() {
+        this.clearUpdateTimeout();
+        if (!this.active) {
+            return;
+        }
+
+        var _delayThenMonitorAgain = () => {
+            this.updateTimeoutId = setTimeout(() => {
+                this.monitor();
+            }, UPDATE_DELAY);
+        };
+
+        var nonTerminalModels = this.models.filter(model => {
+            return !model.terminal();
+        });
+
+        if (nonTerminalModels.length > 0 && !BATCH_FETCH_STATE) {
+            // Allow models to fetch their own details.
+            var updateFunctions = nonTerminalModels.map(summary => {
+                return () => {
+                    return summary.fetch();
+                };
+            });
+
+            return new AJAX_QUEUE.AjaxQueue(updateFunctions).done(_delayThenMonitorAgain);
+        } else if (nonTerminalModels.length > 0) {
+            // Batch fetch updated state...
+            this.fetch({ remove: false }).done(_delayThenMonitorAgain);
+        } else {
+            _delayThenMonitorAgain();
+        }
+    },
+
+    /** clear the timeout and the cached timeout id */
+    clearUpdateTimeout: function() {
+        if (this.updateTimeoutId) {
+            clearTimeout(this.updateTimeoutId);
+            this.updateTimeoutId = null;
+        }
+    },
+
+    toString: function() {
+        return `JobStatesSummaryCollection()`;
+    }
+});
+
+export default { JobStatesSummary, JobStatesSummaryCollection, FETCH_STATE_ON_ADD };
diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index 91e81ed22cd..2652d7c243c 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -1,6 +1,7 @@
 import _l from "utils/localization";
 import HISTORY_MODEL from "mvc/history/history-model";
 import HISTORY_VIEW_EDIT from "mvc/history/history-view-edit";
+import JOB_STATES_MODEL from "mvc/history/job-states-model";
 import historyCopyDialog from "mvc/history/copy-dialog";
 import ERROR_MODAL from "mvc/ui/error-modal";
 import baseMVC from "mvc/base-mvc";
@@ -733,9 +734,16 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             this.hdaQueue.add({
                 name: column.model.id,
                 fn: function() {
-                    return contents.fetchCurrentPage(fetchOptions).done(() => {
-                        column.panel.renderItems();
-                    });
+                    return contents
+                        .fetchCurrentPage(fetchOptions)
+                        .done(() => {
+                            column.panel.renderItems();
+                        })
+                        .done(() => {
+                            if (!JOB_STATES_MODEL.FETCH_STATE_ON_ADD) {
+                                contents.jobStateSummariesCollection.fetch();
+                            }
+                        });
                 }
             });
             // the queue is re-used, so if it's not processing requests - start it again
diff --git a/client/galaxy/style/less/base.less b/client/galaxy/style/less/base.less
index c04ac237568..f5ba8069140 100644
--- a/client/galaxy/style/less/base.less
+++ b/client/galaxy/style/less/base.less
@@ -1108,6 +1108,37 @@ ul.manage-table-actions li {
     margin-left: 0.5em;
 }
 
+.state-progress {
+    border: 1px solid gray;
+    position: relative;
+
+    margin-top: 2px;
+    margin-bottom: 1px;
+
+    .info {
+        color: @black;
+        background: @white;
+    }
+
+    .new {
+        background: @state-default-bg;
+    }
+
+    .running {
+        background: @state-running-bg;
+    }
+
+    .ok {
+        background: @state-success-bg;
+    }
+
+    .note {
+        margin-left: 1em;
+        position: absolute;
+    }
+
+}
+
 // State colors
 
 .state-color-new {
diff --git a/client/galaxy/style/less/list-item.less b/client/galaxy/style/less/list-item.less
index ca5f61b487f..36abdaea718 100644
--- a/client/galaxy/style/less/list-item.less
+++ b/client/galaxy/style/less/list-item.less
@@ -86,6 +86,13 @@
                 color: inherit;
             }
         }
+        .state-description {
+            color: #777;
+            font-size: 90%;
+            a {
+                color: inherit;
+            }
+        }
     }
 
     .primary-actions {
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index b967f897c9e..b17fa922f1b 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -8,6 +8,7 @@ from sqlalchemy.orm import aliased
 from sqlalchemy.sql import select
 
 from galaxy import model
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.lddas import LDDAManager
@@ -246,6 +247,31 @@ class JobSearch(object):
         return None
 
 
+def fetch_job_states(app, sa_session, job_source_ids, job_source_types):
+    decode = app.security.decode_id
+    assert len(job_source_ids) == len(job_source_types)
+    job_ids = set()
+    implicit_collection_job_ids = set()
+
+    for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
+        if job_source_type == "Job":
+            job_ids.add(job_source_id)
+        elif job_source_type == "ImplicitCollectionJobs":
+            implicit_collection_job_ids.add(job_source_id)
+        else:
+            raise RequestParameterInvalidException("Invalid job source type %s found." % job_source_type)
+
+    # TODO: use above sets and optimize queries on second pass.
+    rval = []
+    for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
+        if job_source_type == "Job":
+            rval.append(summarize_jobs_to_dict(sa_session, sa_session.query(model.Job).get(decode(job_source_id))))
+        else:
+            rval.append(summarize_jobs_to_dict(sa_session, sa_session.query(model.ImplicitCollectionJobs).get(decode(job_source_id))))
+
+    return rval
+
+
 def summarize_jobs_to_dict(sa_session, jobs_source):
     """Proudce a summary of jobs for job summary endpoints.
 
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index f6fc932b5a0..357be202da3 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -21,7 +21,7 @@ from galaxy.managers.collections_util import (
     dictify_dataset_collection_instance,
     get_hda_and_element_identifiers
 )
-from galaxy.managers.jobs import summarize_jobs_to_dict
+from galaxy.managers.jobs import fetch_job_states, summarize_jobs_to_dict
 from galaxy.util.json import safe_dumps
 from galaxy.util.streamball import StreamBall
 from galaxy.web import (
@@ -155,12 +155,50 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         elif contents_type == 'dataset_collection':
             return self.__show_dataset_collection(trans, id, history_id, **kwd)
 
+    @expose_api_anonymous
+    def index_jobs_summary(self, trans, history_id, **kwd):
+        """
+        * GET /api/histories/{history_id}/jobs_summary
+            return detailed information about an HDA or HDCAs jobs
+
+        Warning: We allow anyone to fetch job state information about any object they
+        can guess an encoded ID for - it isn't considered protected data. This keeps
+        polling IDs as part of state calculation for large histories and collections as
+        efficient as possible.
+
+        :type   history_id: str
+        :param  history_id: encoded id string of the HDA's or the HDCA's History
+        :type   ids:        str[]
+        :param  ids:        the encoded ids of job summary objects to return - if ids
+                            is specified types must also be specified and have same length.
+        :type   types:      str[]
+        :param  types:      type of object represented by elements in the ids array - either
+                            Job or ImplicitCollectionJob.
+
+        :rtype:     dict[]
+        :returns:   an array of job summary object dictionaries.
+        """
+        ids = kwd.get("ids", None)
+        types = kwd.get("types", None)
+        if ids is None:
+            assert types is None
+            # TODO: ...
+            pass
+        else:
+            ids = util.listify(ids)
+            types = util.listify(types)
+        return map(lambda s: self.encode_all_ids(trans, s), fetch_job_states(self.app, trans.sa_session, ids, types))
+
     @expose_api_anonymous
     def show_jobs_summary(self, trans, id, history_id, **kwd):
         """
         * GET /api/histories/{history_id}/contents/{type}/{id}/jobs_summary
             return detailed information about an HDA or HDCAs jobs
-        .. note:: Anonymous users are allowed to get their current history contents
+
+        Warning: We allow anyone to fetch job state information about any object they
+        can guess an encoded ID for - it isn't considered protected data. This keeps
+        polling IDs as part of state calculation for large histories and collections as
+        efficient as possible.
 
         :type   id:         str
         :param  id:         the encoded id of the HDA to return
@@ -168,7 +206,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         :param  history_id: encoded id string of the HDA's or the HDCA's History
 
         :rtype:     dict
-        :returns:   dictionary containing
+        :returns:   dictionary containing jobs summary object
         """
         contents_type = self.__get_contents_type(trans, kwd)
         # At most one of job or implicit_collection_jobs should be found.
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index cab77e6cfb4..04f56c0fd5f 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -363,6 +363,11 @@ def populate_api_routes(webapp, app):
                           action='download_dataset_collection',
                           conditions=dict(method=["GET"]))
 
+    webapp.mapper.connect("/api/histories/{history_id}/jobs_summary",
+                          action="index_jobs_summary",
+                          controller='history_contents',
+                          conditions=dict(method=["GET"]))
+
     webapp.mapper.connect("/api/histories/{history_id}/contents/{type:%s}s/{id}/jobs_summary" % "|".join(valid_history_contents_types),
                           action="show_jobs_summary",
                           controller='history_contents',

From e7e659cabcf2a5928ab58e73715c0959c78cc997 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 28 Nov 2017 16:34:45 -0500
Subject: [PATCH 19/22] Better dataset loading description.

---
 client/galaxy/scripts/mvc/history/hdca-li.js |  8 ++++----
 client/galaxy/style/less/dataset.less        | 16 ++++++++++++++++
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js
index ec3f6e443fb..cd207ea15de 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li.js
@@ -51,7 +51,7 @@ var HDCAListItemView = _super.extend(
             var jobStatesSummary = this.model.jobStatesSummary;
             if (jobStatesSummary) {
                 if (jobStatesSummary.new()) {
-                    state = "new";
+                    state = "loading";
                 } else if (jobStatesSummary.errored()) {
                     state = "error";
                 } else if (jobStatesSummary.terminal()) {
@@ -63,7 +63,7 @@ var HDCAListItemView = _super.extend(
                 }
             } else if (this.model.get("job_source_id")) {
                 // Initial rendering - polling will fill in more details in a bit.
-                state = STATES.NEW;
+                state = "loading";
             } else {
                 state = this.model.get("populated_state") ? STATES.OK : STATES.RUNNING;
             }
@@ -101,7 +101,7 @@ var HDCAListItemView = _super.extend(
             } else if (!jobStatesSummary || !jobStatesSummary.hasDetails()) {
                 return `
                     <div class="progress state-progress">
-                        <span class="note">Loading job data for ${collectionTypeDescription}...</span>
+                        <span class="note">Loading job data for ${collectionTypeDescription}.<span class="blinking">..</span></span>
                         <div class="progress-bar info" style="width:100%">
                     </div>`;
             } else {
@@ -110,7 +110,7 @@ var HDCAListItemView = _super.extend(
                 if (isNew) {
                     return `
                         <div class="progress state-progress">
-                            <span class="note">Creating jobs...</span>
+                            <span class="note">Creating jobs.<span class="blinking">..</span></span>
                             <div class="progress-bar info" style="width:100%">
                         </div>`;
                 } else if (jobStatesSummary.errored()) {
diff --git a/client/galaxy/style/less/dataset.less b/client/galaxy/style/less/dataset.less
index 3b88fa3b5ad..196a4451ed3 100644
--- a/client/galaxy/style/less/dataset.less
+++ b/client/galaxy/style/less/dataset.less
@@ -176,6 +176,22 @@
             }
         }
     }
+
+    &.state-loading {
+        background: @state-default-bg;
+        .state-icon {
+            .state-icon-running;
+        }
+    }
+
+}
+
+.blinking {
+  animation: blinker 500ms linear infinite;
+}
+
+@keyframes blinker {
+  50% { opacity: 0; }
 }
 
 // ---------------------------------------------------------------------------- datasets as list-items

From 075d8c1d0ab7dca9c8573fe69a5ef7ec18ab2202 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 15 Nov 2017 10:36:47 -0500
Subject: [PATCH 20/22] Rename huge database migration to reflect new PR topic.

---
 ..._workflow_outputs.py => 0136_collection_and_workflow_state.py} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename lib/galaxy/model/migrate/versions/{0136_record_workflow_outputs.py => 0136_collection_and_workflow_state.py} (100%)

diff --git a/lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
similarity index 100%
rename from lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py
rename to lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py

From 8fa5496ba59e39ce4d16bd7c8da1d92989c7f5da Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 28 Nov 2017 18:41:23 -0500
Subject: [PATCH 21/22] Restructure collection state GUI tests to separate
 flakey tests of running state out.

Paste just sometimes randomly hangs when it is not supposed to.
---
 .../test_history_panel_collections.py         | 57 +++++++++++++++----
 1 file changed, 45 insertions(+), 12 deletions(-)

diff --git a/test/selenium_tests/test_history_panel_collections.py b/test/selenium_tests/test_history_panel_collections.py
index 287345f7aea..f38f344ac8a 100644
--- a/test/selenium_tests/test_history_panel_collections.py
+++ b/test/selenium_tests/test_history_panel_collections.py
@@ -1,6 +1,7 @@
 import time
 
 from base.api_asserts import assert_status_code_is
+from base.populators import flakey
 
 from .framework import (
     selenium_test,
@@ -13,19 +14,43 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
     ensure_registered = True
 
     @selenium_test
-    def test_mapping_collection_states(self):
+    def test_mapping_collection_states_terminal(self):
         history_id = self.current_history_id()
         input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
         input_hid = input_collection["hid"]
 
-        # TODO: okay dataset...
-
         failed_response = self.dataset_populator.run_exit_code_from_file(history_id, input_collection["id"])
         failed_hid = failed_response["implicit_collections"][0]["hid"]
 
+        ok_inputs = {
+            "input1": {'batch': True, 'values': [{"src": "hdca", "id": input_collection["id"]}]},
+            "sleep_time": 0,
+        }
+        ok_response = self.dataset_populator.run_tool(
+            "cat_data_and_sleep",
+            ok_inputs,
+            history_id,
+            assert_ok=True,
+        )
+        ok_hid = ok_response["implicit_collections"][0]["hid"]
+        # sleep really shouldn't be needed :(
+        time.sleep(1)
+
+        self.home()
+
+        self.history_panel_wait_for_hid_state(input_hid, "ok")
+        self.history_panel_wait_for_hid_state(failed_hid, "error")
+        self.history_panel_wait_for_hid_state(ok_hid, "ok")
+        self.screenshot("history_panel_collections_state_mapping_terminal")
+
+    @selenium_test
+    @flakey  # Some times a Paste web thread will stall when jobs are running.
+    def test_mapping_collection_states_running(self):
+        history_id = self.current_history_id()
+        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1"]).json()
         running_inputs = {
             "input1": {'batch': True, 'values': [{"src": "hdca", "id": input_collection["id"]}]},
-            "sleep_time": 180,
+            "sleep_time": 60,
         }
         running_response = self.dataset_populator.run_tool(
             "cat_data_and_sleep",
@@ -42,16 +67,14 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
 
             self.home()
 
-            self.history_panel_wait_for_hid_state(input_hid, "ok")
-            self.history_panel_wait_for_hid_state(failed_hid, "error")
             self.history_panel_wait_for_hid_state(running_hid, "running")
-            self.screenshot("history_panel_collections_state_mapping")
+            self.screenshot("history_panel_collections_state_mapping_running")
         finally:
             for job in running_response.json()["jobs"]:
                 self.dataset_populator.cancel_job(job["id"])
 
     @selenium_test
-    def test_output_collection_states(self):
+    def test_output_collection_states_terminal(self):
         history_id = self.current_history_id()
         input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
 
@@ -72,6 +95,19 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
         )
         failed_hid = failed_response["output_collections"][0]["hid"]
 
+        # sleep really shouldn't be needed :(
+        time.sleep(1)
+
+        self.home()
+
+        self.history_panel_wait_for_hid_state(ok_hid, "ok")
+        self.history_panel_wait_for_hid_state(failed_hid, "error")
+        self.screenshot("history_panel_collections_state_terminal")
+
+    @selenium_test
+    @flakey  # Some times a Paste web thread will stall when jobs are running.
+    def test_output_collection_states_running(self):
+        history_id = self.current_history_id()
         running_inputs = {
             "sleep_time": 180,
         }
@@ -89,11 +125,8 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
             time.sleep(1)
 
             self.home()
-
-            self.history_panel_wait_for_hid_state(ok_hid, "ok")
-            self.history_panel_wait_for_hid_state(failed_hid, "error")
             self.history_panel_wait_for_hid_state(running_hid, "running")
-            self.screenshot("history_panel_collections_state")
+            self.screenshot("history_panel_collections_state_running")
         finally:
             for job in running_response.json()["jobs"]:
                 self.dataset_populator.cancel_job(job["id"])

From c47d8992ba52e5af8eae635a4ce50cca8a6d02c9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 30 Nov 2017 10:03:00 -0500
Subject: [PATCH 22/22] Repack client.

---
 static/scripts/bundled/admin.bundled.js         | 2 +-
 static/scripts/bundled/adminToolshed.bundled.js | 2 +-
 static/scripts/bundled/analysis.bundled.js      | 6 +++---
 static/scripts/bundled/library.bundled.js       | 4 ++--
 static/scripts/bundled/libs.bundled.js          | 8 ++++----
 static/scripts/bundled/login.bundled.js         | 2 +-
 static/scripts/bundled/masthead.bundled.js      | 2 +-
 static/scripts/bundled/viz.bundled.js           | 2 +-
 static/scripts/bundled/workflow.bundled.js      | 2 +-
 static/scripts/mvc/history/hdca-li.js           | 2 +-
 static/scripts/mvc/history/history-contents.js  | 2 +-
 static/scripts/mvc/history/history-model.js     | 2 +-
 static/scripts/mvc/history/history-view.js      | 2 +-
 static/scripts/mvc/history/job-states-model.js  | 1 +
 static/scripts/mvc/history/multi-panel.js       | 2 +-
 static/style/blue/base.css                      | 2 +-
 16 files changed, 22 insertions(+), 21 deletions(-)
 create mode 100644 static/scripts/mvc/history/job-states-model.js

diff --git a/static/scripts/bundled/admin.bundled.js b/static/scripts/bundled/admin.bundled.js
index 055d2fff0bf..28c89a59d08 100644
--- a/static/scripts/bundled/admin.bundled.js
+++ b/static/scripts/bundled/admin.bundled.js
@@ -4,4 +4,4 @@ webpackJsonp([1],[,,,,function(t,e,i){"use strict";(function(t,n,a){function r(t
  * @author   Feross Aboukhadijeh <feross@feross.org> <http://feross.org>
  * @license  MIT
  */
-t.exports=function(t){return null!=t&&(i(t)||n(t)||!!t._isBuffer)}},function(t,e,i){"use strict";function n(t){this.defaults=t,this.interceptors={request:new o,response:new o}}var a=i(16),r=i(5),o=i(85),s=i(86);n.prototype.request=function(t){"string"==typeof t&&(t=r.merge({url:arguments[0]},arguments[1])),t=r.merge(a,this.defaults,{method:"get"},t),t.method=t.method.toLowerCase();var e=[s,void 0],i=Promise.resolve(t);for(this.interceptors.request.forEach(function(t){e.unshift(t.fulfilled,t.rejected)}),this.interceptors.response.forEach(function(t){e.push(t.fulfilled,t.rejected)});e.length;)i=i.then(e.shift(),e.shift());return i},r.forEach(["delete","get","head","options"],function(t){n.prototype[t]=function(e,i){return this.request(r.merge(i||{},{method:t,url:e}))}}),r.forEach(["post","put","patch"],function(t){n.prototype[t]=function(e,i,n){return this.request(r.merge(n||{},{method:t,url:e,data:i}))}}),t.exports=n},function(t,e){function i(){throw new Error("setTimeout has not been 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v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,q-j,$),void 0!==v&&k>x&&!(j>b||q<v)){var D=Math.max(j,v),I=Math.min(q,b);t.fillRect(D,d+1,I-D,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<I&&(D+=2,I-=2),t.fillRect(D,d+1,I-D,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+g;if(p=f(D),_=f(D+q),o([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=q;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+q):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,s-a)));for(var L=Math.max(D,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=q),g+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=q;break;case"D":$.draw_deletion(p,S,q),g+=q;break;case"I":var V=p-b;if(o([D,D+q],m)){var G=h.slice(v,v+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-s);break;case 1005:break;case 1002:G=G.slice(a-D,D-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(D+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=q}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,q),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];S.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&(S<0||x>$)&&(S=k,$=i<0?x:w,i<0?y:b),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&s.push(l[d]);return a(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return r.topLevelReductionCache=o,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=i>0?0:3e8;t.fromRef&&(s=e);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>s)return a(u)}else u.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<s)return a(u)}else u.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(s+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(o(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=r.exec(n);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};n=n.substring(s[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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e=this;e.options={};for(var n in i.defaultOptions)i.defaultOptions.hasOwnProperty(n)&&(e.options[n]=t.hasOwnProperty(n)?t[n]:i.defaultOptions[n]);return e.options.logLevel=e._parseLevel(e.options.logLevel),e.options.consoleLevel=e._parseLevel(e.options.consoleLevel),e._sending=!1,e._waiting=null,e._postSize=e.options.postSize,e._initCache(),e},i.prototype._initCache=function(){try{this.cache=new a({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(t){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",t]),this.options.logLevel=i.NONE}},i.prototype._parseLevel=function(t){var e=void 0===t?"undefined":r(t);if("number"===e)return t;if("string"===e){var n=t.toUpperCase();if(i.hasOwnProperty(n))return i[n]}throw new Error("Unknown log level: "+t)},i.prototype.emit=function(t,e,i){var n=this;return 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r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof r.consoleLogger.log&&r.consoleLogger.log.apply(r.consoleLogger,s),r)},i.prototype.log=function(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.debug=function(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.info=function(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.warn=function(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.error=function(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.metric=function(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},a.defaultOptions={maxSize:5e3},a.prototype._init=function(t){if(!this._hasStorage())throw new Error("LoggingCache needs localStorage");if(!t.key)throw new Error("LoggingCache needs key for localStorage");return this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return localStorage.setItem(this.key,"[]"),this},a.prototype.stringify=function(t){return JSON.stringify(this.get(t))},a.prototype.print=function(){console.log(JSON.stringify(this._fetchAndParse(),null,"  "))},e.default={MetricsLogger:i,LoggingCache:a}}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(160),s=r(o),l=i(176),d=r(l),c=i(9),u=r(c),h=i(3),f=r(h),p=t.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(e){var i=this;this.config=n.defaults(e.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(t){t.title?(f.default.setWindowTitle(t.title),t.allow_title_display=!1):(f.default.setWindowTitle(),t.allow_title_display=!0),i.center.display(t)},Galaxy.router=this.router=e.Router&&new e.Router(i,e),this.masthead=new s.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(t){var n=t.charAt(0).toUpperCase()+t.slice(1),a=e[n];if(a){var r=new a(i,e);i[r.toString()]=r,i.panels[t]=new d.default.SidePanel({id:t,el:i.$("#"+t),view:r})}}),this.render(),this.router&&t.history.start({root:Galaxy.root,pushState:!0})},render:function(){return 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i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var t=window.Galaxy.config.communication_server_host,e=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:t+":"+e}).success(function(t){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(t){n.css("visibility","hidden")}):n.css("visibility","hidden")}});e.default={View:p}}).call(e,i(1),i(2),i(0))},,,function(t,e,i){"use strict";(function(t){function 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a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},e.redirect?window.location=Galaxy.root+e.redirect+"?"+n.param(a):(t.data.matchModel(i,function(e,i){t.field_list[i].value(e.value)}),e._showMessage(t,success_message))}).fail(function(i){e._showMessage(t,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(t,e){t.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),t.message.update(e)}});e.default={View:d}}).call(e,i(1),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,i){"use strict";(function(t){function e(t){return t&&t.__esModule?t:{default:t}}var n=i(0),a=e(n),r=i(177),o=e(r),s=i(277),l=e(s),d=i(197),c=e(d),u=i(26),h=e(u),f=i(4),p=(e(f),i(61)),_=e(p),m=i(182),g=e(m),v=i(3),b=e(v),w=i(179),y=e(w),x=i(142),k=e(x),C=i(278),S=e(C),$=a.default;window.app=function(e,i){window.Galaxy=new 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v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,q-j,$),void 0!==v&&k>x&&!(j>b||q<v)){var D=Math.max(j,v),I=Math.min(q,b);t.fillRect(D,d+1,I-D,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<I&&(D+=2,I-=2),t.fillRect(D,d+1,I-D,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+g;if(p=f(D),_=f(D+q),o([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=q;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+q):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,s-a)));for(var L=Math.max(D,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=q),g+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=q;break;case"D":$.draw_deletion(p,S,q),g+=q;break;case"I":var V=p-b;if(o([D,D+q],m)){var G=h.slice(v,v+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-s);break;case 1005:break;case 1002:G=G.slice(a-D,D-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(D+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=q}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,q),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];S.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&(S<0||x>$)&&(S=k,$=i<0?x:w,i<0?y:b),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&s.push(l[d]);return a(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return r.topLevelReductionCache=o,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=i>0?0:3e8;t.fromRef&&(s=e);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>s)return a(u)}else u.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<s)return a(u)}else u.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(s+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(o(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=r.exec(n);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};n=n.substring(s[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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e=this;e.options={};for(var n in i.defaultOptions)i.defaultOptions.hasOwnProperty(n)&&(e.options[n]=t.hasOwnProperty(n)?t[n]:i.defaultOptions[n]);return e.options.logLevel=e._parseLevel(e.options.logLevel),e.options.consoleLevel=e._parseLevel(e.options.consoleLevel),e._sending=!1,e._waiting=null,e._postSize=e.options.postSize,e._initCache(),e},i.prototype._initCache=function(){try{this.cache=new a({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(t){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",t]),this.options.logLevel=i.NONE}},i.prototype._parseLevel=function(t){var e=void 0===t?"undefined":r(t);if("number"===e)return t;if("string"===e){var n=t.toUpperCase();if(i.hasOwnProperty(n))return i[n]}throw new Error("Unknown log level: "+t)},i.prototype.emit=function(t,e,i){var n=this;return 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r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof r.consoleLogger.log&&r.consoleLogger.log.apply(r.consoleLogger,s),r)},i.prototype.log=function(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.debug=function(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.info=function(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.warn=function(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.error=function(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.metric=function(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},a.defaultOptions={maxSize:5e3},a.prototype._init=function(t){if(!this._hasStorage())throw new Error("LoggingCache needs localStorage");if(!t.key)throw new Error("LoggingCache needs key for localStorage");return this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return localStorage.setItem(this.key,"[]"),this},a.prototype.stringify=function(t){return JSON.stringify(this.get(t))},a.prototype.print=function(){console.log(JSON.stringify(this._fetchAndParse(),null,"  "))},e.default={MetricsLogger:i,LoggingCache:a}}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(160),s=r(o),l=i(176),d=r(l),c=i(9),u=r(c),h=i(3),f=r(h),p=t.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(e){var i=this;this.config=n.defaults(e.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(t){t.title?(f.default.setWindowTitle(t.title),t.allow_title_display=!1):(f.default.setWindowTitle(),t.allow_title_display=!0),i.center.display(t)},Galaxy.router=this.router=e.Router&&new e.Router(i,e),this.masthead=new s.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(t){var n=t.charAt(0).toUpperCase()+t.slice(1),a=e[n];if(a){var r=new a(i,e);i[r.toString()]=r,i.panels[t]=new d.default.SidePanel({id:t,el:i.$("#"+t),view:r})}}),this.render(),this.router&&t.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var t=this.config.message_box_content||"",e=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+e+"-message").html(t).toggle(!!t).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var t=this.config.inactivity_box_content||"",e=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(t+" ").append(e).toggle(!!t).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var t=this;return n.each(this._panelids,function(e){var i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var t=window.Galaxy.config.communication_server_host,e=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:t+":"+e}).success(function(t){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(t){n.css("visibility","hidden")}):n.css("visibility","hidden")}});e.default={View:p}}).call(e,i(1),i(2),i(0))},,,function(t,e,i){"use strict";(function(t){function 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a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},e.redirect?window.location=Galaxy.root+e.redirect+"?"+n.param(a):(t.data.matchModel(i,function(e,i){t.field_list[i].value(e.value)}),e._showMessage(t,success_message))}).fail(function(i){e._showMessage(t,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(t,e){t.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),t.message.update(e)}});e.default={View:d}}).call(e,i(1),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,i){"use strict";(function(t){function e(t){return t&&t.__esModule?t:{default:t}}var n=i(0),a=e(n),r=i(177),o=e(r),s=i(278),l=e(s),d=i(197),c=e(d),u=i(26),h=e(u),f=i(4),p=(e(f),i(61)),_=e(p),m=i(182),g=e(m),v=i(3),b=e(v),w=i(179),y=e(w),x=i(142),k=e(x),C=i(279),S=e(C),$=a.default;window.app=function(e,i){window.Galaxy=new o.default.GalaxyApp(e,i),Galaxy.debug("admin app");var n=g.default.extend({routes:{"(/)admin(/)users":"show_users","(/)admin(/)roles":"show_roles","(/)admin(/)groups":"show_groups","(/)admin(/)tool_versions":"show_tool_versions","(/)admin(/)quotas":"show_quotas","(/)admin(/)repositories":"show_repositories","(/)admin(/)forms":"show_forms","(/)admin(/)form(/)(:form_id)":"show_form","(/)admin/api_keys":"show_user_api_keys"},authenticate:function(t,e){return Galaxy.user&&Galaxy.user.id&&Galaxy.user.get("is_admin")},show_users:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/users_list",url_data:Galaxy.params,dict_format:!0}))},show_roles:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/roles_list",url_data:Galaxy.params,dict_format:!0}))},show_groups:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/groups_list",url_data:Galaxy.params,dict_format:!0}))},show_repositories:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin_toolshed/browse_repositories",url_data:Galaxy.params,dict_format:!0}))},show_tool_versions:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/tool_versions_list",url_data:Galaxy.params,dict_format:!0}))},show_quotas:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/quotas_list",url_data:Galaxy.params,dict_format:!0}))},show_user_api_keys:function(){var t=document.createElement("div");this.page.display(t),new k.default(S.default).$mount(t)},show_forms:function(){this.page.display(new h.default({url_base:Galaxy.root+"forms/forms_list",url_data:Galaxy.params,dict_format:!0}))},show_form:function(t){var e="?id="+_.default.get("id"),i={reset_user_password:{title:"Reset passwords",url:"admin/reset_user_password"+e,icon:"fa-user",submit_title:"Save new 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diff --git a/static/scripts/bundled/adminToolshed.bundled.js b/static/scripts/bundled/adminToolshed.bundled.js
index e67e77f0a0b..0732a93d49c 100644
--- a/static/scripts/bundled/adminToolshed.bundled.js
+++ b/static/scripts/bundled/adminToolshed.bundled.js
@@ -46,4 +46,4 @@ r=i,l=e("<div />",{css:{position:"absolute",top:"-200px",left:s?"0px":"-1000px",
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e=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var e=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=s("<select/>")).append(this.$dropdown=s("<div/>")).append(this.$resize=s("<div/>").append(this.$resize_icon=s("<i/>"))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(t){var i=t.pageY,n=e.$select.height();e.minHeight=e.minHeight||n,s("#dd-helper").show().on("mousemove",function(t){e.$select.height(Math.max(n+(t.pageY-i),e.minHeight))}).on("mouseup mouseleave",function(){s("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var e=this;this.$el.append(this.$select=s("<div/>")).append(this.$dropdown=s("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){e.$select.select2&&e.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var t=[];0!==e.all_button.value()&&n.each(e.model.get("data"),function(e){t.push(e.value)}),e.value(t),e.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(e,t){return!e||""==e||String(t).toUpperCase().indexOf(e.toUpperCase())>=0},_changeData:function(){var e=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:e.model.get("empty_text")}),n.each(this.model.get("data"),function(t){e.data.push(t)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],n.each(this.data,function(t,i){e.data2.push({order:i,id:t.value,text:t.label,tags:t.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:e.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(t){e.matched_tags={};var i=e.model.get("pagesize"),s=n.filter(e.data2,function(i){var s=!1;return n.each(i.tags,function(i){e._match(t.term,i)&&(s=e.matched_tags[i]=!0)}),s||e._match(t.term,i.text)});t.callback({results:s.slice((t.page-1)*i,t.page*i),more:s.length>=t.page*i})},formatResult:function(t){return n.escape(t.text)+'<div class="ui-tags">'+n.reduce(t.tags,function(t,i){return e.matched_tags[i]?t+'&nbsp;<div class="label label-info">'+n.escape(i)+"</div>":t},"")+"</div>"}}),this.$(".select2-container .select2-search 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null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return n.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(s.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){n.each(this.model.get("data"),function(t){t.keep&&!n.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return s.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=s.isArray(e)?e:[e]:s.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(s.isArray(e)){var i=[];n.each(e,function(e){var s=n.findWhere(t.data2,{id:e});s&&i.push(s)}),e=i}else{e=n.findWhere(this.data2,{id:e})}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var e=null;if(this.model.get("searchable")){var t=this.$select.select2("data");t&&(s.isArray(t)?(e=[],t.sort(function(e,t){return e.order-t.order}),n.each(t,function(t){e.push(t.id)})):e=t.id)}else e=this.$select.val();return r.default.isEmpty(e)?null:e}});t.default={View:c}}).call(t,i(1),i(0),i(2))},23:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(12),d=a(l),c=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({visible:!0,data:[],id:r.default.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(t),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var e=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=s("<div/>")).append(this.$menu=s("<div/>").addClass("ui-options-menu")).append(this.$options=s(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new d.default.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):n.each(this.model.get("data"),function(t){e.$options.append(s(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(s.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=s.isArray(e)?e:[e];n.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(s(this).val())}),r.default.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return s("<div/>").addClass("ui-options-list")}}),h=c.extend({_templateOption:function(e){var t=r.default.uid();return s("<div/>").addClass("ui-option").append(s("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(s("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),u={};u.View=h.extend({initialize:function(e){e.type="radio",h.prototype.initialize.call(this,e)}});var p={};p.View=h.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,h.prototype.initialize.call(this,e)}});var _={};_.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=s("<label/>").addClass("btn btn-default");return e.icon&&t.append(s("<i/>").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(s("<input/>").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return s("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),t.default={Base:c,BaseIcons:h,Radio:u,RadioButton:_,Checkbox:p}}).call(t,i(1),i(0),i(2))},24:function(e,t,i){"use strict";(function(e,s){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),o=n(a),r=i(11),l=n(r),d=i(4),c=n(d),h=e.View.extend({initialize:function(e){var t=this;this.options=e,this.name=e.name||"element",this.multiple=e.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:e.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new "+this.name,onclick:function(){t.add({id:t.select.value(),name:t.select.text()})}}),this.setElement(this._template(e)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(e){if(void 0!==e){if(this.portlet.empty(),s.isArray(e))for(var t in e){var i=e[t],n=null,a=null;"string"!=s.type(i)?(n=i.id,a=i.name):n=a=i,null!=n&&this.add({id:n,name:a})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:s(this).prop("id"),name:s(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var t=this;if(0===this.$('[id="'+e.id+'"]').length)if(o.default.isEmpty(e.id))this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else{var i=s(this._templateRow({id:e.id,name:e.name}));i.on("click",function(){i.remove(),t._refresh()}),i.on("mouseover",function(){i.addClass("portlet-highlight")}),i.on("mouseout",function(){i.removeClass("portlet-highlight")}),this.portlet.append(i),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(e){this.select.update(e)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(e){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(e){return'<div id="'+e.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span class="ui-list-name">'+e.name+"</span></div>"}});t.default={View:h}}).call(t,i(1),i(0))},308:function(e,t,i){"use strict";function s(e){new a.default.GalaxyApp(e)}Object.defineProperty(t,"__esModule",{value:!0}),t.App=s;var n=i(309),a=function(e){return e&&e.__esModule?e:{default:e}}(n);window.adminToolshedApp=s},309:function(e,t,i){"use strict";(function(e){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(310),a=s(n),o=i(311),r=s(o),l=i(312),d=s(l),c=i(313),h=s(c),u=i(314),p=s(u),_=i(315),f=s(_),g=i(316),m=s(g),v=e.Router.extend({initialize:function(){this.routesHit=0,e.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}}),b=e.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new v,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new p.default.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new a.default.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new r.default.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,t){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:t}):Galaxy.admintoolshedapp.adminShedCategoryView=new d.default.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:t})}),this.admin_toolshed_router.on("route:repository",function(e,t){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:t}):Galaxy.admintoolshedapp.adminRepositoryView=new h.default.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:t})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new f.default.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new m.default.Workflows}),e.history.start({pushState:!1})}});t.default={GalaxyApp:b}}).call(t,i(1))},310:function(e,t,i){"use strict";(function(e,s){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(167),o=n(a),r=i(168),l=n(r),d=e.View.extend({defaults:{tool_sheds:[{url:"https://toolshed.g2.bx.psu.edu/",name:"Galaxy Main Tool Shed"}]},initialize:function(e){this.options=s.defaults(this.options||{},this.defaults),this.model=new o.default.ShedsCollection,this.listenTo(this.model,"sync",this.render),this.model.fetch()},el:"#center",render:function(e){this.options=s.defaults(this.options||{},e,this.defaults);var t=this.templateToolshedList;this.$el.html(t({title:"Configured Galaxy Tool 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strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l);i(157);var c=e.View.extend({el:"#center",defaults:{tool_shed:"https://toolshed.g2.bx.psu.edu/"},initialize:function(e){var t=e.tool_shed.replace(/\//g,"%2f");this.options=s.defaults(this.options||e,this.defaults),this.model=new r.default.Categories,this.listenTo(this.model,"sync",this.render),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.model.tool_shed=t,this.model.fetch()},render:function(e){this.options=s.extend(this.options,e),this.options.categories=this.model.models,this.options.queue=d.default.queueLength();var t=this.templateCategoryList;this.$el.html(t(this.options)),n("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){var t=this;n("#search_box").autocomplete({source:function(e,i){var s=t.model.tool_shed.replace(/%2f/g,"/"),a=Galaxy.root+"api/tool_shed/search",o={term:e.term,tool_shed_url:s};n.post(a,o,function(e){console.log(e);var t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a=(Galaxy.root,t.model.tool_shed,"repository/s/"+t.model.tool_shed+"/r/"+n);e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.initialize(e)},templateCategoryList:s.template(['<style type="text/css">',".ui-autocomplete { background-color: #fff; }","li.ui-menu-item { list-style-type: none; }","</style>",'<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner" style="layout: inline;">Categories in <%= tool_shed.replace(/%2f/g, "/") %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="unified-panel-body" id="list_categories">','<div id="standard-search" style="height: 2em; margin: 1em;">','<span class="ui-widget" >','<input class="search-box-input" id="search_box" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" name="search" placeholder="Search repositories by name or id" size="60" type="text" />',"</span>","</div>",'<div style="clear: both; margin-top: 1em;">','<table class="grid">','<thead id="grid-table-header">',"<tr>","<th>Name</th>","<th>Description</th>","<th>Repositories</th>","</tr>","</thead>","<% _.each(categories, function(category) { %>","<tr>","<td>",'<a href="#/category/s/<%= tool_shed %>/c/<%= category.get("id") %>"><%= category.get("name") %></a>',"</td>",'<td><%= category.get("description") %></td>','<td><%= category.get("repositories") %></td>',"</tr>","<% }); %>","</table>","</div>","</div>"].join(""))});t.default={CategoryView:c}}).call(t,i(1),i(2),i(0))},312:function(e,t,i){"use 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t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a="repository/s/"+t.model.tool_shed+"/r/"+n;e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateCategoryContents:s.template(['<style type="text/css">',".ui-autocomplete { background-color: #fff; }","li.ui-menu-item { list-style-type: none; }","</style>",'<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner">Repositories in <%= category.get("name") %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="unified-panel-body" id="list_repositories">','<div id="standard-search" style="height: 2em; margin: 1em;">','<span class="ui-widget" >','<input class="search-box-input" id="search_box" name="search" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" 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o=i(167),r=a(o),l=i(198),d=(a(l),i(3)),c=a(d),h=i(9),u=a(h),p=i(20),_=a(p),f=i(168),g=a(f),m=e.View.extend({el:"#center",initialize:function(e){this.options=s.defaults(this.options||{},this.defaults),this.model=new r.default.RepositoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&repository_id="+e.repository_id,this.model.tool_shed_url=e.tool_shed.replace(/%2f/g,"/"),this.model.tool_shed=t,this.model.category=e.repository_id,this.model.fetch()},render:function(e){var t=this.templateRepoDetails,i=this.model.models[0];this.options={repository:i.get("repository"),tool_shed:this.model.tool_shed,queue:g.default.queueLength()};var a=Object.keys(this.options.repository.metadata);this.options.current_changeset=this.options.current_changeset||a[a.length-1],this.options.current_metadata=this.options.repository.metadata[this.options.current_changeset],this.options.current_metadata.tool_shed_url=this.model.tool_shed_url,this.options.tools=this.options.current_metadata.tools,this.options.repository_dependencies_template=this.templateRepoDependencies,this.options.repository_dependency_template=this.templateRepoDependency,this.options.tps_template_global_select=this.templateGlobalSectionSelect,this.options.tps_template_tool_select=this.templateToolSectionSelect,this.options.tps_select_options=this.templatePanelSelectOptions,this.options.tool_dependencies=i.get("tool_dependencies"),this.options.shed_tool_conf=this.templateShedToolConf({stc_html:i.get("shed_conf")}),this.options.panel_section_dict=i.get("panel_section_dict"),this.options.api_url=Galaxy.root+"api/tool_shed_repositories/install?async=True",this.options=s.extend(this.options,e),this.$el.html(t(this.options)),this.checkInstalled(this.options.current_metadata),this.bindEvents(),n("#center").css("overflow","auto")},bindEvents:function(){var e=this;n("#changeset").on("change",function(){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),n("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),n("#install_repository").on("click",function(t){n("#repository_installation");t.preventDefault();var i={};i.repositories=JSON.stringify([[n("#install_repository").attr("data-tsrid"),n("#changeset").find("option:selected").val()]]),i.tool_shed_repository_ids=JSON.stringify([n("#install_repository").attr("data-tsrid")]),i.tool_shed_url=e.model.tool_shed_url,i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val();e.panelSelect(i);i.tool_panel_section=JSON.stringify(e.panelSelect(i)),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.changeset=n("#changeset").find("option:selected").val();var s=n("#repository_installation").attr("action");e.prepareInstall(i,s)}),n("#queue_install").on("click",function(t){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];var i=(e.options.current_changeset,{});s.each(Object.keys(e.options.current_metadata),function(t){i[t]||(i[t]=e.options.current_metadata[t])}),i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val(),i.tool_panel_section=JSON.stringify(e.panelSelect({})),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.tool_shed_url=e.model.tool_shed_url,"/"==i.tool_shed_url.substr(-1)&&(i.tool_shed_url=i.tool_shed_url.substr(0,i.tool_shed_url.length-1)),g.default.addToQueue(i),e.checkInstalled(i)}),n(".tool_panel_section_picker").on("change",function(){n(this).find("option:selected").val()==n("#tool_panel_section_select").find("option:selected").val()?n(this).attr("default","active"):n(this).removeAttr("default")}),n(function(){n("#repository_dependencies").jstree()}),n(".tool_form").on("click",function(){var t=n(this).attr("data-guid"),i=(n(this).attr("data-clean"),n(this).attr("data-name")),s=n(this).attr("data-desc"),a=e.model.tool_shed_url,o=n("#repository_details").attr("data-tsrid"),r=n("#changeset").find("option:selected").val(),l=Galaxy.root+"api/tool_shed/tool_json",d={guid:t,tool_shed_url:a,tsr_id:o,changeset:r};n.get(l,d,function(e){e.cls="ui-portlet-plain";var t=new _.default(e);c.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+c.default.textify(e.extensions)+")")});var n=new u.default.View,a="<u>"+i+"</u> "+s;n.show({closing_events:!0,title:a,body:t.$el,buttons:{Close:function(){n.hide()}}})})})},checkInstalled:function(e){var t=this,i={name:e.name,owner:e.owner},s=!1;t.repoQueued(e);n.get(Galaxy.root+"api/tool_shed_repositories",i,function(i){for(var a=0;a<i.length;a++){var o=i[a],r=!o.deleted&&!o.uninstalled,l=o.changeset_revision==e.changeset_revision||o.installed_changeset_revision==e.changeset_revision;o.name==e.repository.name&&o.owner==e.repository.owner&&r&&l&&(s=!0),s?(n("#install_repository").prop("disabled",!0),n("#install_repository").val("This revision is already installed")):(n("#install_repository").prop("disabled",!1),n("#install_repository").val("Install this revision"))}t.repoQueued(e)||s?(n("#queue_install").hide(),n("#queue_install").val("This revision is already in the queue")):(n("#queue_install").show(),n("#queue_install").val("Install this revision later"))})},panelSelect:function(e){var t={};return n("#tool_panel_section_select").length?e.tool_panel_section_id=n("#tool_panel_section_select").find("option:selected").val():e.new_tool_panel_section=n("#new_tool_panel_section").val(),n(".tool_panel_section_picker").each(function(){var e=n(this).attr("name"),i=n(this).attr("data-toolguid");t[i]="tool_panel_section_id"===e?{tool_panel_section:n(this).find("option:selected").val(),action:"append"}:{tool_panel_section:n(this).val(),action:"create"}}),t},reDraw:function(e){this.$el.empty(),this.initialize(e)},repoQueued:function(e){var t=this;if(localStorage.repositories){var i=(JSON.parse(localStorage.repositories),e.changeset_revision,t.queueKey(e));return localStorage.repositories&&(queued_repos=JSON.parse(localStorage.repositories)),!!queued_repos.hasOwnProperty(i)}},queueKey:function(e){var t=this.model.tool_shed_url;return"/"==t.substr(-1)&&(t=t.substr(0,t.length-1)),t+"|"+e.repository_id+"|"+e.changeset_revision},tpsSelection:function(){new_tps=n("#tool_panel_section_select").find("option:selected").val(),n('.tool_panel_section_picker[default="active"]').each(function(){n(this).val(new_tps)})},prepareInstall:function(e,t){var i=this;n.post(t,e,function(e){var t=JSON.parse(e);i.doInstall(t)})},doInstall:function(t){var i=Galaxy.root+"admin_toolshed/install_repositories",s=t.repositories,a="status/r/"+s.join("|");n.post(i,t,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})},templateRepoDetails:s.template(['<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner">Repository information for <strong><%= repository.name %></strong> from <strong><%= repository.owner %></strong></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="unified-panel-body" id="repository_details" data-tsrid="<%= repository.id %>">','<form id="repository_installation" name="install_repository" method="post" action="<%= api_url %>">','<input type="hidden" id="repositories" name="<%= repository.id %>" value="ID" 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class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">','<th style="padding-left: 40px;">Name</th>',"<th>Description</th>","<th>Version</th>","<th><%= tps_template_global_select({tps: panel_section_dict, tps_select_options: tps_select_options}) %></tr>","</thead>",'<tbody id="tools_in_repo">',"<% _.each(current_metadata.tools, function(tool) { %>",'<tr id="libraryItem-<%= tool.clean %>" class="tool_row" style="display: table-row;" style="width: 15%">','<td style="padding-left: 40px;">','<div id="tool-<%= tool.clean %>" class="menubutton split popup" style="float: left;">','<a class="tool_form view-info" data-toggle="modal" data-target="toolform_<%= tool.clean %>" data-clean="<%= tool.clean %>" data-guid="<%= tool.guid %>" data-name="<%= tool.name %>" data-desc="<%= tool.description %>"><%= tool.name %></a>',"</div>","</td>","<td><%= tool.description %></td>",'<td style="width: 15%"><%= tool.version %></td>','<td style="width: 35%" id="tool_tps_<%= tool.clean %>">',"<%= tps_template_tool_select({tool: tool, tps: panel_section_dict, tps_select_options: tps_select_options}) %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>","</div>","<% } %>","</form>","</div>"].join("")),templateRepoDependencies:s.template(['<div class="toolFormTitle">Repository Dependencies</div>','<div class="toolFormBody tables container-table" id="repository_dependencies">',"<ul>","<li>Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>","</li>","</ul>","</div>"].join("")),templateRepoDependency:s.template(['<li id="metadata_<%= id %>" class="datasetRow repository_dependency_row">',"Repository <b><%= repository.name %></b> revision <b><%= changeset_revision %></b> owned by <b><%= repository.owner %></b>","<% if (has_repository_dependencies) { %>",'<ul class="child_dependencies">',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","</ul>","<% } %>","</li>"].join("")),templateShedToolConf:s.template(['<div class="toolFormTitle">Shed tool configuration file:</div>','<div class="toolFormBody">','<div class="form-row">',"<%= stc_html %>",'<div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>',"</div>","</div>"].join("")),templateToolDependency:s.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:s.template(['<div id="tool_panel_section">','<div class="form-row" id="new_tps">','<input id="new_tool_panel_section" name="new_tool_panel_section" type="textfield" value="" size="40"/>','<input class="btn btn-primary" type="button" id="select_existing" value="Select existing" />','<div class="toolParamHelp" style="clear: both;">',"Add a new tool panel section to contain the installed tools (optional).","</div>","</div>","</div>"].join("")),templateGlobalSectionSelect:s.template(['<div id="tool_panel_section">','<div class="toolFormTitle">Tool Panel Section</div>','<div class="toolFormBody">','<div class="tab-pane" id="select_tps">','<select name="<%= name %>" id="<%= tps.id %>">',"<%= tps_select_options({sections: tps.sections}) %>","</select>",'<input class="btn btn-primary" type="button" id="create_new" value="Create new" />','<div class="toolParamHelp" style="clear: both;">',"Select an existing tool panel section to contain the installed 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this.flat_dict&&this.flat_dict[e]},matchCase:function(e,t){return r(e,t)},matchModel:function(e,t){var i=this;l(e.inputs,function(e,s){i.flat_dict[s]&&t(e,i.flat_dict[s])})},matchResponse:function(e){function t(e,n){if("string"==typeof n){var a=s.flat_dict[e];a&&(i[a]=n)}else for(var o in n){var r=o;if(""!==e){var l="|";n instanceof Array&&(l="_"),r=e+l+r}t(r,n[o])}}var i={},s=this;return t("",e),i},_iterate:function(e,t){var i=this;s(e).children().each(function(){var e=this,n=s(e).attr("id");if(s(e).hasClass("section-row")){var a=i.app.input_list[n];t[n]=a&&{input:a}||{},i._iterate(e,t[n])}else i._iterate(e,t)})}})),r=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},l=function e(t,i,a,o){o=s.extend(!0,{},o),n.each(t,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var l in t){var d=t[l];d.name=d.name||l;var 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r=o.step;r||(r=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div 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i=e.find(".button-"+t);i.on("click",function(){s._setState(t,!i.data("is_expanded"))})}function i(n,a,r){r=r||[];for(var l in a){var d=a[l],c=d.options&&d.options.length>0,h=r.slice(0);s.header_index[d.value]=h.slice(0);var u=e("<div/>");if(c){var p=o.default.uid(),_=e("<span/>").addClass("button-"+p).addClass("ui-drilldown-button fa fa-plus-square"),f=e("<div/>").addClass("subgroup-"+p).addClass("ui-drilldown-subgroup");u.append(e("<div/>").append(_).append(s._templateOption({label:d.name,value:d.value}))),h.push(p),i(f,d.options,h),u.append(f),t(u,p)}else u.append(s._templateOption({label:d.name,value:d.value}));n.append(u)}}var s=this;this.header_index={};var n=e("<div/>");return i(n,this.model.get("data")),n},_template:function(){return e("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});t.default={View:d}}).call(t,i(0),i(2))},48:function(e,t,i){"use strict";(function(e,s,n,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(4),c=(o(d),i(11)),h=o(c),u=i(49),p=o(u),_=i(50),f=o(_),g=i(51),m=o(g),v=e.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new m.default,this.setElement(s("<div/>")),this.render()},render:function(){var e=this;this.$el.empty(),n.each(this.inputs,function(t){e.add(t)})},add:function(e){var t=a.extend(!0,{},e);switch(t.id=e.id=l.default.uid(),this.app.input_list[t.id]=t,t.type){case"conditional":this._addConditional(t);break;case"repeat":this._addRepeat(t);break;case"section":this._addSection(t);break;default:this._addRow(t)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var s=t.app.data.matchCase(e,i);for(var n in e.cases){var a=e.cases[n],o=t.$("#"+e.id+"-section-"+n),r=!1;for(var l in 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v(this.app,{inputs:e.inputs}).$el),t.append(s("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var s=this.parameters.create(e);this.app.field_list[i]=s;var n=new f.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:s});return this.app.element_list[i]=n,this._append(n.$el,e.id),s},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},49:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(11),d=a(l),c=i(4),h=a(c),u=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new h.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(s("<div/>").append(this.$list=s("<div/>")).append(s("<div/>").append(this.button_new.$el)))},size:function(){return n.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new h.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),n.each(this.list,function(e){e.hideOperation("button_delete")}),n.isEmpty(this.list)&&this.$el.append(s("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:u}}).call(t,i(1),i(0),i(2))},50:function(e,t,i){"use strict";(function(e,i,s){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var s=this.model.get("collapsible_value");this.field.collapsed=void 0!==s&&JSON.stringify(this.model.get("value"))==JSON.stringify(s),this.listenTo(this.model,"change",this.render,this),this.render();var n=this;this.$collapsible.on("click",function(){n.field.collapsed=!n.field.collapsed,t.trigger&&t.trigger("change"),n.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){n.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(s.escape(this.model.get("text_value")));var n=this.model.get("error_text");if(this.$error[n?"show":"hide"](),this.$el[n?"addClass":"removeClass"]("ui-error"),this.$error_text.html(n),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},51:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(4),d=a(l),c=i(52),h=a(c),u=i(53),p=a(u),_=i(54),f=a(_),g=i(55),m=a(g),v=i(57),b=a(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new h.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],s.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(n.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new b.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new p.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new m.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},52:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(4),d=a(l),c=i(22),h=a(c),u={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},p={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:u.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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Separate jobs will be triggered for each dataset selection."));this.$batch={linked:n.clone(),enabled:n.clone().append(s("<div/>").append(s("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(s("<div/>").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple 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e=this;n.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),n.each(e.$batch,function(t,s){t[e.config[i].batch==s?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var e=this,t=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");p[t]?this.config=p[t]:(this.config=p.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+t+"'."));var i=e.model.get("data"),s=r.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],n.each(this.config,function(t,n){e.button_data.push({value:n,icon:t.icon,tooltip:t.tooltip}),e.fields.push(new h.default.View({optional:e.model.get("optional"),multiple:t.multiple,searchable:!t.multiple||i&&i[t.src]&&i[t.src].length>e.model.get("pagelimit"),individual:!0,error_text:"No "+(s?s+" ":"")+(a[t.src]||"content")+" 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n=i(3),a=(s(n),i(4)),o=s(a),r=i(43),l=(s(r),i(24)),d=s(l),c=e.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),h=e.Collection.extend({initialize:function(){var t=this;this.config=new e.Model({library_id:null}),this.config.on("change",function(){t.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),u=e.View.extend({initialize:function(e){var t=this;this.libraries=new c,this.datasets=new h,this.options=e,this.library_select=new o.default.Select.View({onchange:function(e){t.datasets.config.set("library_id",e)}}),this.dataset_list=new d.default.View({name:"dataset",optional:e.optional,multiple:e.multiple,onchange:function(){t.trigger("change")}}),this.libraries.on("reset",function(){var e=[];t.libraries.each(function(t){e.push({value:t.id,label:t.get("name")})}),t.library_select.update(e)}),this.datasets.on("reset",function(){var e=[];null!==t.library_select.text()&&t.datasets.each(function(t){"file"===t.get("type")&&e.push({value:t.id,label:t.get("name")})}),t.dataset_list.update(e)}),this.on("change",function(){e.onchange&&e.onchange(t.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){t.library_select.trigger("change"),void 0!==t.options.value&&t.value(t.options.value)}})},value:function(e){return this.dataset_list.value(e)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});t.default={View:u}}).call(t,i(1))},54:function(e,t,i){"use strict";(function(e){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),a=s(n),o=i(24),r=s(o),l=e.View.extend({initialize:function(e){var t=this;this.ftpfile_list=new r.default.View({name:"file",optional:e.optional,multiple:e.multiple,onchange:function(){e.onchange&&e.onchange(t.value())}}),this.setElement(this.ftpfile_list.$el),a.default.get({url:Galaxy.root+"api/remote_files",success:function(e){var i=[];for(var s in e)i.push({value:e[s].path,label:e[s].path});t.ftpfile_list.update(i)}})},value:function(e){return this.ftpfile_list.value(e)}});t.default={View:l}}).call(t,i(1))},55:function(e,t,i){"use strict";(function(e){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),a=(s(n),i(4)),o=s(a),r=i(56),l=s(r),d=e.View.extend({initialize:function(e){var t=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){t.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new o.default.Input({type:"password"}),this.setElement(this._template(e)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(e){var t=this;l.default.openFileBrowser({successCallback:function(e){t.value(e.destination+"^"+e.token)}})},_template:function(e){return'<div class="ui-gs-select-file"><div class="ui-gs-browse-field"><span class="ui-gs-browse-button" /><span class="ui-gs-filename-textbox" /></div><div class="ui-gs-token-field"><span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span><span class="ui-gs-token-textbox" /></div></div>'},value:function(e){if(void 0===e)return this._getValue();this._setValue(e)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(e){e&&(values=e.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});t.default={View:d}}).call(t,i(1))},56:function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.default={openFileBrowser:function(e){var t=window.Galaxy.config.genomespace_ui_url,i=t+"upload/loadUrlToGenomespace.html?getLocation=true",s=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=e.successCallback,window.addEventListener("message",function(e){successCalBack(e.data)},!1),s.focus(),null!=e.errorCallback&&(s.setCallbackOnGSUploadError=config.errorCallback)}}},57:function(e,t,i){"use strict";(function(e,s){Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),a=function(e){return e&&e.__esModule?e:{default:e}}(n);t.default=e.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},initialize:function(e){this.options=a.default.merge(e,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var t=this;this.$boxes.on("click",function(){t.value(s(this).css("background-color")),t.$header.trigger("click")}),this.$header.on("click",function(){t.visible=!t.visible,t.visible?t.$view.fadeIn("fast"):t.$view.fadeOut("fast")})},value:function(e){return void 0!==e&&null!==e&&(this.$value.css("background-color",e),this.$(".ui-color-picker-box").empty(),this.$(this._getValue()).html(this._templateCheck()),this.options.onchange&&this.options.onchange(e)),this._getValue()},_getValue:function(){var e=this.$value.css("background-color");if(e=e.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/)){var t=function(e){return("0"+parseInt(e).toString(16)).slice(-2)};return"#"+t(e[1])+t(e[2])+t(e[3])}return null},_build:function(){this._content({colors:this.colors.base});for(var e in this.colors.theme){var t={};0==e?t.bottom=!0:e!=this.colors.theme.length-1?(t.top=!0,t.bottom=!0):t.top=!0,t.colors=this.colors.theme[e],this._content(t)}this._content({colors:this.colors.standard})},_content:function(e){var t=e.colors,i=s(this._templateContent()),n=i.find(".line");this.$panel.append(i);for(var a in t){var o=s(this._templateBox(t[a]));e.top&&(o.css("border-top","none"),o.css("border-top-left-radius","0px"),o.css("border-top-right-radius","0px")),e.bottom&&(o.css("border-bottom","none"),o.css("border-bottom-left-radius","0px"),o.css("border-bottom-right-radius","0px")),n.append(o)}return i},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="line"/></div>'},_templateBox:function(e){return'<div id="'+e+'" class="ui-color-picker-box" style="background-color: #'+e+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div 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n=e.data.checksum();n!=t&&(t=n,e.model.get("onchange")())}}),this.on("reset",function(){s.each(e.element_list,function(e){e.reset()})}),this},_renderForm:function(){n(".tooltip").remove();var e=this.model.attributes;this.message=new c.default.UnescapedMessage,this.section=new u.default.View(this,{inputs:e.inputs}),this.portlet=new l.default.View({icon:e.icon,title:e.title,cls:e.cls,operations:!e.hide_operations&&e.operations,buttons:e.buttons,collapsible:e.collapsible,collapsed:e.collapsed,onchange_title:e.onchange_title}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),e.inputs&&this.$el.append(this.portlet.$el),e.message&&this.message.update({persistent:!0,status:e.status,message:e.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}).call(t,i(1),i(2),i(0))},22:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(s.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=s.isArray(e)?e:[e];n.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(s(this).val())}),r.default.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return s("<div/>").addClass("ui-options-list")}}),h=c.extend({_templateOption:function(e){var t=r.default.uid();return s("<div/>").addClass("ui-option").append(s("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(s("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),u={};u.View=h.extend({initialize:function(e){e.type="radio",h.prototype.initialize.call(this,e)}});var p={};p.View=h.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,h.prototype.initialize.call(this,e)}});var _={};_.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=s("<label/>").addClass("btn btn-default");return e.icon&&t.append(s("<i/>").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(s("<input/>").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return s("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),t.default={Base:c,BaseIcons:h,Radio:u,RadioButton:_,Checkbox:p}}).call(t,i(1),i(0),i(2))},24:function(e,t,i){"use strict";(function(e,s){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),o=n(a),r=i(11),l=n(r),d=i(4),c=n(d),h=e.View.extend({initialize:function(e){var t=this;this.options=e,this.name=e.name||"element",this.multiple=e.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:e.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new "+this.name,onclick:function(){t.add({id:t.select.value(),name:t.select.text()})}}),this.setElement(this._template(e)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(e){if(void 0!==e){if(this.portlet.empty(),s.isArray(e))for(var t in e){var i=e[t],n=null,a=null;"string"!=s.type(i)?(n=i.id,a=i.name):n=a=i,null!=n&&this.add({id:n,name:a})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:s(this).prop("id"),name:s(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var t=this;if(0===this.$('[id="'+e.id+'"]').length)if(o.default.isEmpty(e.id))this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else{var i=s(this._templateRow({id:e.id,name:e.name}));i.on("click",function(){i.remove(),t._refresh()}),i.on("mouseover",function(){i.addClass("portlet-highlight")}),i.on("mouseout",function(){i.removeClass("portlet-highlight")}),this.portlet.append(i),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(e){this.select.update(e)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(e){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(e){return'<div id="'+e.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span class="ui-list-name">'+e.name+"</span></div>"}});t.default={View:h}}).call(t,i(1),i(0))},309:function(e,t,i){"use strict";function s(e){new a.default.GalaxyApp(e)}Object.defineProperty(t,"__esModule",{value:!0}),t.App=s;var n=i(310),a=function(e){return e&&e.__esModule?e:{default:e}}(n);window.adminToolshedApp=s},310:function(e,t,i){"use strict";(function(e){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(311),a=s(n),o=i(312),r=s(o),l=i(313),d=s(l),c=i(314),h=s(c),u=i(315),p=s(u),_=i(316),f=s(_),g=i(317),m=s(g),v=e.Router.extend({initialize:function(){this.routesHit=0,e.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}}),b=e.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new v,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new p.default.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new a.default.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new r.default.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,t){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:t}):Galaxy.admintoolshedapp.adminShedCategoryView=new d.default.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:t})}),this.admin_toolshed_router.on("route:repository",function(e,t){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:t}):Galaxy.admintoolshedapp.adminRepositoryView=new h.default.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:t})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new f.default.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new m.default.Workflows}),e.history.start({pushState:!1})}});t.default={GalaxyApp:b}}).call(t,i(1))},311:function(e,t,i){"use strict";(function(e,s){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(167),o=n(a),r=i(168),l=n(r),d=e.View.extend({defaults:{tool_sheds:[{url:"https://toolshed.g2.bx.psu.edu/",name:"Galaxy Main Tool Shed"}]},initialize:function(e){this.options=s.defaults(this.options||{},this.defaults),this.model=new o.default.ShedsCollection,this.listenTo(this.model,"sync",this.render),this.model.fetch()},el:"#center",render:function(e){this.options=s.defaults(this.options||{},e,this.defaults);var t=this.templateToolshedList;this.$el.html(t({title:"Configured Galaxy Tool 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strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l);i(157);var c=e.View.extend({el:"#center",defaults:{tool_shed:"https://toolshed.g2.bx.psu.edu/"},initialize:function(e){var t=e.tool_shed.replace(/\//g,"%2f");this.options=s.defaults(this.options||e,this.defaults),this.model=new r.default.Categories,this.listenTo(this.model,"sync",this.render),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.model.tool_shed=t,this.model.fetch()},render:function(e){this.options=s.extend(this.options,e),this.options.categories=this.model.models,this.options.queue=d.default.queueLength();var t=this.templateCategoryList;this.$el.html(t(this.options)),n("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){var t=this;n("#search_box").autocomplete({source:function(e,i){var s=t.model.tool_shed.replace(/%2f/g,"/"),a=Galaxy.root+"api/tool_shed/search",o={term:e.term,tool_shed_url:s};n.post(a,o,function(e){console.log(e);var t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a=(Galaxy.root,t.model.tool_shed,"repository/s/"+t.model.tool_shed+"/r/"+n);e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.initialize(e)},templateCategoryList:s.template(['<style type="text/css">',".ui-autocomplete { background-color: #fff; }","li.ui-menu-item { list-style-type: none; }","</style>",'<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner" style="layout: inline;">Categories in <%= tool_shed.replace(/%2f/g, "/") %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue 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t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a="repository/s/"+t.model.tool_shed+"/r/"+n;e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateCategoryContents:s.template(['<style type="text/css">',".ui-autocomplete { background-color: #fff; }","li.ui-menu-item { list-style-type: none; }","</style>",'<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner">Repositories in <%= category.get("name") %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="unified-panel-body" id="list_repositories">','<div id="standard-search" style="height: 2em; margin: 1em;">','<span class="ui-widget" >','<input class="search-box-input" id="search_box" name="search" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" 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a=Object.keys(this.options.repository.metadata);this.options.current_changeset=this.options.current_changeset||a[a.length-1],this.options.current_metadata=this.options.repository.metadata[this.options.current_changeset],this.options.current_metadata.tool_shed_url=this.model.tool_shed_url,this.options.tools=this.options.current_metadata.tools,this.options.repository_dependencies_template=this.templateRepoDependencies,this.options.repository_dependency_template=this.templateRepoDependency,this.options.tps_template_global_select=this.templateGlobalSectionSelect,this.options.tps_template_tool_select=this.templateToolSectionSelect,this.options.tps_select_options=this.templatePanelSelectOptions,this.options.tool_dependencies=i.get("tool_dependencies"),this.options.shed_tool_conf=this.templateShedToolConf({stc_html:i.get("shed_conf")}),this.options.panel_section_dict=i.get("panel_section_dict"),this.options.api_url=Galaxy.root+"api/tool_shed_repositories/install?async=True",this.options=s.extend(this.options,e),this.$el.html(t(this.options)),this.checkInstalled(this.options.current_metadata),this.bindEvents(),n("#center").css("overflow","auto")},bindEvents:function(){var e=this;n("#changeset").on("change",function(){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),n("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),n("#install_repository").on("click",function(t){n("#repository_installation");t.preventDefault();var i={};i.repositories=JSON.stringify([[n("#install_repository").attr("data-tsrid"),n("#changeset").find("option:selected").val()]]),i.tool_shed_repository_ids=JSON.stringify([n("#install_repository").attr("data-tsrid")]),i.tool_shed_url=e.model.tool_shed_url,i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val();e.panelSelect(i);i.tool_panel_section=JSON.stringify(e.panelSelect(i)),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.changeset=n("#changeset").find("option:selected").val();var s=n("#repository_installation").attr("action");e.prepareInstall(i,s)}),n("#queue_install").on("click",function(t){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];var i=(e.options.current_changeset,{});s.each(Object.keys(e.options.current_metadata),function(t){i[t]||(i[t]=e.options.current_metadata[t])}),i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val(),i.tool_panel_section=JSON.stringify(e.panelSelect({})),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.tool_shed_url=e.model.tool_shed_url,"/"==i.tool_shed_url.substr(-1)&&(i.tool_shed_url=i.tool_shed_url.substr(0,i.tool_shed_url.length-1)),g.default.addToQueue(i),e.checkInstalled(i)}),n(".tool_panel_section_picker").on("change",function(){n(this).find("option:selected").val()==n("#tool_panel_section_select").find("option:selected").val()?n(this).attr("default","active"):n(this).removeAttr("default")}),n(function(){n("#repository_dependencies").jstree()}),n(".tool_form").on("click",function(){var t=n(this).attr("data-guid"),i=(n(this).attr("data-clean"),n(this).attr("data-name")),s=n(this).attr("data-desc"),a=e.model.tool_shed_url,o=n("#repository_details").attr("data-tsrid"),r=n("#changeset").find("option:selected").val(),l=Galaxy.root+"api/tool_shed/tool_json",d={guid:t,tool_shed_url:a,tsr_id:o,changeset:r};n.get(l,d,function(e){e.cls="ui-portlet-plain";var t=new _.default(e);c.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+c.default.textify(e.extensions)+")")});var n=new u.default.View,a="<u>"+i+"</u> "+s;n.show({closing_events:!0,title:a,body:t.$el,buttons:{Close:function(){n.hide()}}})})})},checkInstalled:function(e){var t=this,i={name:e.name,owner:e.owner},s=!1;t.repoQueued(e);n.get(Galaxy.root+"api/tool_shed_repositories",i,function(i){for(var a=0;a<i.length;a++){var o=i[a],r=!o.deleted&&!o.uninstalled,l=o.changeset_revision==e.changeset_revision||o.installed_changeset_revision==e.changeset_revision;o.name==e.repository.name&&o.owner==e.repository.owner&&r&&l&&(s=!0),s?(n("#install_repository").prop("disabled",!0),n("#install_repository").val("This revision is already installed")):(n("#install_repository").prop("disabled",!1),n("#install_repository").val("Install this revision"))}t.repoQueued(e)||s?(n("#queue_install").hide(),n("#queue_install").val("This revision is already in the queue")):(n("#queue_install").show(),n("#queue_install").val("Install this revision later"))})},panelSelect:function(e){var t={};return n("#tool_panel_section_select").length?e.tool_panel_section_id=n("#tool_panel_section_select").find("option:selected").val():e.new_tool_panel_section=n("#new_tool_panel_section").val(),n(".tool_panel_section_picker").each(function(){var e=n(this).attr("name"),i=n(this).attr("data-toolguid");t[i]="tool_panel_section_id"===e?{tool_panel_section:n(this).find("option:selected").val(),action:"append"}:{tool_panel_section:n(this).val(),action:"create"}}),t},reDraw:function(e){this.$el.empty(),this.initialize(e)},repoQueued:function(e){var t=this;if(localStorage.repositories){var i=(JSON.parse(localStorage.repositories),e.changeset_revision,t.queueKey(e));return localStorage.repositories&&(queued_repos=JSON.parse(localStorage.repositories)),!!queued_repos.hasOwnProperty(i)}},queueKey:function(e){var t=this.model.tool_shed_url;return"/"==t.substr(-1)&&(t=t.substr(0,t.length-1)),t+"|"+e.repository_id+"|"+e.changeset_revision},tpsSelection:function(){new_tps=n("#tool_panel_section_select").find("option:selected").val(),n('.tool_panel_section_picker[default="active"]').each(function(){n(this).val(new_tps)})},prepareInstall:function(e,t){var i=this;n.post(t,e,function(e){var t=JSON.parse(e);i.doInstall(t)})},doInstall:function(t){var i=Galaxy.root+"admin_toolshed/install_repositories",s=t.repositories,a="status/r/"+s.join("|");n.post(i,t,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})},templateRepoDetails:s.template(['<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner">Repository information for <strong><%= repository.name %></strong> from <strong><%= repository.owner %></strong></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="unified-panel-body" id="repository_details" data-tsrid="<%= repository.id %>">','<form id="repository_installation" name="install_repository" method="post" action="<%= api_url %>">','<input type="hidden" id="repositories" name="<%= repository.id %>" value="ID" />','<input type="hidden" id="tool_shed_url" name="tool_shed_url" value="<%= tool_shed %>" />','<div class="toolForm">','<div class="toolFormTitle">Changeset</div>','<div class="toolFormBody changeset">','<select id="changeset" name="changeset" style="margin: 5px;">',"<% _.each(Object.keys(repository.metadata), function(changeset) { %>",'<% if (changeset == current_changeset) { var selected = "selected "; } else { var selected = ""; } %>','<option <%= selected %>value="<%= changeset.split(":")[1] %>"><%= changeset %></option>',"<% }); %>","</select>",'<input class="btn btn-primary preview-button" data-tsrid="<%= current_metadata.repository.id %>" type="submit" id="install_repository" name="install_repository" value="Install this revision now" />','<input class="btn btn-primary preview-button" type="button" id="queue_install" name="queue_install" value="Install this revision later" />','<div class="toolParamHelp" style="clear: both;">Please select a revision and review the settings below before installing.</div>',"</div>","</div>","<%= shed_tool_conf %>","<% if (current_metadata.has_repository_dependencies) { %>",'<div class="toolFormTitle">Repository dependencies for <strong id="current_changeset"><%= current_changeset %></strong></div>','<div class="toolFormBody">','<p id="install_repository_dependencies_checkbox">','<input type="checkbox" checked id="install_repository_dependencies" />','<label for="install_repository_dependencies">Install repository dependencies</label>',"</p>","<% current_metadata.repository_dependency_template = repository_dependency_template; %>",'<div class="tables container-table" id="repository_dependencies">','<div class="expandLink">','<a class="toggle_folder" data_target="repository_dependencies_table">',"Repository dependencies &ndash; <em>installation of these additional repositories is required</em>","</a>","</div>","<%= repository_dependencies_template(current_metadata) %>","</div>","</div>","<% } %>","<% if (current_metadata.includes_tool_dependencies) { %>",'<div class="toolFormTitle">Tool dependencies</div>','<div class="toolFormBody">','<p id="install_resolver_dependencies_checkbox">','<input type="checkbox" checked id="install_resolver_dependencies" />','<label for="install_resolver_dependencies">Install resolver dependencies</label>',"</p>",'<p id="install_tool_dependencies_checkbox">','<input type="checkbox" checked id="install_tool_dependencies" />','<label for="install_tool_dependencies">Install tool dependencies</label>',"</p>",'<div class="tables container-table" id="tool_dependencies">','<div class="expandLink">','<a class="toggle_folder" data_target="tool_dependencies_table">',"Tool dependencies &ndash; <em>repository tools require handling of these dependencies</em>","</a>","</div>",'<table class="tables container-table" id="tool_dependencies_table" border="0" cellpadding="2" cellspacing="2" width="100%">',"<thead>",'<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">','<th style="padding-left: 40px;">Name</th>',"<th>Version</th>","<th>Type</th>","</tr>","</thead>",'<tbody id="tool_deps">',"<% _.each(tool_dependencies[current_changeset], function(dependency) { %>",'<tr class="datasetRow tool_dependency_row" style="display: table-row;">','<td style="padding-left: 40px;">',"<%= dependency.name %></td>","<td><%= dependency.version %></td>","<td><%= dependency.type %></td>","</tr>","<% }); %>","</tbody>","</table>","</div>","</div>","<% } %>","<% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>",'<div class="toolFormTitle">Tools &ndash; <em>click the name to preview the tool and use the pop-up menu to inspect all metadata</em></div>','<div class="toolFormBody">','<div class="tables container-table" id="tools_toggle">','<table class="tables container-table" id="valid_tools" border="0" cellpadding="2" cellspacing="2" width="100%">',"<thead>",'<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">','<th style="padding-left: 40px;">Name</th>',"<th>Description</th>","<th>Version</th>","<th><%= tps_template_global_select({tps: panel_section_dict, tps_select_options: tps_select_options}) %></tr>","</thead>",'<tbody id="tools_in_repo">',"<% _.each(current_metadata.tools, function(tool) { %>",'<tr id="libraryItem-<%= tool.clean %>" class="tool_row" style="display: table-row;" style="width: 15%">','<td style="padding-left: 40px;">','<div id="tool-<%= tool.clean %>" class="menubutton split popup" style="float: left;">','<a class="tool_form view-info" data-toggle="modal" data-target="toolform_<%= tool.clean %>" data-clean="<%= tool.clean %>" data-guid="<%= tool.guid %>" data-name="<%= tool.name %>" data-desc="<%= tool.description %>"><%= tool.name %></a>',"</div>","</td>","<td><%= tool.description %></td>",'<td style="width: 15%"><%= tool.version %></td>','<td style="width: 35%" id="tool_tps_<%= tool.clean %>">',"<%= tps_template_tool_select({tool: tool, tps: panel_section_dict, tps_select_options: tps_select_options}) %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>","</div>","<% } %>","</form>","</div>"].join("")),templateRepoDependencies:s.template(['<div class="toolFormTitle">Repository Dependencies</div>','<div class="toolFormBody tables container-table" id="repository_dependencies">',"<ul>","<li>Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>","</li>","</ul>","</div>"].join("")),templateRepoDependency:s.template(['<li id="metadata_<%= id %>" class="datasetRow repository_dependency_row">',"Repository <b><%= repository.name %></b> revision <b><%= changeset_revision %></b> owned by <b><%= repository.owner %></b>","<% if (has_repository_dependencies) { %>",'<ul class="child_dependencies">',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","</ul>","<% } %>","</li>"].join("")),templateShedToolConf:s.template(['<div class="toolFormTitle">Shed tool configuration file:</div>','<div class="toolFormBody">','<div class="form-row">',"<%= stc_html %>",'<div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>',"</div>","</div>"].join("")),templateToolDependency:s.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:s.template(['<div id="tool_panel_section">','<div class="form-row" id="new_tps">','<input id="new_tool_panel_section" name="new_tool_panel_section" type="textfield" value="" size="40"/>','<input class="btn btn-primary" type="button" id="select_existing" value="Select existing" />','<div class="toolParamHelp" style="clear: both;">',"Add a new tool panel section to contain the installed tools (optional).","</div>","</div>","</div>"].join("")),templateGlobalSectionSelect:s.template(['<div id="tool_panel_section">','<div class="toolFormTitle">Tool Panel Section</div>','<div class="toolFormBody">','<div class="tab-pane" id="select_tps">','<select name="<%= name %>" id="<%= tps.id %>">',"<%= tps_select_options({sections: tps.sections}) %>","</select>",'<input class="btn btn-primary" type="button" id="create_new" value="Create new" />','<div class="toolParamHelp" style="clear: both;">',"Select an existing tool panel section to contain the installed tools (optional).","</div>","</div>","</div>","</div>"].join("")),templateToolSectionCreate:s.template(['<div id="new_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="form-row">','<input data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" size="40" name="new_tool_panel_section" id="new_tool_panel_section_<%= tool.clean %>" type="text">','<input id="per_tool_select_<%= tool.clean %>" class="btn btn-primary" data-toolguid="<%= tool.guid %>" value="Select existing" id="select_existing_<%= tool.clean %>" type="button">',"</div>"].join("")),templateToolSectionSelect:s.template(['<div id="select_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="tps_creator">','<select default="active" style="width: 30em;" data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" name="tool_panel_section_id" id="tool_panel_section_select_<%= tool.clean %>">',"<%= tps_select_options({sections: tps.sections}) %>","</select>",'<input id="per_tool_create_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="btn btn-primary create-tps-button" data-toolguid="<%= tool.guid %>" value="Create new" id="create_new_<%= tool.clean %>" type="button">','<div style="clear: both;" class="toolParamHelp"></div>',"</div>"].join("")),templatePanelSelectOptions:s.template(["<% _.each(sections, function(section) { %>",'<option value="<%= section.id %>"><%= section.name %></option>',"<% }); %>"].join(""))});t.default={RepoDetails:m}}).call(t,i(1),i(2),i(0))},315:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l),c=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new r.default.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,i=t.templateRepoQueue,n=t.model.models;t.$el.html(i({title:"Repository Installation Queue",repositories:n,queue:d.default.queueLength()})),s("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t=this;s(".install_one").on("click",function(){var e=t.loadFromQueue(s(this).attr("data-repokey"));t.installFromQueue(e,s(this).attr("data-repokey"))}),s(".remove_one").on("click",function(){var e=s(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var i=t[e].repository.id;delete t[e],s("#queued_repository_"+i).remove()}localStorage.repositories=JSON.stringify(t)}),s("#clear_queue").on("click",function(){localStorage.repositories="{}"}),s("#from_workflow").on("click",function(){e.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(t,i){var n=Object();n.install_tool_dependencies=t.install_tool_dependencies,n.install_repository_dependencies=t.install_repository_dependencies,n.install_resolver_dependencies=t.install_resolver_dependencies,n.tool_panel_section=t.tool_panel_section,n.shed_tool_conf=t.shed_tool_conf,n.repositories=JSON.stringify([[t.repository.id,t.changeset_revision]]),n.tool_shed_repository_ids=JSON.stringify([t.repository.id]),n.tool_shed_url=i.split("|")[0],n.changeset=t.changeset_revision;var a=Galaxy.root+"api/tool_shed_repositories/install?async=True";if(s("#queued_repository_"+t.repository.id).remove(),localStorage.repositories){void 0===i&&(i=d.default.queueKey(t));var o=JSON.parse(localStorage.repositories);o.hasOwnProperty(i)&&(delete o[i],localStorage.repositories=JSON.stringify(o))}s.post(a,n,function(t){var i=JSON.parse(t),n=i.repositories,a="status/r/"+n.join("|");s.post(Galaxy.root+"admin_toolshed/install_repositories",i,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:n.template(['<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner"><%= title %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="tab-pane" id="panel_header" id="repository_queue">','<table id="queued_repositories" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">','<thead id="grid-table-header">',"<tr>",'<th class="datasetRow">Name</th>','<th class="datasetRow">Owner</th>','<th class="datasetRow">Revision</th>','<th class="datasetRow">ToolShed</th>','<th class="datasetRow">Install</th>','<th class="datasetRow"><input class="btn btn-primary" type="submit" id="clear_queue" name="clear_queue" value="Clear queue" /></th>',"</tr>","</thead>","<tbody>","<% _.each(repositories, function(repository) { %>",'<tr id="queued_repository_<%= repository.get("id") %>">','<td class="datasetRow"><%= repository.get("repository").name %></td>','<td class="datasetRow"><%= repository.get("repository").owner %></td>','<td class="datasetRow"><%= repository.get("changeset_revision") %></td>','<td class="datasetRow"><%= repository.get("tool_shed_url") %></td>','<td class="datasetRow">','<input class="btn btn-primary install_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />',"</td>",'<td class="datasetRow">','<input class="btn btn-primary remove_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />',"</td>","</tr>","<% }); %>","</tbody>","</table>",'<input type="button" class="btn btn-primary" id="from_workflow" value="Add from workflow" />',"</div>"].join(""))});t.default={RepoQueueView:c}}).call(t,i(1),i(0),i(2))},316:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l),c=e.View.extend({el:"#center",initialize:function(e){this.options=s.defaults(this.options||[{}],e,this.defaults),this.model=new r.default.RepoStatus,this.listenTo(this.model,"sync",this.render),this.model.url+="?repositories="+this.options.repositories.join("|"),this.model.fetch(),this.timer=setInterval(function(e){var t=["installed","error"],i=!0;s.some(e.model.models,function(e){repo_id=e.get("id");var s=e.get("status").toLowerCase();if(-1===t.indexOf(s))return 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}",".state-color-cloning,",".state-color-setting-tool-versions,",".state-color-installing-repository-dependencies,",".state-color-installing-tool-dependencies,",".state-color-loading-proprietary-datatypes { border-color:#AAAA66; background:#FFFFCC }",".state-color-installed { border-color:#20b520; background:#b0f1b0 }",".state-color-error { border-color:#dd1b15; background:#f9c7c5 }","</style>",'<table id="grid-table" class="grid">','<thead id="grid-table-header">',"<tr>",'<th id="null-header">Name<span class="sort-arrow"></span></th>','<th id="null-header">Description<span class="sort-arrow"></span></th>','<th id="null-header">Owner<span class="sort-arrow"></span></th>','<th id="null-header">Revision<span class="sort-arrow"></span></th>','<th id="null-header">Installation Status<span class="sort-arrow"></span></th>',"</tr>","</thead>",'<tbody id="grid-table-body">',"<% _.each(repositories, function(repository) { %>","<tr>","<td>",'<div id="" class="">','<label id="repo-name-<%= 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a.inputs)if(!a.inputs[l].hidden){r=!0;break}n==s&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var s in e.cases){var n=new v(this.app,{inputs:e.cases[s].inputs});this._append(n.$el.addClass("ui-form-section"),e.id+"-section-"+s)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+s++,o=new v(i.app,{inputs:t});a.add({id:n,$el:o.$el,ondel:function(){a.del(n),i.app.trigger("change")}})}for(var i=this,s=0,a=new p.default.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),o=n.size(e.cache),r=0;r<Math.max(Math.max(o,e.min||0),e.default||0);r++)t(r<o?e.cache[r]:e.inputs);this.app.model.get("sustain_repeats")&&a.hideOptions();var l=new f.default(this.app,{label:e.title||e.name,help:e.help,field:a});this._append(l.$el,e.id)},_addSection:function(e){var t=new h.default.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new v(this.app,{inputs:e.inputs}).$el),t.append(s("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var s=this.parameters.create(e);this.app.field_list[i]=s;var n=new f.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:s});return this.app.element_list[i]=n,this._append(n.$el,e.id),s},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},49:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(11),d=a(l),c=i(4),h=a(c),u=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new h.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(s("<div/>").append(this.$list=s("<div/>")).append(s("<div/>").append(this.button_new.$el)))},size:function(){return n.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new h.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),n.each(this.list,function(e){e.hideOperation("button_delete")}),n.isEmpty(this.list)&&this.$el.append(s("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:u}}).call(t,i(1),i(0),i(2))},50:function(e,t,i){"use strict";(function(e,i,s){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var s=this.model.get("collapsible_value");this.field.collapsed=void 0!==s&&JSON.stringify(this.model.get("value"))==JSON.stringify(s),this.listenTo(this.model,"change",this.render,this),this.render();var n=this;this.$collapsible.on("click",function(){n.field.collapsed=!n.field.collapsed,t.trigger&&t.trigger("change"),n.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){n.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(s.escape(this.model.get("text_value")));var n=this.model.get("error_text");if(this.$error[n?"show":"hide"](),this.$el[n?"addClass":"removeClass"]("ui-error"),this.$error_text.html(n),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},51:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(4),d=a(l),c=i(52),h=a(c),u=i(53),p=a(u),_=i(54),f=a(_),g=i(55),m=a(g),v=i(57),b=a(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new h.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],s.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(n.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new b.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new p.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new m.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},52:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=a(o),l=i(4),d=a(l),c=i(22),h=a(c),u={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},p={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:u.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:u.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:u.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:u.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:u.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:u.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:u.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:u.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:u.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:u.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:u.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:u.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:u.ENABLED}]},_=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(t),this.setElement(s("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var n=s("<div/>").addClass("ui-form-info").append(s("<i/>").addClass("fa fa-sitemap")).append(s("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:n.clone(),enabled:n.clone().append(s("<div/>").append(s("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(s("<div/>").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){t.onchange&&t.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=s.isArray(i)?i:[i],i.length>0)){var n=this._batch({values:[]});for(var a in i){var o=this.history[i[a]+"_"+this.config[t].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[a]+"'."),null;n.values.push(o)}return n.values.sort(function(e,t){return e.hid-t.hid}),n}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;n.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),n.each(e.$batch,function(t,s){t[e.config[i].batch==s?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var e=this,t=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");p[t]?this.config=p[t]:(this.config=p.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+t+"'."));var i=e.model.get("data"),s=r.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],n.each(this.config,function(t,n){e.button_data.push({value:n,icon:t.icon,tooltip:t.tooltip}),e.fields.push(new h.default.View({optional:e.model.get("optional"),multiple:t.multiple,searchable:!t.multiple||i&&i[t.src]&&i[t.src].length>e.model.get("pagelimit"),individual:!0,error_text:"No "+(s?s+" ":"")+(a[t.src]||"content")+" available.",onchange:function(){e.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(t){e.model.set("current",t),e.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),n.each(this.fields,function(t){e.$el.append(t.$el.css({"margin-left":o}))}),n.each(this.$batch,function(t,i){e.$el.append(t.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;n.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};n.each(e,function(e,s){i[s]=[],n.each(e,function(e){i[s].push({hid:e.hid,keep:e.keep,label:e.hid+": "+e.name,value:e.id,tags:e.tags}),t.history[e.id+"_"+s]=e})}),n.each(this.config,function(e,s){i[e.src]&&t.fields[s].add(i[e.src],function(e,t){return t.hid-e.hid})})},_changeValue:function(){var e=this.model.get("value");if(e&&e.values&&e.values.length>0){var t=[];n.each(e.values,function(e){t.push(e.id)});for(var i=e.values[0].src,s=e.values.length>1,a=0;a<this.config.length;a++){var o=this.fields[a],r=this.config[a];if(r.src==i&&-1!==[s,!0].indexOf(r.multiple)){this.model.set("current",a),o.value(t);break}}}else n.each(this.fields,function(e){e.value(null)})},_handleDrop:function(e){try{var t=this.model.get("data"),i=this.model.get("current"),s=this.config[i],a=this.fields[i],o=JSON.parse(e.originalEvent.dataTransfer.getData("text"))[0],r=o.id,l="dataset"==o.history_content_type?"hda":"hdca",d={id:r,src:l};if(t&&n.findWhere(t[l],d)){if(s.src==l){var c=a.value();c&&s.multiple?-1==c.indexOf(r)&&c.push(r):c=r,a.value(c)}else 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diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index 19cc5341583..45dfece8d3f 100644
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t=this.attributes.obj_cache,i=this.attributes.key_ary,n=e.toString(),a=o.indexOf(i,function(e){return e.toString()===n});return-1!==a&&(t[n].stale?(i.splice(a,1),delete t[n]):this.move_key_to_end(e,a)),t[n]},set_elt:function(e,t){var i=this.attributes.obj_cache,n=this.attributes.key_ary,a=e.toString(),s=this.attributes.num_elements;if(!i[a]){if(n.length>=s){delete i[n.shift().toString()]}n.push(e)}return i[a]=t,t},move_key_to_end:function(e,t){this.attributes.key_ary.splice(t,1),this.attributes.key_ary.push(e)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(e,t){return!0},can_subset:function(e){return!1}}),initialize:function(e){y.prototype.initialize.call(this);var t=this.get("init_data");t&&this.add_data(t)},add_data:function(e){this.get("num_elements")<e.length&&this.set("num_elements",e.length);var t=this;o.each(e,function(e){t.set_data(e.region,e)})},data_is_ready:function(){var t=this.get("dataset"),i=e.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:t.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(e){return"pending"!==e}});return 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r=t.get("start");s===this.DEEP_DATA_REQ?e.extend(a,{start_val:o.data.length+1}):s===this.BROAD_DATA_REQ&&(r=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=t.copy().set("start",r),d=this,c=this.load_data(l,i,n,a),u=e.Deferred();return this.set_data(t,u),e.when(c).then(function(e){e.data&&(e.data=o.data.concat(e.data),e.max_low&&(e.max_low=o.max_low),e.message&&(e.message=e.message.replace(/[0-9]+/,e.data.length))),d.set_data(t,e),u.resolve(e)}),u},can_get_more_detailed_data:function(e){var t=this.get_elt(e);return"bigwig"===t.dataset_type&&t.data.length<8e3},get_more_detailed_data:function(e,t,i,n,a){var s=this._mark_stale(e);return s?(a||(a={}),"bigwig"===s.dataset_type&&(a.num_samples=1e3*n),this.load_data(e,t,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(e){var t=this.get_elt(e);return t||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),e.toString()),t.stale=!0,t},get_genome_wide_data:function(t){var i=this,n=!0,a=o.map(t.get("chroms_info").chrom_info,function(e){var t=i.get_elt(new $({chrom:e.chrom,start:0,end:e.len}));return t||(n=!1),t});if(n)return a;var s=e.Deferred();return e.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(e){i.add_data(e.data),s.resolve(e.data)}),s},subset_entry:function(e,t){var i={bigwig:function(e,t){return o.filter(e,function(e){return e[0]>=t.get("start")&&e[0]<=t.get("end")})},refseq:function(t,i){var n=i.get("start")-e.region.get("start");return e.data.slice(n,n+i.length())}},n=e.data;return!e.region.same(t)&&e.dataset_type in i&&(n=i[e.dataset_type](e.data,t)),{region:t,data:n,dataset_type:e.dataset_type}}}),k=x.extend({initialize:function(e){var t=new n.Model;t.urlRoot=e.data_url,this.set("dataset",t)},load_data:function(e,t,i,n){return e.length()<=1e5?x.prototype.load_data.call(this,e,t,i,n):{data:null,region:e}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(e){this.id=e.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(e){var t=o.find(this.get_chroms_info(),function(t){return t.chrom===e});return new $({chrom:t.chrom,end:t.len})},get_chrom_len:function(e){return o.find(this.get_chroms_info(),function(t){return t.chrom===e}).len}}),$=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(e){return this.attributes.chrom===e.get("chrom")&&this.attributes.start===e.get("start")&&this.attributes.end===e.get("end")},initialize:function(e){if(e.from_str){var t=e.from_str.split(":"),i=t[0],n=t[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new $({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(e){var t=this.get("chrom"),i=e.get("chrom"),n=this.get("start"),a=e.get("start"),s=this.get("end"),o=e.get("end");return t&&i&&t!==i?$.overlap_results.DIF_CHROMS:n<a?s<a?$.overlap_results.BEFORE:s<o?$.overlap_results.OVERLAP_START:$.overlap_results.CONTAINS:n>a?n>o?$.overlap_results.AFTER:s<=o?$.overlap_results.CONTAINED_BY:$.overlap_results.OVERLAP_END:s>=o?$.overlap_results.CONTAINS:$.overlap_results.CONTAINED_BY},trim:function(e){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var t=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>t&&(this.attributes.end=t-1)}return this},contains:function(e){return this.compute_overlap(e)===$.overlap_results.CONTAINS},overlaps:function(e){return 0===o.intersection([this.compute_overlap(e)],[$.overlap_results.DIF_CHROMS,$.overlap_results.BEFORE,$.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=n.Collection.extend({model:$}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(e){this.set("region",new $(e.region))}}),M=n.Collection.extend({model:T}),E=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(e){this.set("dataset",new l.default.Dataset(e.dataset));var t=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(e,t){return 0===o.size(e)&&(e={name:t.get("config").get("name").get("value"),color:t.get("config").get("color").get("value")}),e},dataset:function(e){return{id:e.id,hda_ldda:e.get("hda_ldda")}}}}),P=n.Collection.extend({model:E}),O=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return e.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),A=O.extend(v).extend({defaults:o.extend({},O.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(e){this.set("drawables",new P(e.tracks));var t=[];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs)),this.unset("tracks"),this.get("drawables").each(function(e){e.unset("preloaded_data")})},add_tracks:function(e){this.get("drawables").add(e)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(e,t){return{obj_type:"View",prefs:{name:t.get("title"),content_visible:!0},drawables:t.get("drawables")}}}}),D=n.Router.extend({initialize:function(e){this.view=e.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(e){t.navigate(e)})},change_location:function(e){this.view.go_to(e)}});t.default={BackboneTrack:E,BrowserBookmark:T,BrowserBookmarkCollection:M,Cache:y,CanvasManager:b,Genome:C,GenomeDataManager:x,GenomeRegion:$,GenomeRegionCollection:S,GenomeVisualization:A,GenomeReferenceDataManager:k,TrackBrowserRouter:D,Visualization:O,select_datasets:w}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,i){function n(e){e+="";for(var t=/(\d+)(\d{3})/;t.test(e);)e=e.replace(t,"$1,$2");return e}Object.defineProperty(t,"__esModule",{value:!0});var a=function(e){return"promise"in e},s=e.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(e){return!0}},go:function(){var e=i.Deferred(),t=this,n=t.get("ajax_settings"),a=t.get("success_fn"),s=t.get("interval");return function t(){i.ajax(n).success(function(i){a(i)?e.resolve(i):setTimeout(t,s)})}(),e}}),o=function(e){e||(e="#ffffff"),"string"==typeof e&&(e=[e]);for(var 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g({model:e.model,$el:this.$el})},expand_to_container:function(){this.$el.height()<this.scroll_elt.height()&&this.attempt_to_fetch()},attempt_to_fetch:function(e){var t=this;!this.loading_chunk&&this.scrolled_to_bottom()&&(this.loading_chunk=!0,this.loading_indicator.show(),a.when(t.model.get_next_chunk()).then(function(e){e&&(t._renderChunk(e),t.loading_chunk=!1),t.loading_indicator.hide(),t.expand_to_container()}))},render:function(){this.loading_indicator=a("<div/>").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var e=a("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(e);var t=this.model.get_metadata("column_names"),i=a("<thead/>").appendTo(e),n=a("<tr/>").appendTo(i);if(t)n.append("<th>"+t.join("</th><th>")+"</th>");else for(var s=1;s<=this.model.get_metadata("columns");s++)n.append("<th>"+s+"</th>");var o=this,r=this.model.get("first_data_chunk");r?this._renderChunk(r):a.when(o.model.get_next_chunk()).then(function(e){o._renderChunk(e)}),this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(e,t,i){var n=a("<td>").text(e),s=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):s&&t<s.length&&("str"!==s[t]&&"list"!==s[t]||n.addClass("stringalign")),n},_renderRow:function(e){var t=e.split("\t"),i=a("<tr>"),s=this.model.get_metadata("columns");return 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this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),_=p.extend({initialize:function(e){p.prototype.initialize.call(this,e),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:e.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),g=e.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(e){var t=parent.Galaxy;if(t&&t.modal&&(this.modal=t.modal),t&&t.frame&&(this.frame=t.frame),this.modal&&this.frame){var i=e.model,n=i.get("metadata");if(i.get("file_ext")){if(this.file_ext=i.get("file_ext"),"bed"==this.file_ext){if(!(n.get("chromCol")&&n.get("startCol")&&n.get("endCol")))return void console.log("TabularButtonTrackster : Bed-file metadata incomplete.");this.col.chrom=n.get("chromCol")-1,this.col.start=n.get("startCol")-1,this.col.end=n.get("endCol")-1}if("vcf"==this.file_ext){var 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i=t.pageY,a=e.$select.height();e.minHeight=e.minHeight||a,n("#dd-helper").show().on("mousemove",function(t){e.$select.height(Math.max(a+(t.pageY-i),e.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var e=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){e.$select.select2&&e.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var t=[];0!==e.all_button.value()&&a.each(e.model.get("data"),function(e){t.push(e.value)}),e.value(t),e.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(e,t){return!e||""==e||String(t).toUpperCase().indexOf(e.toUpperCase())>=0},_changeData:function(){var e=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:e.model.get("empty_text")}),a.each(this.model.get("data"),function(t){e.data.push(t)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(t,i){e.data2.push({order:i,id:t.value,text:t.label,tags:t.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:e.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(t){e.matched_tags={};var i=e.model.get("pagesize"),n=a.filter(e.data2,function(i){var n=!1;return a.each(i.tags,function(i){e._match(t.term,i)&&(n=e.matched_tags[i]=!0)}),n||e._match(t.term,i.text)});t.callback({results:n.slice((t.page-1)*i,t.page*i),more:n.length>=t.page*i})},formatResult:function(t){return a.escape(t.text)+'<div class="ui-tags">'+a.reduce(t.tags,function(t,i){return e.matched_tags[i]?t+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":t},"")+"</div>"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),a.each(this.data,function(t){e.$select.append(n("<option/>").attr("value",t.value).html(a.escape(t.label)))})),this.model.set("disabled",this.model.get("readonly")||0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var e=this._getValue();this.all_button.value(n.isArray(e)?e.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return a.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(n.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){a.each(this.model.get("data"),function(t){t.keep&&!a.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return n.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=n.isArray(e)?e:[e]:n.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(n.isArray(e)){var i=[];a.each(e,function(e){var n=a.findWhere(t.data2,{id:e});n&&i.push(n)}),e=i}else{e=a.findWhere(this.data2,{id:e})}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var e=null;if(this.model.get("searchable")){var t=this.$select.select2("data");t&&(n.isArray(t)?(e=[],t.sort(function(e,t){return e.order-t.order}),a.each(t,function(t){e.push(t.id)})):e=t.id)}else e=this.$select.val();return r.default.isEmpty(e)?null:e}});t.default={View:c}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(12),d=s(l),c=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({visible:!0,data:[],id:r.default.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(t),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var e=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=n("<div/>")).append(this.$menu=n("<div/>").addClass("ui-options-menu")).append(this.$options=n(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new d.default.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):a.each(this.model.get("data"),function(t){e.$options.append(n(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=n.isArray(e)?e:[e];a.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(n(this).val())}),r.default.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(e){var t=r.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(n("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),h={};h.View=u.extend({initialize:function(e){e.type="radio",u.prototype.initialize.call(this,e)}});var f={};f.View=u.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,u.prototype.initialize.call(this,e)}});var p={};p.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=n("<label/>").addClass("btn btn-default");return e.icon&&t.append(n("<i/>").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(n("<input/>").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),t.default={Base:c,BaseIcons:u,Radio:h,RadioButton:p,Checkbox:f}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(11),l=a(r),d=i(4),c=a(d),u=e.View.extend({initialize:function(e){var t=this;this.options=e,this.name=e.name||"element",this.multiple=e.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:e.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new "+this.name,onclick:function(){t.add({id:t.select.value(),name:t.select.text()})}}),this.setElement(this._template(e)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(e){if(void 0!==e){if(this.portlet.empty(),n.isArray(e))for(var t in e){var i=e[t],a=null,s=null;"string"!=n.type(i)?(a=i.id,s=i.name):a=s=i,null!=a&&this.add({id:a,name:s})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:n(this).prop("id"),name:n(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var t=this;if(0===this.$('[id="'+e.id+'"]').length)if(o.default.isEmpty(e.id))this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else{var i=n(this._templateRow({id:e.id,name:e.name}));i.on("click",function(){i.remove(),t._refresh()}),i.on("mouseover",function(){i.addClass("portlet-highlight")}),i.on("mouseout",function(){i.removeClass("portlet-highlight")}),this.portlet.append(i),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(e){this.select.update(e)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(e){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(e){return'<div id="'+e.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span class="ui-list-name">'+e.name+"</span></div>"}});t.default={View:u}}).call(t,i(1),i(0))},function(e,t,i){"use strict";var n=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default;s.fn.make_text_editable=function(e){var t="num_cols"in e?e.num_cols:30,i="num_rows"in e?e.num_rows:4,n="use_textarea"in e&&e.use_textarea,a="on_finish"in e?e.on_finish:null,o="help_text"in e?e.help_text:null,r=s(this);return r.addClass("editable-text").click(function(o){if(!(s(this).children(":input").length>0)){r.removeClass("editable-text");var l,d,c=function(e){r.find(":input").remove(),""!==e?r.text(e):r.html("<br>"),r.addClass("editable-text"),a&&a(e)},u="cur_text"in e?e.cur_text:r.text();n?(l=s("<textarea/>").attr({rows:i,cols:t}).text(s.trim(u)).keyup(function(e){27===e.keyCode&&c(u)}),d=s("<button/>").text("Done").click(function(){return c(l.val()),!1})):l=s("<input type='text'/>").attr({value:s.trim(u),size:t}).blur(function(){c(u)}).keyup(function(e){27===e.keyCode?s(this).trigger("blur"):13===e.keyCode&&c(s(this).val()),e.stopPropagation()}),r.text(""),r.append(l),d&&r.append(d),l.focus(),l.select(),o.stopPropagation()}}),o&&r.attr("title",o).tooltip(),r}},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(143),c=o(d),u=i(144),h=o(u),f=i(67),p=o(f);e.ajaxSettings.traditional=!0,t.default=n.View.extend({grid:null,initialize:function(e){this.grid=new c.default,this.dict_format=e.dict_format,this.title=e.title;var t=this;if(window.add_tag_to_grid_filter=function(e,i){var n=e+(void 0!==i&&""!==i?":"+i:"");a("#advanced-search").is(":visible")||(a("#standard-search").slideToggle("fast"),a("#advanced-search").slideToggle("fast")),t.add_filter_condition("tags",n)},this.dict_format)if(this.setElement("<div/>"),e.url_base&&!e.items){var i=e.url_data||{};s.each(e.filters,function(e,t){i["f-"+t]=e}),a.ajax({url:e.url_base+"?"+a.param(i),success:function(i){i.embedded=e.embedded,i.filters=e.filters||{},t.init_grid(i)}})}else this.init_grid(e);else this.setElement("#grid-container"),this.init_grid(e);e.use_panels&&a("#center").css({padding:"10px",overflow:"auto"})},handle_refresh:function(e){e&&a.inArray("history",e)>-1&&window.top.Galaxy&&window.top.Galaxy.currHistoryPanel&&window.top.Galaxy.currHistoryPanel.loadCurrentHistory()},init_grid:function(e){this.grid.set(e);var t=this.grid.attributes;this.allow_title_display&&t.title&&l.default.setWindowTitle(t.title),this.handle_refresh(t.refresh_frames);var i=this.grid.get("url_base");if(i=i.replace(/^.*\/\/[^\/]+/,""),this.grid.set("url_base",i),this.$el.html(h.default.grid(t)),this.$el.find("#grid-table-header").html(h.default.header(t)),this.$el.find("#grid-table-body").html(h.default.body(t)),this.$el.find("#grid-table-footer").html(h.default.footer(t)),t.message){this.$el.find("#grid-message").html(h.default.message(t));var n=this;t.use_hide_message&&setTimeout(function(){n.$el.find("#grid-message").html("")},5e3)}this.init_grid_elements(),this.init_grid_controls(),init_refresh_on_change()},init_grid_controls:function(){var e=this;this.$el.find(".operation-button").each(function(){a(this).off(),a(this).click(function(){return e.submit_operation(this),!1})}),this.$el.find("input[type=text]").each(function(){a(this).off(),a(this).click(function(){a(this).select()}).keyup(function(){a(this).css("font-style","normal")})}),this.$el.find(".sort-link").each(function(){a(this).off(),a(this).click(function(){return e.set_sort_condition(a(this).attr("sort_key")),!1})}),this.$el.find(".text-filter-form").each(function(){a(this).off(),a(this).submit(function(){var t=a(this).attr("column_key"),i=a("#input-"+t+"-filter"),n=i.val();return i.val(""),e.add_filter_condition(t,n),!1})}),this.$el.find(".text-filter-val > a").each(function(){a(this).off(),a(this).click(function(){return a(this).parent().remove(),e.remove_filter_condition(a(this).attr("filter_key"),a(this).attr("filter_val")),!1})}),this.$el.find(".categorical-filter > a").each(function(){a(this).off(),a(this).click(function(){return e.set_categorical_filter(a(this).attr("filter_key"),a(this).attr("filter_val")),!1})}),this.$el.find(".advanced-search-toggle").each(function(){a(this).off(),a(this).click(function(){return e.$el.find("#standard-search").slideToggle("fast"),e.$el.find("#advanced-search").slideToggle("fast"),!1})}),this.$el.find("#check_all").off(),this.$el.find("#check_all").on("click",function(){e.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var e=a(this).find("input.grid-row-select-checkbox"),t=a(this).find("span.grid-selected-count"),i=function(){t.text(a(e).filter(":checked").length)};a(e).each(function(){a(this).change(i)}),i()}),0!==this.$el.find(".community_rating_star").length&&this.$el.find(".community_rating_star").rating({});var e=this.grid.attributes,t=this;this.$el.find(".page-link > a").each(function(){a(this).click(function(){return t.set_page(a(this).attr("page_num")),!1})}),this.$el.find(".use-target").each(function(){a(this).click(function(e){return t.execute({href:a(this).attr("href"),target:a(this).attr("target")}),!1})}),0!=e.items.length&&s.each(e.items,function(i,n){var a=t.$("#grid-"+n+"-popup").off(),o=new 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e=this;i(".frame").promise().done(function(){e._panelScroll(0,!0)})},_panelScroll:function(e,t){var i=this.top-this.options.scroll*e;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var s={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,s,t)}}this.top=i}this.render()},_frameInit:function(e,t){e.id=t,e.screen_location={},e.grid_location={},e.grid_rank=null,e.$el.attr("id",t.substring(1))},_frameInsert:function(e,t,a){var s=this,o=[];e&&(e.grid_location=null,o.push([e,this._locationRank(t)])),n.each(this.frame_list,function(e){null!==e.grid_location&&(e.grid_location=null,o.push([e,e.grid_rank]))}),o.sort(function(e,t){return e[1]<t[1]?-1:e[1]>t[1]?1:0}),n.each(o,function(e){s._framePlace(e[0],a)}),this.top_max=0,n.each(this.frame_list,function(e){null!==e.grid_location&&(s.top_max=Math.max(s.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a<this.options.rows;a++){for(var s=0;s<Math.max(1,this.cols-i.width);s++)if(i.top=a,i.left=s,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(e,i,t):console.log("Grid dimensions exceeded.")},_frameFocus:function(e,t){e.$el.css("z-index",this.frame_z+(t?1:0))},_frameOffset:function(e,t,i){if(e.screen_location.left=t.left,e.screen_location.top=t.top,i){this._frameFocus(e,!0);var n=this;e.$el.animate({top:t.top,left:t.left},"fast",function(){n._frameFocus(e,!1)})}else e.$el.css({top:t.top,left:t.left})},_frameResize:function(e,t){e.$el.css({width:t.width,height:t.height}),e.screen_location.width=t.width,e.screen_location.height=t.height},_frameGrid:function(e,t,i){e.grid_location=t,this._frameOffset(e,this._toPixel(t),i),e.grid_rank=this._locationRank(t)},_frameScreen:function(e){var t=e.screen_location;return{top:t.top,left:t.left,width:t.width,height:t.height}}});t.default={View:s}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({id:s.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(t),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(e){a[e.which]=!1}).on("keydown",function(e){var t=e.which;a[t]=!0,i.model.get("is_workflow")&&a[16]&&52==t?(i.value("$"),event.preventDefault()):8==t||9==t||13==t||37==t||39==t||t>=48&&t<=57&&!a[16]||t>=96&&t<=105||(190==t||110==t)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==t||109==t)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var r=o.step;r||(r=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});t.default={View:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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f=o.default.uid(),p=e("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),m=e("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(e("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(m,d.options,u),h.append(m),t(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=e("<div/>");return i(a,this.model.get("data")),a},_template:function(){return e("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});t.default={View:d}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),m=o(p),_=i(51),g=o(_),v=e.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var e=this;this.$el.empty(),a.each(this.inputs,function(t){e.add(t)})},add:function(e){var t=s.extend(!0,{},e);switch(t.id=e.id=l.default.uid(),this.app.input_list[t.id]=t,t.type){case"conditional":this._addConditional(t);break;case"repeat":this._addRepeat(t);break;case"section":this._addSection(t);break;default:this._addRow(t)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var a in e.cases){var s=e.cases[a],o=t.$("#"+e.id+"-section-"+a),r=!1;for(var l in s.inputs)if(!s.inputs[l].hidden){r=!0;break}a==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var a=new v(this.app,{inputs:e.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var a=e.id+"-section-"+n++,o=new v(i.app,{inputs:t});s.add({id:a,$el:o.$el,ondel:function(){s.del(a),i.app.trigger("change")}})}for(var i=this,n=0,s=new f.default.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),o=a.size(e.cache),r=0;r<Math.max(Math.max(o,e.min||0),e.default||0);r++)t(r<o?e.cache[r]:e.inputs);this.app.model.get("sustain_repeats")&&s.hideOptions();var l=new m.default(this.app,{label:e.title||e.name,help:e.help,field:s});this._append(l.$el,e.id)},_addSection:function(e){var t=new u.default.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new v(this.app,{inputs:e.inputs}).$el),t.append(n("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var a=new m.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(11),d=s(l),c=i(4),u=s(c),h=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(e){e.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:h}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,t.trigger&&t.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var s=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+s)).attr("data-original-title",this.model.get("text_"+s)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(52),u=s(c),h=i(53),f=s(h),p=i(54),m=s(p),_=i(55),g=s(_),v=i(57),w=s(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new u.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],n.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(a.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new w.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new m.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new g.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(22),u=s(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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fa").addClass(e.icon),this.$title.addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right")}}),c=o.extend({$menu:null,initialize:function(t){this.model=t&&t.model||new e.Model({id:"",title:"",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(t),this.collection=new e.Collection,this.setElement(n("<div/>").append(this.$root=n("<div/>").append(this.$icon=n("<i/>")).append(this.$title=n("<span/>")))),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"change add remove reset",this.render,this),this.render()},render:function(){var e=this,t=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(t.cls).attr("id",t.id).css({display:t.visible&&this.collection.where({visible:!0}).length>0?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:t.tooltip,placement:"bottom"}).off("click").on("click",function(e){n(".tooltip").hide(),e.preventDefault(),t.onclick&&t.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(t.icon),this.$title.removeClass().addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=n("<ul/>").addClass("menu dropdown-menu").addClass("pull-"+e.model.get("pull")).attr("role","menu"),this.$el.append(this.$menu)),this.collection.each(function(t){var i=t.attributes;if(i.visible){var a=n("<a/>").addClass("dropdown-item").attr({href:i.href,target:i.target}).append(n("<i/>").addClass("fa").addClass(i.icon).css("display",i.icon?"inline-block":"none")).append(i.title).on("click",function(e){i.onclick&&(e.preventDefault(),i.onclick())});e.$menu.append(n("<li/>").append(a)),i.divider&&e.$menu.append(n("<li/>").addClass("divider"))}})},addMenu:function(e){this.collection.add(s.default.merge(e,{title:"",target:"",href:"",onclick:null,divider:!1,visible:!0,icon:null,cls:"button-menu btn-group"}))}});t.default={ButtonDefault:o,ButtonLink:r,ButtonIcon:d,ButtonCheck:l,ButtonMenu:c}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return 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t=[];s.$("input.grid-row-select-checkbox[name=id]:checked").each(function(){window.console.log(e(this).val()),t[t.length]=e.ajax({url:Galaxy.root+"api/datasets/"+e(this).val(),dataType:"json",data:{data_type:"track_config",hda_ldda:"histories"==s.current()?"hda":"ldda"}})}),e.when.apply(e,t).then(function(){var t=arguments[0]instanceof Array?e.map(arguments,function(e){return e[0]}):[arguments[0]];i(t)}),Galaxy.modal.hide()}}})},b=function(e){this.default_font=void 0!==e?e:"9px Monaco, Lucida Console, 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t=this.attributes.obj_cache,i=this.attributes.key_ary,n=e.toString(),a=o.indexOf(i,function(e){return e.toString()===n});return-1!==a&&(t[n].stale?(i.splice(a,1),delete t[n]):this.move_key_to_end(e,a)),t[n]},set_elt:function(e,t){var i=this.attributes.obj_cache,n=this.attributes.key_ary,a=e.toString(),s=this.attributes.num_elements;if(!i[a]){if(n.length>=s){delete i[n.shift().toString()]}n.push(e)}return i[a]=t,t},move_key_to_end:function(e,t){this.attributes.key_ary.splice(t,1),this.attributes.key_ary.push(e)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(e,t){return!0},can_subset:function(e){return!1}}),initialize:function(e){y.prototype.initialize.call(this);var t=this.get("init_data");t&&this.add_data(t)},add_data:function(e){this.get("num_elements")<e.length&&this.set("num_elements",e.length);var t=this;o.each(e,function(e){t.set_data(e.region,e)})},data_is_ready:function(){var t=this.get("dataset"),i=e.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:t.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(e){return"pending"!==e}});return e.when(a.go()).then(function(e){i.resolve("ok"===e||"data"===e)}),i},search_features:function(t){var i=this.get("dataset"),n={query:t,hda_ldda:i.get("hda_ldda"),data_type:"features"};return e.getJSON(i.url(),n)},load_data:function(t,i,n,a){var s=this.get("dataset"),o={data_type:this.get("data_type"),chrom:t.get("chrom"),low:t.get("start"),high:t.get("end"),mode:i,resolution:n,hda_ldda:s.get("hda_ldda")};e.extend(o,a);var r=this.get("filters_manager");if(r){for(var l=[],d=r.filters,c=0;c<d.length;c++)l.push(d[c].name);o.filter_cols=JSON.stringify(l)}var u=this,h=e.getJSON(s.url(),o,function(e){e.region=t,u.set_data(t,e)});return this.set_data(t,h),h},get_data:function(e,t,i,n){var a=this.get_elt(e);if(a&&(c.default.is_deferred(a)||this.get("data_mode_compatible")(a,t)))return a;for(var s,o,r=this.get("key_ary"),l=this.get("obj_cache"),d=0;d<r.length;d++)if(s=r[d],s.contains(e)&&(o=!0,a=l[s.toString()],c.default.is_deferred(a)||this.get("data_mode_compatible")(a,t)&&this.get("can_subset")(a))){if(this.move_key_to_end(s,d),!c.default.is_deferred(a)){var u=this.subset_entry(a,e);this.set_data(e,u),a=u}return a}if(!o&&e.length()<this.attributes.min_region_size){e=e.copy();var h=this.most_recently_added();!h||e.get("start")>h.get("start")?e.set("end",e.get("start")+this.attributes.min_region_size):e.set("start",e.get("end")-this.attributes.min_region_size),e.set("genome",this.attributes.genome),e.trim()}return this.load_data(e,t,i,n)},set_data:function(e,t){this.set_elt(e,t)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(t,i,n,a,s){var o=this._mark_stale(t);if(!o||!this.get("data_mode_compatible")(o,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var r=t.get("start");s===this.DEEP_DATA_REQ?e.extend(a,{start_val:o.data.length+1}):s===this.BROAD_DATA_REQ&&(r=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=t.copy().set("start",r),d=this,c=this.load_data(l,i,n,a),u=e.Deferred();return this.set_data(t,u),e.when(c).then(function(e){e.data&&(e.data=o.data.concat(e.data),e.max_low&&(e.max_low=o.max_low),e.message&&(e.message=e.message.replace(/[0-9]+/,e.data.length))),d.set_data(t,e),u.resolve(e)}),u},can_get_more_detailed_data:function(e){var t=this.get_elt(e);return"bigwig"===t.dataset_type&&t.data.length<8e3},get_more_detailed_data:function(e,t,i,n,a){var s=this._mark_stale(e);return s?(a||(a={}),"bigwig"===s.dataset_type&&(a.num_samples=1e3*n),this.load_data(e,t,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(e){var t=this.get_elt(e);return t||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),e.toString()),t.stale=!0,t},get_genome_wide_data:function(t){var i=this,n=!0,a=o.map(t.get("chroms_info").chrom_info,function(e){var t=i.get_elt(new $({chrom:e.chrom,start:0,end:e.len}));return t||(n=!1),t});if(n)return a;var s=e.Deferred();return e.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(e){i.add_data(e.data),s.resolve(e.data)}),s},subset_entry:function(e,t){var i={bigwig:function(e,t){return o.filter(e,function(e){return e[0]>=t.get("start")&&e[0]<=t.get("end")})},refseq:function(t,i){var n=i.get("start")-e.region.get("start");return e.data.slice(n,n+i.length())}},n=e.data;return!e.region.same(t)&&e.dataset_type in i&&(n=i[e.dataset_type](e.data,t)),{region:t,data:n,dataset_type:e.dataset_type}}}),k=x.extend({initialize:function(e){var t=new n.Model;t.urlRoot=e.data_url,this.set("dataset",t)},load_data:function(e,t,i,n){return e.length()<=1e5?x.prototype.load_data.call(this,e,t,i,n):{data:null,region:e}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(e){this.id=e.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(e){var t=o.find(this.get_chroms_info(),function(t){return t.chrom===e});return new $({chrom:t.chrom,end:t.len})},get_chrom_len:function(e){return o.find(this.get_chroms_info(),function(t){return t.chrom===e}).len}}),$=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(e){return this.attributes.chrom===e.get("chrom")&&this.attributes.start===e.get("start")&&this.attributes.end===e.get("end")},initialize:function(e){if(e.from_str){var t=e.from_str.split(":"),i=t[0],n=t[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new $({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(e){var t=this.get("chrom"),i=e.get("chrom"),n=this.get("start"),a=e.get("start"),s=this.get("end"),o=e.get("end");return t&&i&&t!==i?$.overlap_results.DIF_CHROMS:n<a?s<a?$.overlap_results.BEFORE:s<o?$.overlap_results.OVERLAP_START:$.overlap_results.CONTAINS:n>a?n>o?$.overlap_results.AFTER:s<=o?$.overlap_results.CONTAINED_BY:$.overlap_results.OVERLAP_END:s>=o?$.overlap_results.CONTAINS:$.overlap_results.CONTAINED_BY},trim:function(e){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var t=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>t&&(this.attributes.end=t-1)}return this},contains:function(e){return this.compute_overlap(e)===$.overlap_results.CONTAINS},overlaps:function(e){return 0===o.intersection([this.compute_overlap(e)],[$.overlap_results.DIF_CHROMS,$.overlap_results.BEFORE,$.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=n.Collection.extend({model:$}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(e){this.set("region",new $(e.region))}}),M=n.Collection.extend({model:T}),E=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(e){this.set("dataset",new l.default.Dataset(e.dataset));var t=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(e,t){return 0===o.size(e)&&(e={name:t.get("config").get("name").get("value"),color:t.get("config").get("color").get("value")}),e},dataset:function(e){return{id:e.id,hda_ldda:e.get("hda_ldda")}}}}),P=n.Collection.extend({model:E}),O=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return e.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),A=O.extend(v).extend({defaults:o.extend({},O.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(e){this.set("drawables",new P(e.tracks));var t=[];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs)),this.unset("tracks"),this.get("drawables").each(function(e){e.unset("preloaded_data")})},add_tracks:function(e){this.get("drawables").add(e)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(e,t){return{obj_type:"View",prefs:{name:t.get("title"),content_visible:!0},drawables:t.get("drawables")}}}}),D=n.Router.extend({initialize:function(e){this.view=e.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(e){t.navigate(e)})},change_location:function(e){this.view.go_to(e)}});t.default={BackboneTrack:E,BrowserBookmark:T,BrowserBookmarkCollection:M,Cache:y,CanvasManager:b,Genome:C,GenomeDataManager:x,GenomeRegion:$,GenomeRegionCollection:S,GenomeVisualization:A,GenomeReferenceDataManager:k,TrackBrowserRouter:D,Visualization:O,select_datasets:w}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,i){function n(e){e+="";for(var t=/(\d+)(\d{3})/;t.test(e);)e=e.replace(t,"$1,$2");return e}Object.defineProperty(t,"__esModule",{value:!0});var a=function(e){return"promise"in e},s=e.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(e){return!0}},go:function(){var e=i.Deferred(),t=this,n=t.get("ajax_settings"),a=t.get("success_fn"),s=t.get("interval");return function t(){i.ajax(n).success(function(i){a(i)?e.resolve(i):setTimeout(t,s)})}(),e}}),o=function(e){e||(e="#ffffff"),"string"==typeof e&&(e=[e]);for(var 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counts",type:"bool",default_value:!0},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0}],function(e){return e.key===t});i&&this.set(o.extend({},i,e)),void 0===this.get("value")&&void 0!==this.get("default_value")&&(this.set_value(this.get("default_value")),this.get("value")||"color"!==this.get("type")||this.set("value",l.default.get_random_color()))},set_value:function(e,t){var i=this.get("type");"float"===i?e=parseFloat(e):"int"===i&&(e=parseInt(e,10)),this.set({value:e},t)}})),u=e.Collection.extend({model:c,to_key_value_dict:function(){var e={};return this.each(function(t){e[t.get("key")]=t.get("value")}),e},get_value:function(e){var t=this.get(e);if(t)return t.get("value")},set_value:function(e,t,i){var n=this.get(e);if(n)return n.set_value(t,i)},set_default_value:function(e,t){var i=this.get(e);if(i)return i.set("default_value",t)}},{from_models_and_saved_values:function(e,t){return t&&(e=o.map(e,function(e){return o.extend({},e,{value:t[e.key]})})),new u(e)}}),h=e.View.extend({className:"config-settings-view",render:function(){var e=this.$el;return this.collection.each(function(t,i){if(!t.get("hidden")){var a="param_"+i,s=t.get("type"),r=t.get("value"),d=n("<div class='form-row' />").appendTo(e);if(d.append(n("<label />").attr("for",a).text(t.get("label")+":")),"bool"===s)d.append(n('<input type="checkbox" />').attr("id",a).attr("name",a).attr("checked",r));else if("text"===s)d.append(n('<input type="text"/>').attr("id",a).val(r).click(function(){n(this).select()}));else if("select"===s){var c=n("<select />").attr("id",a);o.each(t.get("options"),function(e){n("<option/>").text(e.label).attr("value",e.value).appendTo(c)}),c.val(r),d.append(c)}else if("color"===s){var u=n("<div/>").appendTo(d),h=n("<input 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d.append(n("<input />").attr("id",a).attr("name",a).val(r));t.help&&d.append(n("<div class='help'/>").text(t.help))}}),this},render_in_modal:function(e){var t=this,i=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc")},a=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc"),t.update_from_form()},s=function(e){27===(e.keyCode||e.which)?i():13===(e.keyCode||e.which)&&a()};n(window).bind("keypress.check_enter_esc",s),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:e||"Configure",body:this.$el,buttons:{Cancel:i,OK:a}})},update_from_form:function(){var e=this;this.collection.each(function(t,i){if(!t.get("hidden")){var n="param_"+i,a=e.$el.find("#"+n).val();"bool"===t.get("type")&&(a=e.$el.find("#"+n).is(":checked")),t.set_value(a)}})}});t.default={ConfigSetting:c,ConfigSettingCollection:u,ConfigSettingCollectionView:h}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(12),d=s(l),c=e.View.extend({initialize:function(t){var i=this;this.data=[],this.data2=[],this.model=t&&t.model||new e.Model({id:r.default.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,readonly:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(t),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls 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i=t.pageY,a=e.$select.height();e.minHeight=e.minHeight||a,n("#dd-helper").show().on("mousemove",function(t){e.$select.height(Math.max(a+(t.pageY-i),e.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var e=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){e.$select.select2&&e.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var t=[];0!==e.all_button.value()&&a.each(e.model.get("data"),function(e){t.push(e.value)}),e.value(t),e.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(e,t){return!e||""==e||String(t).toUpperCase().indexOf(e.toUpperCase())>=0},_changeData:function(){var e=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:e.model.get("empty_text")}),a.each(this.model.get("data"),function(t){e.data.push(t)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(t,i){e.data2.push({order:i,id:t.value,text:t.label,tags:t.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:e.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(t){e.matched_tags={};var i=e.model.get("pagesize"),n=a.filter(e.data2,function(i){var n=!1;return a.each(i.tags,function(i){e._match(t.term,i)&&(n=e.matched_tags[i]=!0)}),n||e._match(t.term,i.text)});t.callback({results:n.slice((t.page-1)*i,t.page*i),more:n.length>=t.page*i})},formatResult:function(t){return a.escape(t.text)+'<div class="ui-tags">'+a.reduce(t.tags,function(t,i){return e.matched_tags[i]?t+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":t},"")+"</div>"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),a.each(this.data,function(t){e.$select.append(n("<option/>").attr("value",t.value).html(a.escape(t.label)))})),this.model.set("disabled",this.model.get("readonly")||0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var e=this._getValue();this.all_button.value(n.isArray(e)?e.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return a.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(n.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){a.each(this.model.get("data"),function(t){t.keep&&!a.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return n.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=n.isArray(e)?e:[e]:n.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(n.isArray(e)){var i=[];a.each(e,function(e){var n=a.findWhere(t.data2,{id:e});n&&i.push(n)}),e=i}else{e=a.findWhere(this.data2,{id:e})}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var e=null;if(this.model.get("searchable")){var t=this.$select.select2("data");t&&(n.isArray(t)?(e=[],t.sort(function(e,t){return e.order-t.order}),a.each(t,function(t){e.push(t.id)})):e=t.id)}else e=this.$select.val();return r.default.isEmpty(e)?null:e}});t.default={View:c}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(12),d=s(l),c=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({visible:!0,data:[],id:r.default.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(t),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var e=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=n("<div/>")).append(this.$menu=n("<div/>").addClass("ui-options-menu")).append(this.$options=n(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new d.default.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):a.each(this.model.get("data"),function(t){e.$options.append(n(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=n.isArray(e)?e:[e];a.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(n(this).val())}),r.default.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(e){var t=r.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(n("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),h={};h.View=u.extend({initialize:function(e){e.type="radio",u.prototype.initialize.call(this,e)}});var f={};f.View=u.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,u.prototype.initialize.call(this,e)}});var p={};p.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=n("<label/>").addClass("btn btn-default");return e.icon&&t.append(n("<i/>").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(n("<input/>").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),t.default={Base:c,BaseIcons:u,Radio:h,RadioButton:p,Checkbox:f}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(11),l=a(r),d=i(4),c=a(d),u=e.View.extend({initialize:function(e){var t=this;this.options=e,this.name=e.name||"element",this.multiple=e.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:e.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new "+this.name,onclick:function(){t.add({id:t.select.value(),name:t.select.text()})}}),this.setElement(this._template(e)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(e){if(void 0!==e){if(this.portlet.empty(),n.isArray(e))for(var t in e){var i=e[t],a=null,s=null;"string"!=n.type(i)?(a=i.id,s=i.name):a=s=i,null!=a&&this.add({id:a,name:s})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:n(this).prop("id"),name:n(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var t=this;if(0===this.$('[id="'+e.id+'"]').length)if(o.default.isEmpty(e.id))this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else{var 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frame-shadow")}),this.$el.append(this.frame_shadow.$el),this._frameInit(this.frame_shadow,"#frame-shadow"),this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list["#frame-shadow"]=this.frame_shadow,this.visible?this.show():this.hide(),this._panelRefresh(),i(window).resize(function(){a.visible&&a._panelRefresh()})},render:function(){this.$(".frame-scroll-up")[this.top!=this.options.top_min&&"show"||"hide"](),this.$(".frame-scroll-down")[this.top!=this.top_max&&"show"||"hide"]()},add:function(e){if(this.frame_counter>=this.options.frame_max)Galaxy.modal.show({title:"Warning",body:"You have reached the maximum number of allowed frames ("+this.options.frame_max+").",buttons:{Close:function(){Galaxy.modal.hide()}}});else{var t="#frame-"+this.frame_uid++;if(0!==i(t).length)Galaxy.modal.show({title:"Error",body:"This frame already exists. This page might contain multiple frame managers.",buttons:{Close:function(){Galaxy.modal.hide()}}});else{this.top=this.options.top_min;var n=new a(e);this.$el.append(n.$el),e.width=this._toPixelCoord("width",this.options.frame.cols),e.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt(n.$el.css("z-index")),this.frame_list[t]=n,this.frame_counter++,this._frameInit(n,t),this._frameResize(n,{width:e.width,height:e.height}),this._frameInsert(n,{top:0,left:0},!0),!this.visible&&this.show(),this.trigger("add")}}},del:function(e){var t=this,i=e.$el;i.fadeOut("fast",function(){i.remove(),delete t.frame_list[e.id],t.frame_counter--,t._panelRefresh(!0),t._panelAnimationComplete(),t.trigger("remove")})},show:function(){this.visible=!0,this.$el.fadeIn("fast"),this.trigger("show")},hide:function(){this.event.type||(this.visible=!1,this.$el.fadeOut("fast",function(){i(this).hide()}),this.trigger("hide"))},length:function(){return this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(e){i(".tooltip").hide(),this.event.type||((i(e.target).hasClass("f-header")||i(e.target).hasClass("f-title"))&&(this.event.type="drag"),i(e.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(e.preventDefault(),this.event.target=this._frameIdentify(e.target),this.event.xy={x:e.originalEvent.pageX,y:e.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(e){if(this.event.type){var t={x:e.originalEvent.pageX,y:e.originalEvent.pageY},i={x:t.x-this.event.xy.x,y:t.y-this.event.xy.y};this.event.xy=t;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var s={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==s.left&&s.left++,this._frameInsert(this.frame_shadow,s)}}},_eventFrameMouseUp:function(e){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(e){this.event.type||(e.preventDefault(),this.del(this._frameIdentify(e.target)))},_eventHide:function(e){!this.event.type&&this.hide()},_eventPanelScroll:function(e){if(!this.event.type&&this.visible){0!==i(e.srcElement).parents(".frame").length?e.stopPropagation():(e.preventDefault(),this._panelScroll(e.originalEvent.detail?e.originalEvent.detail:e.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(e){this.event.type||(e.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(e){this.event.type||(e.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(e){return this.frame_list["#"+i(e).closest(".frame").attr("id")]},_frameDragStart:function(e){this._frameFocus(e,!0);var t=this._frameScreen(e);this._frameResize(this.frame_shadow,t),this._frameGrid(this.frame_shadow,e.grid_location),e.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(e){this._frameFocus(e,!1);var t=this._frameScreen(this.frame_shadow);this._frameResize(e,t),this._frameGrid(e,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(e,t){var i="width"==e||"height"==e?1:-1;return"top"==e&&(t-=this.top),parseInt((t+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(e,t){var i="width"==e||"height"==e?1:-1,n=t*this.options.cell-i*this.options.margin;return"top"==e&&(n+=this.top),n},_toGrid:function(e){return{top:this._toGridCoord("top",e.top),left:this._toGridCoord("left",e.left),width:this._toGridCoord("width",e.width),height:this._toGridCoord("height",e.height)}},_toPixel:function(e){return{top:this._toPixelCoord("top",e.top),left:this._toPixelCoord("left",e.left),width:this._toPixelCoord("width",e.width),height:this._toPixelCoord("height",e.height)}},_isCollision:function(e){for(var t in this.frame_list){var i=this.frame_list[t];if(null!==i.grid_location&&function(e,t){return!(e.left>t.left+t.width-1||e.left+e.width-1<t.left||e.top>t.top+t.height-1||e.top+e.height-1<t.top)}(e,i.grid_location))return!0}return!1},_locationRank:function(e){return e.top*this.cols+e.left},_panelRefresh:function(e){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,e)},_panelAnimationComplete:function(){var e=this;i(".frame").promise().done(function(){e._panelScroll(0,!0)})},_panelScroll:function(e,t){var i=this.top-this.options.scroll*e;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var s={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,s,t)}}this.top=i}this.render()},_frameInit:function(e,t){e.id=t,e.screen_location={},e.grid_location={},e.grid_rank=null,e.$el.attr("id",t.substring(1))},_frameInsert:function(e,t,a){var s=this,o=[];e&&(e.grid_location=null,o.push([e,this._locationRank(t)])),n.each(this.frame_list,function(e){null!==e.grid_location&&(e.grid_location=null,o.push([e,e.grid_rank]))}),o.sort(function(e,t){return e[1]<t[1]?-1:e[1]>t[1]?1:0}),n.each(o,function(e){s._framePlace(e[0],a)}),this.top_max=0,n.each(this.frame_list,function(e){null!==e.grid_location&&(s.top_max=Math.max(s.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a<this.options.rows;a++){for(var s=0;s<Math.max(1,this.cols-i.width);s++)if(i.top=a,i.left=s,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(e,i,t):console.log("Grid dimensions exceeded.")},_frameFocus:function(e,t){e.$el.css("z-index",this.frame_z+(t?1:0))},_frameOffset:function(e,t,i){if(e.screen_location.left=t.left,e.screen_location.top=t.top,i){this._frameFocus(e,!0);var n=this;e.$el.animate({top:t.top,left:t.left},"fast",function(){n._frameFocus(e,!1)})}else e.$el.css({top:t.top,left:t.left})},_frameResize:function(e,t){e.$el.css({width:t.width,height:t.height}),e.screen_location.width=t.width,e.screen_location.height=t.height},_frameGrid:function(e,t,i){e.grid_location=t,this._frameOffset(e,this._toPixel(t),i),e.grid_rank=this._locationRank(t)},_frameScreen:function(e){var t=e.screen_location;return{top:t.top,left:t.left,width:t.width,height:t.height}}});t.default={View:s}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({id:s.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(t),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(e){a[e.which]=!1}).on("keydown",function(e){var t=e.which;a[t]=!0,i.model.get("is_workflow")&&a[16]&&52==t?(i.value("$"),event.preventDefault()):8==t||9==t||13==t||37==t||39==t||t>=48&&t<=57&&!a[16]||t>=96&&t<=105||(190==t||110==t)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==t||109==t)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var r=o.step;r||(r=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});t.default={View:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(23),l=a(r),d=l.default.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple="checkbox"==e.type,l.default.BaseIcons.prototype.initialize.call(this,e)},_setValue:function(t){if(l.default.BaseIcons.prototype._setValue.call(this,t),void 0!==t&&null!==t&&this.header_index){var i=this,a=e.isArray(t)?t:[t];n.each(a,function(e){var t=i.header_index[e];n.each(t,function(e){i._setState(e,!0)})})}},_setState:function(e,t){var i=this.$(".button-"+e),n=this.$(".subgroup-"+e);i.data("is_expanded",t),t?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function t(e,t){var i=e.find(".button-"+t);i.on("click",function(){n._setState(t,!i.data("is_expanded"))})}function i(a,s,r){r=r||[];for(var l in s){var d=s[l],c=d.options&&d.options.length>0,u=r.slice(0);n.header_index[d.value]=u.slice(0);var h=e("<div/>");if(c){var f=o.default.uid(),p=e("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),m=e("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(e("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(m,d.options,u),h.append(m),t(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=e("<div/>");return i(a,this.model.get("data")),a},_template:function(){return e("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});t.default={View:d}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),m=o(p),_=i(51),g=o(_),v=e.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var e=this;this.$el.empty(),a.each(this.inputs,function(t){e.add(t)})},add:function(e){var t=s.extend(!0,{},e);switch(t.id=e.id=l.default.uid(),this.app.input_list[t.id]=t,t.type){case"conditional":this._addConditional(t);break;case"repeat":this._addRepeat(t);break;case"section":this._addSection(t);break;default:this._addRow(t)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var a in e.cases){var s=e.cases[a],o=t.$("#"+e.id+"-section-"+a),r=!1;for(var l in s.inputs)if(!s.inputs[l].hidden){r=!0;break}a==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var a=new v(this.app,{inputs:e.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var a=e.id+"-section-"+n++,o=new v(i.app,{inputs:t});s.add({id:a,$el:o.$el,ondel:function(){s.del(a),i.app.trigger("change")}})}for(var i=this,n=0,s=new f.default.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),o=a.size(e.cache),r=0;r<Math.max(Math.max(o,e.min||0),e.default||0);r++)t(r<o?e.cache[r]:e.inputs);this.app.model.get("sustain_repeats")&&s.hideOptions();var l=new m.default(this.app,{label:e.title||e.name,help:e.help,field:s});this._append(l.$el,e.id)},_addSection:function(e){var t=new u.default.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new v(this.app,{inputs:e.inputs}).$el),t.append(n("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var a=new m.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(11),d=s(l),c=i(4),u=s(c),h=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(e){e.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:h}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,t.trigger&&t.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var s=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+s)).attr("data-original-title",this.model.get("text_"+s)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(52),u=s(c),h=i(53),f=s(h),p=i(54),m=s(p),_=i(55),g=s(_),v=i(57),w=s(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new u.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],n.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(a.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new w.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new m.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new g.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(22),u=s(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(t),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){t.onchange&&t.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var s in i){var o=this.history[i[s]+"_"+this.config[t].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[s]+"'."),null;a.values.push(o)}return a.values.sort(function(e,t){return e.hid-t.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;a.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),a.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var e=this,t=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[t]?this.config=f[t]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+t+"'."));var i=e.model.get("data"),n=r.default.textify(this.model.get("extensions")),s=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(t,a){e.button_data.push({value:a,icon:t.icon,tooltip:t.tooltip}),e.fields.push(new u.default.View({optional:e.model.get("optional"),multiple:t.multiple,searchable:!t.multiple||i&&i[t.src]&&i[t.src].length>e.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(s[t.src]||"content")+" available.",onchange:function(){e.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(t){e.model.set("current",t),e.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(t){e.$el.append(t.$el.css({"margin-left":o}))}),a.each(this.$batch,function(t,i){e.$el.append(t.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;a.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};a.each(e,function(e,n){i[n]=[],a.each(e,function(e){i[n].push({hid:e.hid,keep:e.keep,label:e.hid+": 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this.model.set("value",{values:[d]}),this.model.trigger("change:value");this.trigger("change"),this._handleDropStatus("success")}else this._handleDropStatus("danger")}catch(e){this._handleDropStatus("danger")}e.preventDefault()},_handleDropStatus:function(e){var t=this;this.$el.removeClass("ui-dragover").addClass("ui-dragover-"+e),setTimeout(function(){t.$el.removeClass("ui-dragover-"+e)},this.model.get("statustimer"))},_batch:function(e){e.batch=!1;var t=this.model.get("current"),i=this.config[t];if("hdca"==i.src&&!i.multiple){var n=this.history[this.fields[t].value()+"_hdca"];n&&n.map_over_type&&(e.batch=!0)}return i.batch!=h.LINKED&&i.batch!=h.ENABLED||(e.batch=!0,i.batch==h.ENABLED&&"true"===this.button_product.value()&&(e.product=!0)),e}});t.default={View:p}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=(n(a),i(4)),o=n(s),r=i(43),l=(n(r),i(24)),d=n(l),c=e.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=e.Collection.extend({initialize:function(){var t=this;this.config=new e.Model({library_id:null}),this.config.on("change",function(){t.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=e.View.extend({initialize:function(e){var t=this;this.libraries=new c,this.datasets=new u,this.options=e,this.library_select=new o.default.Select.View({onchange:function(e){t.datasets.config.set("library_id",e)}}),this.dataset_list=new d.default.View({name:"dataset",optional:e.optional,multiple:e.multiple,onchange:function(){t.trigger("change")}}),this.libraries.on("reset",function(){var e=[];t.libraries.each(function(t){e.push({value:t.id,label:t.get("name")})}),t.library_select.update(e)}),this.datasets.on("reset",function(){var e=[];null!==t.library_select.text()&&t.datasets.each(function(t){"file"===t.get("type")&&e.push({value:t.id,label:t.get("name")})}),t.dataset_list.update(e)}),this.on("change",function(){e.onchange&&e.onchange(t.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){t.library_select.trigger("change"),void 0!==t.options.value&&t.value(t.options.value)}})},value:function(e){return this.dataset_list.value(e)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});t.default={View:h}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=n(a),o=i(24),r=n(o),l=e.View.extend({initialize:function(e){var t=this;this.ftpfile_list=new r.default.View({name:"file",optional:e.optional,multiple:e.multiple,onchange:function(){e.onchange&&e.onchange(t.value())}}),this.setElement(this.ftpfile_list.$el),s.default.get({url:Galaxy.root+"api/remote_files",success:function(e){var i=[];for(var n in e)i.push({value:e[n].path,label:e[n].path});t.ftpfile_list.update(i)}})},value:function(e){return this.ftpfile_list.value(e)}});t.default={View:l}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=(n(a),i(4)),o=n(s),r=i(56),l=n(r),d=e.View.extend({initialize:function(e){var t=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){t.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new o.default.Input({type:"password"}),this.setElement(this._template(e)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(e){var t=this;l.default.openFileBrowser({successCallback:function(e){t.value(e.destination+"^"+e.token)}})},_template:function(e){return'<div class="ui-gs-select-file"><div class="ui-gs-browse-field"><span class="ui-gs-browse-button" /><span class="ui-gs-filename-textbox" /></div><div class="ui-gs-token-field"><span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span><span class="ui-gs-token-textbox" /></div></div>'},value:function(e){if(void 0===e)return this._getValue();this._setValue(e)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(e){e&&(values=e.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});t.default={View:d}}).call(t,i(1))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.default={openFileBrowser:function(e){var t=window.Galaxy.config.genomespace_ui_url,i=t+"upload/loadUrlToGenomespace.html?getLocation=true",n=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=e.successCallback,window.addEventListener("message",function(e){successCalBack(e.data)},!1),n.focus(),null!=e.errorCallback&&(n.setCallbackOnGSUploadError=config.errorCallback)}}},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return 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x?e.clear_search_results():e.show()})},apply_search_results:function(){var e=this.get("tool_search").get("results");if(null===e)return void this.clear_search_results();var t=null;this.get("layout").each(function(i){i instanceof y?(t=i,t.hide()):i instanceof w?i.apply_search_results(e)&&t&&t.show():(t=null,i.apply_search_results(e))})}}),$=e.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),S=$.extend({tagName:"div",render:function(){var e=n("<div/>");e.append(A.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return 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this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),P=e.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new E({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof x){var i=new M({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof w){var n=new S({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof y){var a=new T({model:t});a.render(),e.$el.append(a.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=n(this).attr("class").split(/\s+/)[0],a=e.model.get("tools").get(i);e.trigger("tool_link_click",t,a)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?n("#search-no-results").show():n("#search-no-results").hide()}}),O=e.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(A.tool_form(this.model.toJSON()))}}),A=(e.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new P({collection:this.collection}),this.tool_form_view=new O},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" 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o=i(3),r=s(o),l=i(4),d=s(l),c=i(9),u=s(c),h=i(63),f=s(h),p=i(40),m=s(p),_=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(r.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),r.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),r.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("<input/>").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),r.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new m.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var a in t){var s=t[a],o=this.form.data.match(a),r=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&r){if(!l.optional&&null==s)return this.form.highlight(o),!1;if(s&&s.batch){var d=s.values.length,c=d>0&&s.values[0]&&s.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(e.hid+": "+e.name)))}),s.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("<pre/>").text(JSON.stringify(e,null,4)))}});t.default={View:_}}).call(t,i(1),i(0),i(2))},,function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(e){return-1!==i.indexOf(this.attributes.async_ops,e)},add_filter:function(e,t,i){if(i){var n,a=this.attributes.filters[e];if(null===a||void 0===a)n=t;else if("string"==typeof a)if("All"==a||a==t)n=t;else{var s=[];s[0]=a,s[1]=t,n=s}else n=a,-1===n.indexOf(t)&&n.push(t);this.attributes.filters[e]=n}else this.attributes.filters[e]=t},remove_filter:function(e,t){var n=this.attributes.filters[e];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[e]="";else{var a=i.indexOf(n,t);-1!==a&&(n[a]="")}},get_url_data:function(){var e={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(e.operation=this.attributes.operation),this.attributes.item_ids&&(e.id=this.attributes.item_ids);var t=this;return i.each(i.pairs(t.attributes.filters),function(t){e["f-"+t[0]]=t[1]}),e},get_url:function(e){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(e)}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a);t.default={grid:function(e){var t="";return t=e.embedded?this.grid_header(e)+this.grid_table(e):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(e)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(e),e.info_text&&(t+='<br><div class="toolParamHelp" style="clear: both;">'+e.info_text+"</div>"),t},grid_table:function(e){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(e){var t='<div class="grid-header">';if(e.embedded||(t+="<h2>"+e.title+"</h2>"),e.global_actions){t+='<ul class="manage-table-actions">';var i=e.global_actions.length>=3;i&&(t+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in e.global_actions){var a=e.global_actions[n];t+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(t+="</div>"),t+="</ul>"}return e.insert&&(t+=e.insert),t+=this.grid_filters(e),t+="</div>"},header:function(e){var t="<tr>";e.show_item_checkboxes&&(t+="<th>",e.items.length>0&&(t+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),t+="</th>");for(var i in e.columns){var n=e.columns[i];n.visible&&(t+='<th id="'+n.key+'-header">',n.href?t+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":t+=n.label,t+='<span class="sort-arrow">'+n.extra+"</span></th>")}return t+="</tr>"},body:function(t){var i="",n=0;0==t.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in t.items){var s=t.items[a],o=s.encode_id;i+="<tr ",t.current_item_id==s.id&&(i+='class="current"'),i+=">",t.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var r in t.columns){var l=t.columns[r];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=s.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===e.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",m="";l.attach_popup&&(p="grid-"+a+"-popup",m="menubutton",""!=u&&(m+=" split"),m+=" popup"),i+="<td "+d+">",u?(0!=t.operations.length&&(i+='<div id="'+p+'" class="'+m+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=t.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+m+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(e){var t="";if(e.use_paging&&e.num_pages>1){var i=e.num_page_links,n=e.cur_page_num,a=e.num_pages,s=i/2,o=n-s,r=0;o<=0&&(o=1,r=s-(n-o));var l,d=s+r,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),t+='<tr id="page-links-row">',e.show_item_checkboxes&&(t+="<td></td>"),t+='<td 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f=e.operations[h];f.allow_multiple&&(t+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}t+="</td></tr>"}var p=!1;for(h in e.operations)if(e.operations[h].global_operation){p=!0;break}if(p){t+='<tr><td colspan="100">';for(h in e.operations){var f=e.operations[h];f.global_operation&&(t+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}t+="</td></tr>"}return e.legend&&(t+='<tr><td colspan="100">'+e.legend+"</td></tr>"),t},message:function(e){var t=e.status;return-1!=["success","ok"].indexOf(t)&&(t="done"),'<p><div class="'+t+'message transient-message">'+n.escape(e.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1;for(var s in e.columns){var o=e.columns[s];if("advanced"==o.filterable){var r=o.key,l=i[r],d=t[r];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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class="text-filter-form" column_key="'+s+'" action="'+t.url+'" method="get" >';for(u in t.columns){var r=t.columns[u],l=n[r.key];l&&"All"!=l&&(r.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+r.key+'" name="f-'+r.key+'" value="'+l+'"/>')}o+='<span id="'+s+'-filtering-criteria">';var d=n[s];if(d){var c=e.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(s,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(s,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var m=p.length;m<20&&(m=20),m+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+s+'-filter" name="f-'+s+'" type="text" placeholder="'+p+'" size="'+m+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+s+'-filtering-criteria">';var _=!1;for(var g in t.categorical_filters[s]){var v=t.categorical_filters[s][g],w="",b="";for(var y in v)w=y,b=v[y];_&&(o+=" | "),_=!0;var h=n[s];h&&v[s]&&h==b?o+='<span class="categorical-filter '+s+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+s+'-filter"><a href="javascript:void(0);" filter_key="'+w+'" filter_val="'+b+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(e,t){return'<span class="text-filter-val">'+(t=s.default.sanitize(t))+'<a href="javascript:void(0);" filter_key="'+e+'" filter_val="'+t+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(146),l=a(r),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),m=i(26),_=a(m),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var w=null,b=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=e.Model.extend;var x=y.extend({initialize:function(e){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=e},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var e=[];n(".bookmark").each(function(){e.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var t=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,i={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:t},bookmarks:e};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(e){Galaxy.modal.hide(),b.vis_id=e.vis_id,b.has_changes=!1,window.history.pushState({},"",e.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var e=this,t=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(e){o.each(e,function(e){b.add_drawable(l.default.object_from_template(e,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=e.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){e.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){e.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=t,t},add_bookmark:function(e,t,i){var a=n("#right .unified-panel-body"),s=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(s),r=(n("<a href=''/>").text(e).appendTo(o).click(function(){return b.go_to(e),!1}),n("<div/>").text(t).appendTo(s));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){return s.slideUp("fast"),s.remove(),b.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);r.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,s},create_visualization:function(e,t,i,a,s){var r=this,d=new l.default.TracksterView(o.extend(e,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(e){if(t){var n=t.chrom,o=t.start,c=t.end,u=t.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(e[0].chrom)}else d.change_chrom(e[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],r.add_bookmark(f.position,f.annotation,s);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(t){new c.default.TrackBrowserRouter(t),e.history.start()},init_keyboard_nav:function(e){n(document).keyup(function(t){if(!n(t.srcElement).is(":input"))switch(t.which){case 37:e.move_fraction(.25);break;case 38:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()-20);break;case 39:e.move_fraction(-.25);break;case 40:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(e){if(e.has_changes){var t=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(t.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=e.View.extend({initialize:function(){w=new x(Galaxy.root),w.createButtonMenu(),w.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(w.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var e=this,t=p.default.get("dbkey"),i={},n={dbkey:t,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(t||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){e.view_in_saved(n)},"View in new visualization":function(){e.view_new()}}})},view_in_saved:function(e){var t=new _.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:t.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){e.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(e)})}}})},view_existing:function(){var e=galaxy_config.app.viz_config;b=w.create_visualization({container:n("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,!0),this.init_editor()},view_new:function(){var e=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(t){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(t),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){e.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=t.map(function(e){return e[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(e){for(var t='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<e.length;i++)t+='<option value="'+e[i][1]+'">'+e[i][0]+"</option>";return t+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(e,t){n(document).trigger("convert_to_values"),b=w.create_visualization({container:n("#center .unified-panel-body"),name:e,dbkey:t},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){b.add_drawable(l.default.object_from_template(e,b,b))}}),n("#add-bookmark-button").click(function(){var e=b.chrom+":"+b.low+"-"+b.high;return w.add_bookmark(e,"Bookmark description",!0)}),w.init_keyboard_nav(b),n(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});t.default={TracksterUI:x,GalaxyApp:k}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function o(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var r=i(2),l=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(r),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),m=i(148),_=a(m),g=i(149),v=a(g),w=i(150),b=a(w),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),S=a($),T=i(151),M=a(T);i(25);var E=l.extend,P={},O=function(e,t){P[e.attr("id")]=t},A=function(t,i,n,a){n=".group",P[t.attr("id")]=a,t.bind("drag",{handle:"."+i,relative:!0},function(t,i){var a,s,o,r,l,d=(e(this),e(this).parent()),c=d.children(".track,.group"),u=P[e(this).attr("id")];if(s=e(this).parents(n),0!==s.length){o=s.position().top,r=o+s.outerHeight();var h=P[s.attr("id")];if(i.offsetY<o)return e(this).insertBefore(s),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>r)return e(this).insertAfter(s),h.remove_drawable(u),void h.container.add_drawable(u)}for(s=null,l=0;l<c.length;l++)if(a=e(c.get(l)),o=a.position().top,r=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=r)return i.offsetY-o<r-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void P[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=e(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),P[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(e(this).insertBefore(c.get(l)),P[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})},D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",I=["Histogram","Line","Filled","Intensity"],z=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};z.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(e){new S.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],E(z.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var L=function(e,t,i){z.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};E(L.prototype,z.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i<e.length;i++)t=ne(e[i],this.view,this),this.add_drawable(t)},init:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].init()},_draw:function(e){for(var t=0;t<this.drawables.length;t++)this.drawables[t]._draw(e)},to_dict:function(){for(var e=[],t=0;t<this.drawables.length;t++)e.push(this.drawables[t].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:e}},add_drawable:function(e){this.drawables.push(e),e.container=this,this.changed()},add_drawable_before:function(e,t){this.changed();var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,0,e),!0)},replace_drawable:function(e,t,i){var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables[n]=t,i&&e.container_div.replaceWith(t.container_div),this.changed()),n},remove_drawable:function(e){var t=this.drawables.indexOf(e);return-1!==t&&(this.drawables.splice(t,1),e.container=null,this.changed(),!0)},move_drawable:function(e,t){var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(t,0,e),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(e){for(var t,i=this.drawables.slice(0),n=[];0!==i.length;)t=i.shift(),t instanceof e?n.push(t):t.drawables&&(i=i.concat(t.drawables));return n}});var j=function(t,i,n){if(E(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),L.call(this,t,i,n),this.content_div=e("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),A(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};E(j.prototype,z.prototype,L.prototype,{action_icons_def:[z.prototype.action_icons_def[0],z.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},z.prototype.action_icons_def[2]],build_container_div:function(){var t=e("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i<t;i++){if(a=this.drawables[i],a.get_type()!==s){can_composite=!1;break}a instanceof Z&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),e(".tooltip").remove()),o>1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],l[r.name]=[r];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],r.name in l&&l[r.name].push(r);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new b.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].filters_manager=this.saved_filters_managers[e];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var e=0;e<this.drawables.length;e++){var t=this.drawables[e];this.saved_filters_managers.push(t.filters_manager),t.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var e=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,e,!0);e.request_draw()},add_drawable:function(e){L.prototype.add_drawable.call(this,e),this.update_icons()},remove_drawable:function(e){L.prototype.remove_drawable.call(this,e),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var e=E(L.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),e},request_draw:function(e){l.each(this.drawables,function(t){t.request_draw(e)})}});var R=n.View.extend({initialize:function(e){E(e,{obj_type:"View"}),L.call(this,"View",e.container,e),this.chrom=null,this.vis_id=e.vis_id,this.dbkey=e.dbkey,this.stand_alone=void 0===e.stand_alone||e.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:e.name})},render:function(){this.requested_redraw=!1;var t=this.container,i=this;this.top_container=e("<div/>").addClass("top-container").appendTo(t),this.browser_content_div=e("<div/>").addClass("content").appendTo(t),this.bottom_container=e("<div/>").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,i),this.intro_div=e("<div/>").addClass("intro").appendTo(this.viewport_container);e("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(e){l.each(e,function(e){i.add_drawable(ne(e,i,i))})})});this.nav_container=e("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(Z),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new W(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});E(R.prototype,L.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500)}else view.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(p.default.commatize(e)+" - "+p.default.commatize(t)),this.nav_input.val(this.chrom+":"+p.default.commatize(e)+"-"+p.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){t.num=100;var i=this,n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new X(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e('<option value="">Select Chrom/Contig</option>'));for(var s=0,o=i.chrom_data.length;s<o;s++){var r=i.chrom_data[s].chrom,l=e("<option>");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('<option value="previous">Previous 100</option>')),t.next_chroms&&i.chrom_select.append(e('<option value="next">Next 100</option>')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;o<r;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(e){e=e.replace(/,/g,""),e=e.replace(/:|\-/g," ");var t=e.split(/\s+/),i=t[0],n=t[1]?parseInt(t[1],10):void 0,a=t[2]?parseInt(t[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(e){var t=this,i=t.high-t.low;this.move_delta(e*i)},move_delta:function(e){var t=this,i=t.high-t.low;t.low-e<t.max_low?(t.low=t.max_low,t.high=t.max_low+i):t.high-e>t.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){L.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(L.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;l.each(n,function(t){var n=l.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;e<this.max_low&&(e=this.max_low),t>this.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(t=e+this.min_separation),this.low=Math.floor(e),this.high=Math.ceil(t),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(e){var t=e[0],i=e[1];t&&t._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(e){e._draw()})},zoom_in:function(e,t){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;e&&(n=e/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var e=this.high-this.low,t=e/2+this.low,i=e*this.zoom_factor/2;this.low=Math.round(t-i),this.high=Math.round(t+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(e){if(this.overview_drawable){if(this.overview_drawable.dataset.id===e.dataset.id)return;this.overview_viewport.find(".track").remove()}var t=e.copy({content_div:this.overview_viewport}),i=this;t.header_div.hide(),t.is_overview=!0,i.overview_drawable=t,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){e(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var N=C.default.Tool.extend({defaults:{track:null},initialize:function(e){C.default.Tool.prototype.initialize.call(this,e);var t=!0;void 0!==e.tool_state&&void 0!==e.tool_state.hidden&&(t=e.tool_state.hidden),this.set("hidden",t),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(e){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),V=n.View.extend({events:{"change :input":"update_value"},render:function(){var t=this.$el.addClass("param-row"),i=this.model;e("<div>").addClass("param-label").text(i.get("label")).appendTo(t);e("<div/>").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("<div style='clear: both;'/>").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),G=n.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()});e("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(e){var t=new V({model:e});t.render(),n.append(t.$el)}),n.find("input").click(function(){e(this).select()});var a=e("<div>").addClass("param-row").appendTo(n),s=e("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);e("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e<this.params.length;e++)this.params[e].update_value()},run_on_dataset:function(){var e=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:e.id},null,function(t){Galaxy.modal.show({title:e.get("name")+" is Running",body:e.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var e,t=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:t.view.chrom,start:t.view.low,end:t.view.high}),a={target_dataset_id:t.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},s=t,o=i.get("name")+s.tool_region_and_parameters_str(n);if(s.container===view){var r=new j(view,view,{name:t.config.get_value("name")}),l=s.container.replace_drawable(s,r,!1);r.container_div.insertBefore(s.view.content_div.children()[l]),r.add_drawable(s),s.container_div.appendTo(r.content_div),e=r}else e=s.container;var d=new s.constructor(view,e,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(s.mode),d.set_filters_manager(s.filters_manager.copy(d)),d.update_icons(),e.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(e){d.set_dataset(new x.default.Dataset(e)),d.tiles_div.text("Running job."),d.init()})},run:function(t,i,n){t.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(t),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});e.when(a.go()).then(function(e){"no converter"===e?(i.container_div.addClass("error"),i.content_div.text(D)):e.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+e.message)):n(e)})}}),U=function(e,t){v.default.Scaler.call(this,t),this.filter=e};U.prototype.gen_val=function(e){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(e[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var H=function(t,i,n,a,s){this.track=t,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=e("<div class='track-tile'/>").append(a),this.data=s,this.stale=!1};H.prototype.predisplay_actions=function(){};var F=function(e,t,i,n,a){H.call(this,e,t,i,n,a)};F.prototype.predisplay_actions=function(){};var B=function(e,t,i,n,a,s,o,r,l,d,c){H.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};E(B.prototype,H.prototype),B.prototype.predisplay_actions=function(){};var q=function(t,i,a){E(a,{drag_handle_class:"draghandle"}),z.call(this,t,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};E(q.prototype,z.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},z.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},z.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(t){var i="<strong>Tool</strong>:"+t.tool.get("name")+"<br/><strong>Dataset</strong>:"+t.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},s=function(){var i,a=e('select[name="regions"] option:selected').val(),s=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(e(".bookmark"),function(t){return new c.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===a?[s]:"bookmarks"===a?o:[s].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:s}})}},z.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&z.prototype.can_draw.call(this)},build_container_div:function(){return e("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("<div class='track-resize'>");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof W?"LabelTrack":this instanceof X?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof te?"ReadTrack":this instanceof ee?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Z?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("<span/>").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(D)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+t.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("<span/>").text(" ")),a.append(e("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(t,i,n){q.call(this,t,i,n);var a=this;if(A(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new b.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new N(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new G({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};E(Y.prototype,z.prototype,q.prototype,{action_icons_def:q.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();E(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){if(this.can_draw()){var i=t&&t.clear_after,n=this.view.low,a=this.view.high,s=this.view.container.width(),o=this.view.resolution_px_b,r=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=s/(view.max_high-view.max_low),r=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*r),f=Math.floor(n/h),p=[],m=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,t),p.push(u),e.when(u).then(function(e){m.push(e)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var _=this;e.when.apply(e,p).then(function(){_.tiles_div.children(".remove").remove(),m=l.filter(m,function(e){return null!==e}),0!==m.length&&_.postdraw_actions(m,s,o,i)})}},_add_yaxis_label:function(t,i){var n=this,a="max"===t?"top":"bottom",o="max"===t?"max":"min",r="max"===t?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=s(n.config.get_value(r),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=e("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),n.config.set_value(r,s(t,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){if(l.filter(e,function(e){return e instanceof F}).length>0){this.max_height_px=0;var a=this;l.each(e,function(e){e instanceof F||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(e,function(e){return e.has_icons})&&l.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)})},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){n||(n={});var a=n.force,s=n.mode||this.mode,o=1/i,r=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,t),u=a?void 0:r.tile_cache.get_elt(c);if(u)return function(e){return e&&"track"in e}(u)&&r.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var e=l.find(I,function(e){return e===s})?"Coverage":s,i=l.map(d,function(i){return i.data_manager.get_data(t,e,o,r.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(t,s,o,view.reference_track.data_url_extra_params)),i},f=e.Deferred();return r.tile_cache.set_elt(c,f),e.when.apply(e,h()).then(function(){var a,s=h(),o=s;if(l.find(s,function(e){return p.default.is_deferred(e)}))return r.tile_cache.set_elt(c,void 0),void e.when(r.draw_helper(t,i,n)).then(function(e){f.resolve(e)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(s.pop(),t));var u=[],m=[];l.each(d,function(e,t){var n=e.mode,a=o[t];"Auto"===n&&(n=e.get_mode(a),e.update_auto_mode(n)),u.push(n),m.push(e.get_canvas_height(a,n,i,b))});var _,g=r.view.canvas_manager.new_canvas(),v=t.get("start"),w=t.get("end"),b=Math.ceil((w-v)*i)+r.left_offset,y=l.max(m);g.width=b,g.height=n.height||y;var x=g.getContext("2d");x.translate(r.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(e,n){_=e.draw_tile(o[n],x,u[n],t,i,a)}),void 0!==_&&(r.tile_cache.set_elt(c,_),r.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new v.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new F(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+l.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var W=function(e,t){q.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};E(W.prototype,q.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("<div/>").addClass("label-container");s<i.high;){var l=Math.floor((s-i.low)/n*o);r.append(e("<div/>").addClass("pos-label").text(p.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var J=function(e,t,i){if(Y.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=ne(n,e,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(e){(e instanceof Z||e instanceof te)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};E(J.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:L.prototype.to_dict,add_drawable:L.prototype.add_drawable,unpack_drawables:L.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;l.each(this.drawables,function(t){t.visible_height_px=e}),q.prototype.on_resize.call(this)},change_mode:function(e){Y.prototype.change_mode.call(this,e);for(var t=0;t<this.drawables.length;t++)this.drawables[t].change_mode(e)},init:function(){for(var t=[],i=0;i<this.drawables.length;i++)t.push(this.drawables[i].init());var n=this;e.when.apply(e,t).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:z.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var e,t=new j(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)e=this.drawables[i],e.update_icons(),t.add_drawable(e),e.container=t,t.content_div.append(e.container_div);this.container.replace_drawable(this,t,!0);t.request_draw({clear_tile_cache:!0})},before_draw:function(){var e=l.min(l.map(this.drawables,function(e){return e.config.get_value("min_value")})),t=l.max(l.map(this.drawables,function(e){return e.config.get_value("max_value")}));this.config.set_value("min_value",e),this.config.set_value("max_value",t),l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)})},update_all_min_max:function(){var e=this.config.get_value("min_value"),t=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(e,t,i,n){var a,s=-1;for(a=0;a<e.length;a++){var o=e[a].html_elt.find("canvas").height();o>s&&(s=o)}for(a=0;a<e.length;a++){var r=e[a];r.html_elt.find("canvas").height()!==s&&(this.draw_helper(r.region,i,{force:!0,height:s}),r.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var X=function(e){Y.call(this,e,{content_div:e.top_labeltrack},{resize:!1,header:!1}),this.left_offset=e.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};E(X.prototype,z.prototype,Y.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:z.prototype.can_draw,draw_helper:function(e,t,i){var n,a=this.tiles_div.is(":visible"),s=null;return t>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=Y.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l<d;l++)t.fillStyle=this.view.get_base_color(o[l]),t.fillText(o[l],Math.floor(l*a),10);return new H(this,n,a,r,s)}});var K=function(t,i,n){this.mode="Histogram",Y.call(this,t,i,n),this.left_offset=30;var a=this;e.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(e){e&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};E(K.prototype,z.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(e,t,i,n,a){return this._draw_line_track_tile(e,t,i,n,a)},can_subset:function(e){return e.data[1][0]-e.data[0][0]==1},postdraw_actions:function(e,t,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Q=function(e,t,i){this.mode="Heatmap",Y.call(this,e,t,i)};E(Q.prototype,z.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){e.data})},draw_tile:function(e,t,i,n,a){var s=t.canvas;return new v.default.DiagonalHeatmapPainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new H(this,n,a,s,e.data)}});var Z=function(e,t,i){Y.call(this,e,t,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};E(Z.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s,o=this;if(0===l.filter(t,function(e){return e instanceof F}).length){var r={};l.each(l.pluck(t,"incomplete_features"),function(e){l.each(e,function(e){r[e[0]]=e})});var d=this;l.each(t,function(t){var i=l.omit(r,l.map(t.incomplete_features,function(e){return e[0]}));if(i=l.omit(i,l.keys(t.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),s=a.getContext("2d");a.height=Math.max(t.canvas.height,d.get_canvas_height(n,t.mode,t.w_scale,100)),a.width=t.canvas.width,s.drawImage(t.canvas,0,0),s.translate(o.left_offset,0);var c=d.draw_tile(n,s,t.mode,t.region,t.w_scale,t.seq_data);e(t.canvas).replaceWith(e(c.canvas)),t.canvas=a,l.extend(t.other_tiles_features_drawn,r)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(s=0;s<t.length;s++)if(t[s].data.length)for(h=t[s].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(t[0]instanceof B){var m=!0;for(s=0;s<t.length;s++)if(!t[s].all_slotted){m=!1;break}this.action_icons.show_more_rows_icon.toggle(!m)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(e){"Auto"===this.mode&&("no_detail"===e&&(e="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+e+")"))},incremental_slots:function(e,t,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[e];return a&&a.mode===i||(a=new _.default.FeatureSlotter(e,i,100,function(e){return n.measureText(e)}),this.slotters[e]=a),a.slot_features(t)},get_mode:function(e){return"no_detail"===e.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var m=this.filters_manager.filters,_=0,g=e.data.length;_<g;_++){for(var v,w=e.data[_],b=!1,y=0,x=m.length;y<x;y++)if(v=m[y],v.update_attrs(w),!v.keep(w)){b=!0;break}b||(h.push(w),w[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new U(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new U(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,s,function(e){return r.view.get_base_color(e)}),S=null;if(t.fillStyle=this.config.get_value("block_color"),t.font=t.canvas.manager.default_font,t.textAlign="right",e.data){var T=$.draw(t,l.width,l.height,a,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-u}return o?void 0:new B(r,n,a,l,e.data,i,e.message,p,S,incomplete_features,s)}});var ee=function(e,t,i){Y.call(this,e,t,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};E(ee.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(e,t,i,n,a){if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,"Histogram",n,a);var s=this.view;return new this.painter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(e){return s.get_base_color(e)}).draw(t,t.canvas.width,t.canvas.height,a),new H(this,n,a,t.canvas,e.data)},get_canvas_height:function(e,t,i,n){if("bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==e.data.length&&(a=e.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),t).get_required_height(a)},predraw_init:function(){var e=[q.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||e.push(this.dataset.fetch()),e},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s=l.filter(t,function(e){return e instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===s.length&&this.config.get_value("show_labels")&&o&&o.length>1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(e("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var te=function(e,t,i){Z.call(this,e,t,i),this.painter=v.default.ReadPainter,this.update_icons()};E(te.prototype,z.prototype,Y.prototype,Z.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var ie={CompositeTrack:J,DrawableGroup:j,DiagonalHeatmapTrack:Q,FeatureTrack:Z,LineTrack:K,ReadTrack:te,VariantTrack:ee,VcfTrack:ee},ne=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new ie[n](t,i,e)};t.default={TracksterView:R,DrawableGroup:j,LineTrack:K,FeatureTrack:Z,DiagonalHeatmapTrack:Q,ReadTrack:te,VariantTrack:ee,CompositeTrack:J,object_from_template:ne}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(a),o=e.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(e){e.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var e=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),s.each(this.model.action_icons_def,function(t){e.add_action_icon(t.name,t.title,t.css_class,t.on_click_fn,t.prepend,t.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,t,i,a,s,o){var r=this;this.action_icons[e]=n("<a/>").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(function(){a(r.model)}).appendTo(this.icons_div),o&&this.action_icons[e].hide()},set_display_modes:function(e,t){if(e){this.model.display_modes=e,this.model.mode=t||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,s=i.display_modes.length;a<s;a++){var o=i.display_modes[a];n[o]=function(e){return function(){i.change_mode(e)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});t.default={TrackHeaderView:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e,t){this.slot=e,this.feature=t},r=function(e,t,i,n){this.slots={},this.start_end_dct={},this.w_scale=e,this.mode=t,this.include_label="Pack"===t,this.max_rows=i,this.measureText=n};s(r.prototype,{_get_draw_coords:function(e){var t=Math.floor(e[1]*this.w_scale),i=Math.ceil(e[2]*this.w_scale),n=e[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;t-a>=0?(t-=a,"left"):(i+=a,"right")}return[t,i]},_find_slot:function(e){for(var t=e[0],i=e[1],n=0;n<=this.max_rows;n++){var a=!1,s=this.start_end_dct[n];if(void 0!==s)for(var o=0,r=s.length;o<r;o++){var l=s[o];if(i>l[0]&&t<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(e){for(var t,i,n=this.start_end_dct,a=[],s=0,r=0,l=e.length;r<l;r++){t=e[r],i=t[0];var d=this.slots[i];if(d){if(t[1]<d.feature[1]||d.feature[2]<t[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(t),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}s=Math.max(s,this.slots[i].slot)}else a.push(r)}for(var r=0,l=a.length;r<l;r++){t=e[a[r]],i=t[0];var m=this._get_draw_coords(t),_=this._find_slot(m);_>=0&&(void 0===n[_]&&(n[_]=[]),n[_].push(m),this.slots[i]=new o(_,t),s=Math.max(s,_))}return s+1}}),t.default={FeatureSlotter:r}},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=function(e,t){var i=e[0],n=e[1],a=t[0],s=t[1];return i<a?n<=a?1001:n<=s?1003:1002:i>s?1006:n<=s?1005:1004},o=function(e,t){var i=s(e,t);return 1001!==i&&1006!==i},r=function(e,t,i,n,a,s){void 0===s&&(s=4);var o,r=n-t,l=a-i,d=Math.floor(Math.sqrt(r*r+l*l)/s),c=r/d,u=l/d;for(o=0;o<d;o++,t+=c,i+=u)o%2==0&&e.fillRect(t,i,s,1)},l=function(e,t,i,n){var a=t-n/2,s=t+n/2,o=i-Math.sqrt(3*n/2);e.beginPath(),e.moveTo(a,o),e.lineTo(s,o),e.lineTo(t,i),e.lineTo(a,o),e.strokeStyle=this.fillStyle,e.fill(),e.stroke(),e.closePath()},d=function(e){this.default_val=e||1};d.prototype.gen_val=function(e){return this.default_val};var c=function(e){this.incomplete_features=e.incomplete_features,this.feature_mapper=e.feature_mapper},u=function(e,t,i,n,s){this.data=e,this.view_start=t,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=s};u.prototype.default_prefs={},u.prototype.draw=function(e,t,i,n){},u.prototype.get_start_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,-.5)},u.prototype.get_end_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,.5)},u.prototype.get_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,0)},u.prototype._chrom_pos_to_draw_pos=function(e,t,i){return Math.floor(t*(Math.max(0,e-this.view_start)+i))};var h=function(e,t,i,n,a){u.call(this,e,t,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(e,t,i,n){var s=!1,o=this.prefs.min_value,r=this.prefs.max_value,l=r-o,d=i,c=this.view_start,u=this.mode,h=this.data;e.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(e.fillStyle="#aaa",e.fillRect(0,f,t,1)),e.beginPath();var p,m,_;_=h.length>1?a.map(h.slice(0,-1),function(e,t){return Math.ceil((h[t+1][0]-h[t][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,w=parseInt(v.slice(1),16),b=(16711680&w)>>16,y=(65280&w)>>8,x=255&w,k=!1,C=!1,$=0,S=h.length;$<S;$++)if(e.fillStyle=e.strokeStyle=v,k=C=!1,g=_[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(m=h[$][1])){if(m<o?(C=!0,m=o):m>r&&(k=!0,m=r),"Histogram"===u)m=Math.round(m/l*d),e.fillRect(p,f,g,-m);else if("Intensity"===u){var T=(m-o)/l,M=Math.round(b+(255-b)*(1-T)),E=Math.round(y+(255-y)*(1-T)),P=Math.round(x+(255-x)*(1-T));e.fillStyle="rgb("+M+","+E+","+P+")",e.fillRect(p,0,g,d)}else m=Math.round(d-(m-o)/l*d),s?e.lineTo(p,m):(s=!0,"Filled"===u?(e.moveTo(p,d),e.lineTo(p,m)):e.moveTo(p,m));if(e.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===u||"Intensity"===u?O=g:(p-=2,O=4),k&&e.fillRect(p,0,O,3),C&&e.fillRect(p,d-3,O,3)}e.fillStyle=v}else s&&"Filled"===u&&e.lineTo(p,d),s=!1;"Filled"===u?(s&&(e.lineTo(p,f),e.lineTo(0,f)),e.fill()):e.stroke(),e.restore()};var f=function(e){this.feature_positions={},this.slot_height=e,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(e,t,i,n){this.feature_positions[t]||(this.feature_positions[t]=[]),this.feature_positions[t].push({data:e,x_start:i,x_end:n})},f.prototype.get_feature_data=function(e,t){var i,n=Math.floor((t-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;e+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],e>=i.x_start&&e<=i.x_end)return i.data};var p=function(e,t,i,n,a,s,o){u.call(this,e,t,i,n,a),this.alpha_scaler=s||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(e,t){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=e*n),i+this.get_top_padding(t)},get_top_padding:function(e){return 0},draw:function(e,t,i,n,a){var s=this.data,o=this.view_start,r=this.view_end;e.save(),e.fillStyle=this.prefs.block_color,e.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,m=s.length;p<m;p++){var _=s[p],g=_[0],v=_[1],w=_[2],b=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==b)&&v<r&&w>o&&(l=this.draw_element(e,this.mode,_,b,o,r,n,d,t),u.map_feature_data(_,b,l[0],l[1]),(v<o||w>r)&&h.push(_))}return e.restore(),u.y_translation=this.get_top_padding(t),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(e,t,i,n,a,s,o,r,l){return[0,0]}});var m=function(e,t,i,n,a,s,o){p.call(this,e,t,i,n,a,s,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(m.prototype,p.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"no_detail"===e?3:"Squish"===e?5:10},draw_element:function(e,t,i,n,a,s,o,r,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),m=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),_=p,g=m,d=("Dense"===t?0:0+n)*r+this.get_top_padding(l),v=null,w=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(e.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===t&&(n=1),"no_detail"===t)e.fillStyle=b,e.fillRect(p,d+5,m-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),w=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var S,T;if("Squish"===t?(S=1,T=3,$=!1):(S=5,T=9),C){var M,E;"Squish"===t||"Dense"===t?(M=d+Math.floor(1.5)+1,E=1):f?(M=d,E=T):(M+=2.5,E=1),this.draw_background_connector&&("Squish"===t||"Dense"===t?e.fillStyle="#ccc":f?"+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand")):e.fillStyle="#ccc",e.fillRect(p,M,m-p,E));for(var P=0,O=C.length;P<O;P++){var A,D,I=C[P],z=Math.floor(Math.max(0,(I[0]-a-.5)*o)),L=Math.ceil(Math.min(l,Math.max((I[1]-a-.5)*o)));if(!(z>L)){if(e.fillStyle=b,e.fillRect(z,d+(T-S)/2+1,L-z,S),void 0!==v&&k>x&&!(z>w||L<v)){var j=Math.max(z,v),R=Math.min(L,w);e.fillRect(j,d+1,R-j,T),1===C.length&&"Pack"===t&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),j+14<R&&(j+=2,R-=2),e.fillRect(j,d+1,R-j,T))}this.draw_individual_connectors&&A&&this.draw_connector(e,A,D,z,L,d),A=z,D=L}}if("Pack"===t){e.globalAlpha=1,e.fillStyle="white";var N=this.height_scaler.gen_val(i),V=Math.ceil(T*N),G=Math.round((T-V)/2);1!==N&&(e.fillRect(p,M+1,m-p,G),e.fillRect(p,M+T-G+1,m-p,G))}}else e.fillStyle=b,e.fillRect(p,d+1,m-p,T),f&&$&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),e.fillRect(p,d+1,m-p,T));e.globalAlpha=1,h&&"Pack"===t&&c>a&&(e.fillStyle=y,0===a&&p-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,m+2,d+8,this.max_label_length),g+=e.measureText(h).width+2):(e.textAlign="right",e.fillText(h,p-2,d+8,this.max_label_length),_-=e.measureText(h).width+2))}return e.globalAlpha=1,[_,g]}});var _=function(e,t,i,n,a,s,o,r,l){p.call(this,e,t,i,n,a,s,o),this.ref_seq=r?r.data:null,this.base_color_fn=l};a.extend(_.prototype,p.prototype,{get_row_height:function(){var e,t=this.mode;return"Dense"===t?e=10:"Squish"===t?e=5:(e=10,this.prefs.show_insertions&&(e*=2)),e},_parse_cigar:function(e){var t="MIDNSHP=X",i=[[0,0]],n=i[0],s=0,o=a.map(e.match(/[0-9]+[MIDNSHP=X]/g),function(e){var a=parseInt(e.slice(0,-1),10),o=e.slice(-1);return"N"===o?0!==n[1]&&(n=[s+a,s+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,s+=a),[t.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(e,t,i,n,a,r,d,c,u,h){var f=function(e){return Math.floor(Math.max(0,(e-a-.5)*i))};e.textAlign="center";var p,m,_=[a,r],g=0,v=0,w=Math.round(i/2),b=e.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===t,C=k?9:3,$=n+1,S=new x(e,C,i,t),T=[],M=[],E=this._parse_cigar(c);c=E.cigar,T=E.blocks;for(var P=0;P<T.length;P++){var O=T[P];o([d+O[0],d+O[1]],_)&&(p=f(d+O[0]),m=f(d+O[1]),p===m&&(m+=1),e.fillStyle=y,e.fillRect(p,$,m-p,C))}for(var A=0,D=c.length;A<D;A++){var I=c[A],z="MIDNSHP=X"[I[0]],L=I[1],j=d+g;if(p=f(j),m=f(j+L),o([j,j+L],_))switch(p===m&&(m+=1),z){case"H":case"S":case"P":break;case"M":g+=L;break;case"=":case"X":var R="";"X"===z?R=h.slice(v,v+L):this.ref_seq&&(R=this.ref_seq.slice(Math.max(0,j-a),Math.min(j-a+L,r-a)));for(var N=Math.max(j,a),V=0;V<R.length;V++)if(R&&!this.prefs.show_differences||"X"===z){var G=Math.floor(Math.max(0,(N+V-a)*i));e.fillStyle=this.base_color_fn(R[V]),k&&i>b?e.fillText(R[V],G,n+9):i>.05&&e.fillRect(G-w,$,Math.max(1,Math.round(i)),C)}"X"===z&&(v+=L),g+=L;break;case"N":e.fillStyle="#ccc",e.fillRect(p,$+(C-1)/2,m-p,1),g+=L;break;case"D":S.draw_deletion(p,$,L),g+=L;break;case"I":var U=p-w;if(o([j,j+L],_)){var H=h.slice(v,v+L);if(this.prefs.show_insertions){var F=p-(m-p)/2;if(("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b){switch(e.fillStyle="yellow",e.fillRect(F-w,n-9,m-p,9),M[M.length]={type:"triangle",data:[U,n+4,5]},e.fillStyle="#ccc",s([j,j+L],_)){case 1003:H=H.slice(a-j);break;case 1004:H=H.slice(0,j-r);break;case 1005:break;case 1002:H=H.slice(a-j,j-r)}for(var V=0,B=H.length;V<B;V++){var G=Math.floor(Math.max(0,(j+V-a)*i));e.fillText(H[V],G-(m-p)/2,n)}}else e.fillStyle="yellow",e.fillRect(F,n+("Dense"!==this.mode?2:5),m-p,"Dense"!==t?3:9)}else("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b&&M.push({type:"text",data:[H.length,U,n+9]})}v+=L}else g=function(e,t,i){return-1!=="M=NXD".indexOf(t)&&(e+=i),e}(g,z,L),v=function(e,t,i){return-1!=="IX".indexOf(t)&&(e+=i),e}(v,z,L)}e.fillStyle="yellow";for(var q,Y,W,P=0;P<M.length;P++)q=M[P],Y=q.type,W=q.data,"text"===Y?(e.save(),e.font="bold "+e.font,e.fillText(W[0],W[1],W[2]),e.restore()):"triangle"===Y&&l(e,W[0],W[1],W[2])},draw_element:function(e,t,i,n,a,s,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),m=("Dense"===t?0:0+n)*l,_="Pack"===t?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=s&&i[4][2]?this.draw_read(e,t,o,m,a,s,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=s&&i[5][2]?this.draw_read(e,t,o,m,a,s,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),w=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&w>v){e.fillStyle="#ccc";var b=m+1+(_-1)/2;r(e,v,b,w,b)}}else this.draw_read(e,t,o,m,a,s,c,i[4],i[5],i[6]);return"Pack"===t&&c>=a&&"."!==h&&(e.fillStyle=this.prefs.label_color,0===a&&f-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,p+2,m+9,this.max_label_length)):(e.textAlign="right",e.fillText(h,f-2,m+9,this.max_label_length))),[0,0]}});var g=function(e,t,i,n,a,s,o){m.call(this,e,t,i,n,a,s,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,m.prototype,{calculate_longest_feature_length:function(){for(var e=0,t=0,i=this.data.length;t<i;t++){var n=this.data[t],a=n[1],s=n[2];e=Math.max(e,s-a)}return e},get_top_padding:function(e){var t=this.view_end-this.view_start,i=e/t;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(e,t,i,n,a,s){var o=(i+n)/2,r=n-o;Math.PI;r>0&&(e.beginPath(),e.arc(o,s,n-o,Math.PI,0),e.stroke())}});var v=function(e,t){Array.isArray(e)?this.rgb=e:6==e.length?this.rgb=e.match(/.{2}/g).map(function(e){return parseInt(e,16)}):7==e.length?this.rgb=e.substring(1,7).match(/.{2}/g).map(function(e){return parseInt(e,16)}):this.rgb=e.split("").map(function(e){return parseInt(e+e,16)}),this.alpha="number"==typeof t?t:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(e){return Math.round(e)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},toHSL:function(){var e,t,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,s=this.alpha,o=Math.max(i,n,a),r=Math.min(i,n,a),l=(o+r)/2,d=o-r;if(o===r)e=t=0;else{switch(t=l>.5?d/(2-o-r):d/(o+r),o){case i:e=(n-a)/d+(n<a?6:0);break;case n:e=(a-i)/d+2;break;case a:e=(i-n)/d+4}e/=6}return{h:360*e,s:t,l:l,a:s}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},mix:function(e,t){var i=this,n=t,a=2*n-1,s=i.toHSL().a-e.toHSL().a,o=((a*s==-1?a:(a+s)/(1+a*s))+1)/2,r=1-o,l=[i.rgb[0]*o+e.rgb[0]*r,i.rgb[1]*o+e.rgb[1]*r,i.rgb[2]*o+e.rgb[2]*r],d=i.alpha*n+e.alpha*(1-n);return new v(l,d)}};var w=function(e,t,i,n){this.start_color=new v(e),this.end_color=new v(t),this.start_value=i,this.end_value=n,this.value_range=n-i};w.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e=(e-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-e).toCSS()};var b=function(e,t,i,n,a){this.positive_ramp=new w(t,i,0,a),this.negative_ramp=new w(t,e,0,-n),this.start_value=n,this.end_value=a};b.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e>=0?this.positive_ramp.map_value(e):this.negative_ramp.map_value(-e)};var y=function(e,t,i,n,a){u.call(this,e,t,i,n,a);var s,o;if(void 0===this.prefs.min_value){var r=1/0;for(s=0,o=this.data.length;s<o;s++)r=Math.min(r,this.data[s][6]);this.prefs.min_value=r}if(void 0===this.prefs.max_value){var l=-1/0;for(s=0,o=this.data.length;s<o;s++)l=Math.max(l,this.data[s][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(e,t,i,n){var a,s,o,r,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),m=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),_=function(e){return(e-h)*n};e.save(),e.rotate(-45*Math.PI/180),e.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],s=_(a[1]),o=_(a[2]),r=_(a[4]),l=_(a[5]),d=a[6],e.fillStyle=m.map_value(d),e.fillRect(s,r,o-s,l-r);e.restore()};var x=function(e,t,i,n){this.ctx=e,this.row_height=t,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=e.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(e,t,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;t+=.5*(this.row_height-n),this.ctx.fillRect(e,t,i*this.px_per_base,n)}});var k=function(e,t,i,n,a,s){u.call(this,e,t,i,n,a),this.base_color_fn=s,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"Squish"===e?5:10},get_required_height:function(e){var t=this.prefs.summary_height;return e>1&&this.prefs.show_sample_data&&(t+=this.divider_height+e*this.get_row_height()),t},draw:function(e,t,i,n){e.save();var s,o,r,l,d,c,u,h,f,p,m,_=function(e,t){var i=e.length,n=t.length,a=0,s=1,o=null;return"-"===t?(o="deletion",s=e.length):0===e.indexOf(t)&&i>n?(o="deletion",s=i-n,a=n):0===t.indexOf(e)&&i<n&&(o="insertion",s=n-i,a=n),null!==o?{type:o,start:a,len:s}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,w="Squish"===this.mode?5:10,b=n<.1?w:"Squish"===this.mode?3:9,y=!0,k=new x(e,w,n,this.mode);1===v&&(w=b=n<e.canvas.manager.char_width_px?this.prefs.summary_height:w,k.row_height=w,y=!1),this.prefs.show_sample_data&&y&&(e.fillStyle="#F3F3F3",e.globalAlpha=1,e.fillRect(0,this.prefs.summary_height-this.divider_height,t,this.divider_height)),e.textAlign="center";for(var C=0;C<this.data.length;C++)if(s=this.data[C],o=s[1],r=s[3],l=[s[4].split(",")],d=s[7].split(","),c=s.slice(8),l=a.map(a.flatten(l),function(e){var t={type:"snp",value:e,start:0},i=_(r,e);return a.extend(t,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(e.fillStyle="#999999",e.globalAlpha=1,m=0;m<l.length;m++)for(h=this.get_start_draw_pos(o+l[m].start,n),e.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,m=0;m<l.length;m++){e.fillStyle="deletion"===l[m].type?"black":this.base_color_fn(l[m].value);var $=c/d.length,S=Math.ceil(this.prefs.summary_height*$);e.fillRect(h,f-S,g,S),f-=S}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,m=0;m<d.length;m++,f+=w)if(p=d[m]?d[m].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],e.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],e.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;e.fillStyle=this.base_color_fn(T),k.draw_details?e.fillText(T,this.get_draw_pos(o,n),f+w):e.fillRect(h,f+1,g,b)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}e.restore()}}),t.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:m,ReadPainter:_,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e){this.manager=null,this.name=e.name,this.index=e.index,this.tool_id=e.tool_id,this.tool_exp_name=e.tool_exp_name};s(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var r=function(t,i,n){return e("<a/>").attr("href","javascript:void(0);").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(t){o.call(this,t),this.low="low"in t?t.low:-Number.MAX_VALUE,this.high="high"in t?t.high:Number.MAX_VALUE,this.min="min"in t?t.min:Number.MAX_VALUE,this.max="max"in t?t.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=e("<div/>").addClass("filter-row slider-row");var n=e("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(e("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),e("<span/>").text(this.low+"-"+this.high)),s=e("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=e("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=e("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(e,t){i.slide(e,t)},change:function(e,t){i.control_element.slider("option","slide").call(i.control_element,e,t)}}),i.slider=i.control_element,i.slider_label=a,function(t,i,n){t.click(function(){var t=i.text(),a=parseFloat(n.slider("option","max")),s=a<=1?4:a<=1e6?a.toString().length:6,o=!1,r=e(this).parents(".slider-row");r.addClass("input"),n.slider("option","values")&&(s=2*s+1,o=!0),i.text(""),e("<input type='text'/>").attr("size",s).attr("maxlength",s).attr("value",t).appendTo(i).focus().select().click(function(e){e.stopPropagation()}).blur(function(){e(this).remove(),i.text(t),r.removeClass("input")}).keyup(function(t){if(27===t.keyCode)e(this).trigger("blur");else if(13===t.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),s=function(e){return isNaN(e)||e>a||e<i},l=e(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],s(l[0])||s(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this)}else if(l=parseFloat(l),s(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this);n.slider(o?"values":"value",l),r.removeClass("input")}})})}(s,a,i.control_element);var d=e("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=r("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=r("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),e("<div style='clear: both;'/>").appendTo(i.parent_div)};s(l.prototype,{to_dict:function(){var e=o.prototype.to_dict.call(this);return s(e,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(e,t){return t-e<=2?.01:1},slide:function(e,t){var i=t.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(e){return e.length>this.index},_keep_val:function(e){return isNaN(e)||e>=this.low&&e<=this.high},keep:function(e){if(!this.applies_to(e))return!0;var t=e[this.index];if(t instanceof Array){for(var i=!0,n=0;n<t.length;n++)if(!this._keep_val(t[n])){i=!1;break}return i}return this._keep_val(e[this.index])},update_attrs:function(e){var t=!1;if(!this.applies_to(e))return t;var i=e[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),t=!0),a>this.max&&(this.max=Math.ceil(a),t=!0)}return t},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var e=this.slider.slider("option","min"),t=this.slider.slider("option","max");(this.min<e||this.max>t)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(t,i){if(this.track=t,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=e("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).bind("keydown",function(e){e.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),s=("height_filter"in i?i.height_filter:null),o=i.filters,r=0;r<o.length;r++)"number"===o[r].type?(n=new l(o[r]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===s&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=e("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;e("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};s(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var e,t={},i=[],n=0;n<this.filters.length;n++)e=this.filters[n],i.push(e.to_dict());return t.filters=i,t.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,t.height_filter=this.height_filter?this.height_filter.name:null,t.visible=this.parent_div.is(":visible"),t},copy:function(e){for(var t=new d(e),i=0;i<this.filters.length;i++)t.add_filter(this.filters[i].copy());return t},add_filter:function(e){e.manager=this,this.parent_div.append(e.parent_div),this.filters.push(e)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var e=0;e<this.filters.length;e++){this.filters[e].update_ui_elt()}},clear_filters:function(){for(var e=0;e<this.filters.length;e++){var t=this.filters[e];t.slider.slider("option","values",[t.min,t.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var t,i,n=(function(e,t,i){return t in e||(e[t]=i),e[t]}),a={},s=0;s<this.filters.length;s++)t=this.filters[s],t.tool_id&&(t.min!==t.low&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" >= "+t.low),t.max!==t.high&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" <= "+t.high));var o=[];for(var r in a)o[o.length]=[r,a[r]];!function t(i,n){var a=n[0],s=a[0],o=a[1],r="("+o.join(") and (")+")",l={cond:r,input:i,target_dataset_id:i,tool_id:s};n=n.slice(1),e.getJSON(run_tool_url,l,function(e){e.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+s,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):t(e.dataset_id,n)})}(this.track.dataset_id,o)}}),t.default={FiltersManager:d,NumberFilter:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(13),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=i(152),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=a.default.GenomeDataManager.extend({load_data:function(t,i,n,a){var s=e.Deferred();this.set_data(t,s);var r=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new e.Deferred;return e.when(o.makeBwg(r)).then(function(i,n){e.when(i.readWigData(t.get("chrom"),t.get("start"),t.get("end"))).then(function(e){var i=[],n={max:Number.MIN_VALUE};e.forEach(function(e){n.max!==e.min-1&&(i.push([n.max+1,0]),i.push([e.min-2,0])),i.push([e.min-1,e.score]),i.push([e.max,e.score]),n=e});var a={data:i,region:t,dataset_type:"bigwig"};l.set_data(t,a),s.resolve(a)})}),s}});t.default={BBIDataManager:r}}).call(t,i(0))},function(e,t,i){(function(n){var a,s;a=[i(153),i(154),i(155)],void 0!==(s=function(e,t){"use strict";function i(){}function a(e){e&&(this.id=e)}function s(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function o(e,t,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:e,timeout:5e3,beforeSend:function(e){e.setRequestHeader("Range","bytes="+t+"-"+(t+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function r(e,t){return e[t]+e[t+1]*y+e[t+2]*x+e[t+3]*k+e[t+4]*C}function l(){}function d(e,t,i,n){this.bwg=e,this.cirTreeOffset=t,this.cirTreeLength=i,this.isSummary=n}function c(e){var t=n.Deferred(),i=new l;return i.url=e,n.when(o(i.url,0,512)).then(function(e){if(!e)return t.resolve(null,"Couldn't fetch file");var a=e,s=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=s[0]+y*s[1]+x*s[2]+k*s[3];if(d==g)i.type="bigwig";else{if(d!=w)return d==v||d==b?t.resolve(null,"Currently don't support big-endian BBI files"):t.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=r(s,8),i.unzoomedDataOffset=r(s,16),i.unzoomedIndexOffset=r(s,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=r(s,36),i.totalSummaryOffset=r(s,44),i.uncompressBufSize=l[13],i.extHeaderOffset=r(s,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=r(s,24*c+72),f=r(s,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(e){return i.schema=e,t.resolve(i)})})}),t}function u(e,t,i,n,a){this.bbi=e,this.type=t,this.fieldCount=i,this.offset=n,this.field=a}var h=e.Range,f=e.union,p=e.intersection,m=t.inflateBuffer,_=t.arrayCopy,g=2291137574,v=654086024,w=2273964779,b=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var e=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var t=this.unzoomedDataOffset;return t=t+4-(t-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,t-this.chromTreeOffset)).then(function(t){var i=new Uint8Array(t),n=new Int16Array(t),a=new Int32Array(t),s=(a[0],a[1],a[2]),o=(a[3],r(i,16),function(t){var a=i[t],l=n[t/2+1];t+=4;for(var d=0;d<l;++d)if(0===a){t+=s;var c=r(i,t);t+=8,c-=e.chromTreeOffset,o(c)}else{for(var u="",h=0;h<s;++h){var f=i[t++];0!==f&&(u+=String.fromCharCode(f))}var p=i[t+3]<<24|i[t+2]<<16|i[t+1]<<8|i[t+0];i[t+7],i[t+6],i[t+5],i[t+4],t+=8,e.chromsToIDs[u]=p,0===u.indexOf("chr")&&(e.chromsToIDs[u.substr(3)]=p),e.idsToChroms[p]=u,e.maxID=Math.max(e.maxID,p)}});o(32)})},d.prototype.readWigData=function(e,t,i){var n=this.bwg.chromsToIDs[e];return void 0===n?[]:this.readWigDataById(n,t,i)},d.prototype.readWigDataById=function(e,t,i){var a=this,s=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var r=new Int32Array(a.cirHeader);a.cirBlockSize=r[1],n.when(a.readWigDataById(e,t,i)).then(function(e){s.resolve(e)})}),s;var l=[],d=0,c=(Date.now(),function(n,a,s,o){return(e<0||n==e)&&a<=i&&s>=t}),u=function(e,t){if(a.bwg.instrument&&console.log("level="+t+"; offset="+e+"; time="+(0|Date.now())),d+=e.length,1==e.length&&e[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return m(a.cachedCirRoot,0,t),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}));for(var i,o=4+32*a.cirBlockSize,r=0;r<e.length;++r){var u=new h(e[r],e[r]+o);i=i?f(i,u):u}for(var _=i.ranges(),g=0;g<_.length;++g){var v=_[g];p(e,v,t)}},p=function(e,t,i,r){t.max(),t.min();n.when(o(a.bwg.url,t.min(),t.max()-t.min())).then(function(o){for(var r=0;r<e.length;++r)t.contains(e[r])&&(m(o,e[r]-t.min(),i),e[r]-a.cirTreeOffset==48&&e[r]-t.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}))})},m=function(n,a,s){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16),y=r(o,a+24);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&l.push({offset:b,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&x.push(b),a+=24}x.length>0&&u(x,s+1)}};return u([a.cirTreeOffset+48],1),s},d.prototype.fetchFeatures=function(e,t){var a=this,s=n.Deferred();if(t.sort(function(e,t){return(0|e.offset)-(0|t.offset)}),0===t.length)return[];var r=[],l=function(e,t,n,s){s||(s={});var o=new i;o._chromId=e,o.segment=a.bwg.idsToChroms[e],o.min=t,o.max=n,o.type=a.bwg.type;for(var l in s)o[l]=s[l];r.push(o)},d=function(){if(0===t.length){Date.now();return s.resolve(r)}var i=t[0];if(i.data)a.parseFeatures(i.data,l,e),t.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<t.length&&t[h].offset==c+u;)u+=t[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(e){for(var i=0,n=0;i<u;){var s,o=t[n];if(a.bwg.uncompressBufSize>0)s=m(e,i+2,o.size-2);else{var r=new Uint8Array(o.size);_(new Uint8Array(e,i,o.size),0,r,0,o.size),s=r.buffer}o.data=s,i+=o.size,++n}d()})}};return d(),s},d.prototype.parseFeatures=function(e,t,i){var s=new Uint8Array(e);if(this.isSummary)for(var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),d=e.byteLength/32,c=0;c<d;++c){var u=r[8*c],m=r[8*c+1],_=r[8*c+2],g=r[8*c+3],v=(l[8*c+4],l[8*c+5]),w=l[8*c+6];l[8*c+7];if(i(u,m+1,_)){var b={type:"bigwig",score:w/g,maxScore:v};"bigbed"==this.bwg.type&&(b.type="density"),t(u,m+1,_,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),u=r[0],y=r[1],x=(r[2],r[3]),k=r[4],C=s[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var S=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&t(u,T,M,{score:S})}else if(2==C)for(var c=0;c<d;++c){var m=r[2*c+6]+1,_=m+k-1,S=l[2*c+7];i(u,m,_)&&t(u,m,_,{score:S})}else if(1==C)for(var c=0;c<d;++c){var m=r[3*c+6]+1,_=r[3*c+7],S=l[3*c+8];m>_&&(m=_),i(u,m,_)&&t(u,m,_,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var E=0,P=this.bwg.definedFieldCount,O=this.bwg.schema;E<s.length;){var u=s[E+3]<<24|s[E+2]<<16|s[E+1]<<8|s[E+0],m=s[E+7]<<24|s[E+6]<<16|s[E+5]<<8|s[E+4],_=s[E+11]<<24|s[E+10]<<16|s[E+9]<<8|s[E+8];E+=12;for(var A="";;){var D=s[E++];if(0==D)break;A+=String.fromCharCode(D)}var I,z={};if(I=A.length>0?A.split("\t"):[],I.length>0&&P>3&&(z.label=I[0]),I.length>1&&P>4){var S=parseInt(I[1]);isNaN(S)||(z.score=S)}if(I.length>2&&P>5&&(z.orientation=I[2]),I.length>5&&P>8){var L=I[5];$.test(L)&&(z.itemRgb="rgb("+L+")")}if(I.length>P-3&&O)for(var j=P-3;j<I.length;++j)z[O.fields[j+3].name]=I[j];if(i(u,m+1,_,I))if(P<12)t(u,m+1,_,z);else{var R=0|I[3],N=0|I[4],V=0|I[6],G=I[7].split(","),U=I[8].split(",");if(z.exonFrames){var H=z.exonFrames.split(",");z.exonFrames=void 0}z.type="transcript";var F=new a;for(var B in z)F[B]=z[B];if(F.id=I[0],F.segment=this.bwg.idsToChroms[u],F.min=m+1,F.max=_,F.notes=[],z.groups=[F],I.length>9){var q=z.geneName||I[9],Y=q;I.length>10&&(Y=I[10]),z.geneName2&&(Y=z.geneName2);var W=n.extend({},F);W.id=q,W.label=Y,W.type="gene",z.groups.push(W)}for(var J=[],X=0;X<V;++X){var K=(0|U[X])+m,Q=K+(0|G[X]),Z=new h(K,Q);J.push(Z)}for(var ee=f(J),te=ee.ranges(),ie=0;ie<te.length;++ie){var ne=te[ie];t(u,ne.min()+1,ne.max(),z)}if(N>R){var ae="+"==z.orientation?new h(R,N+3):new h(R-3,N),se=p(ee,ae);if(se){z.type="translation";for(var oe=se.ranges(),re=0,le=0;oe[0].min()>te[le].max();)le++;for(var ie=0;ie<oe.length;++ie){var de=ie;"-"==z.orientation&&(de=oe.length-ie-1);var ne=oe[de];if(z.readframe=re,H){var ce=parseInt(H[de+le]);"number"==typeof ce&&ce>=0&&ce<=2&&(z.readframe=ce,z.readframeExplicit=!0)}var ue=ne.max()-ne.min();re=(re+ue)%3,t(u,ne.min()+1,ne.max(),z)}}}}}}},d.prototype.getFirstAdjacent=function(e,t,i,n){var a=this.bwg.chromsToIDs[e];if(void 0===a)return n([]);this.getFirstAdjacentById(a,t,i,n)},d.prototype.getFirstAdjacentById=function(e,t,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(e,t,i,n)});var s=null,o=-1,l=-1,d=0,c=(Date.now(),function(e,t){d+=e.length;for(var i,n=4+32*a.cirBlockSize,s=0;s<e.length;++s){var o=new h(e[s],e[s]+n);i=i?f(i,o):o}for(var r=i.ranges(),l=0;l<r.length;++l){var c=r[l];u(e,c,t)}}),u=function(o,r,l,c){r.max(),r.min();a.bwg.data.slice(r.min(),r.max()-r.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(r.contains(o[u])&&(p(c,o[u]-r.min(),l),0==--d)){if(!s)return i>0&&(0!=e||t>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(e!=a.bwg.maxID||t<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,s,o){return i<0&&(n<e||s<t)||i>0&&(n>e||a>t)},[s],function(e){for(var t=null,a=-1,s=-1,o=0;o<e.length;++o){var r=e[o],l=r._chromId,d=r.min,c=r.max;(null==t||i<0&&(l>a||c>s)||i>0&&(l<a||d<s))&&(t=r,s=i<0?c:d,a=l)}return n(null!=t?[t]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),m=h[d],_=f[d/2+1];if(d+=4,0!=m)for(var g=0;g<_;++g){var v=d/4,w=p[v],b=p[v+1],y=p[v+2],x=p[v+3],k=r(h,d+16),C=r(h,d+24);(i<0&&(w<e||w==e&&b<=t)||i>0&&(y>e||y==e&&x>=t))&&(/_random/.exec(a.bwg.idsToChroms[w])||(null==s||i<0&&(y>o||y==o&&x>l)||i>0&&(w<o||w==o&&b<l))&&(s={offset:k,size:C},l=i<0?x:b,o=i<0?y:w)),d+=32}else{for(var $=-1,S=-1,g=0;g<_;++g){var 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e||(e=c),i&&(i=!1),this.istate=new t,this.istate.inflateInit(this,i?-e:e)},e.prototype.inflate=function(e){return null==this.istate?-2:this.istate.inflate(this,e)},e.prototype.inflateEnd=function(){if(null==this.istate)return-2;var e=istate.inflateEnd(this);return this.istate=null,e},e.prototype.inflateSync=function(){return istate.inflateSync(this)},e.prototype.inflateSetDictionary=function(e,t){return istate.inflateSetDictionary(this,e,t)},t.prototype.inflateReset=function(e){return null==e||null==e.istate?-2:(e.total_in=e.total_out=0,e.msg=null,e.istate.mode=0!=e.istate.nowrap?7:0,e.istate.blocks.reset(e,null),f)},t.prototype.inflateEnd=function(e){return null!=this.blocks&&this.blocks.free(e),this.blocks=null,f},t.prototype.inflateInit=function(e,t){return e.msg=null,this.blocks=null,nowrap=0,t<0&&(t=-t,nowrap=1),t<8||t>15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<<t),this.inflateReset(e),f)},t.prototype.inflate=function(e,t){var i,n;if(null==e||null==e.istate||null==e.next_in)return-2;for(t=4==t?m:f,i=m;;)switch(e.istate.mode){case 0:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,8!=(15&(e.istate.method=e.next_in[e.next_in_index++]))){e.istate.mode=13,e.msg="unknown compression method",e.istate.marker=5;break}if(8+(e.istate.method>>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<<e.istate.wbits&&(a=(1<<e.istate.wbits)-1,n=i-a),e.istate.blocks.set_dictionary(t,n,a),e.istate.mode=7,f)};var S=[0,0,255,255];t.prototype.inflateSync=function(e){var t,i,n,a,s;if(null==e||null==e.istate)return-2;if(13!=e.istate.mode&&(e.istate.mode=13,e.istate.marker=0),0==(t=e.avail_in))return m;for(i=e.next_in_index,n=e.istate.marker;0!=t&&n<4;)e.next_in[i]==S[n]?n++:n=0!=e.next_in[i]?0:4-n,i++,t--;return e.total_in+=i-e.next_in_index,e.next_in_index=i,e.avail_in=t,e.istate.marker=n,4!=n?-3:(a=e.total_in,s=e.total_out,this.inflateReset(e),e.total_in=a,e.total_out=s,e.istate.mode=7,f)},t.prototype.inflateSyncPoint=function(e){return null==e||null==e.istate||null==e.istate.blocks?-2:e.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(e,t){t&&(t[0]=this.check),6==this.mode&&this.codes.free(e),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(e.adler=this.check=e._adler.adler32(0,null,0,0))},i.prototype.proc=function(e,t){var i,n,a,r,l,d,c;for(r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),m=[],v=[];s(u,h,m,v,e),this.codes.init(u[0],h[0],m[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(t=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var w=0;w<i;w++)this.blens[w]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,b,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&_[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&_[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(w=18==y?7:y-14,b=18==y?11:3;a<i+w;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(n>>>=i,a-=i,b+=n&_[w],n>>>=w,a-=w,w=this.index,i=this.table,w+b>258+(31&i)+(i>>5&31)||16==y&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);y=16==y?this.blens[w-1]:0;do{this.blens[w++]=y}while(0!=--b);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),m=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,m,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,m[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);mode=12;case 8:return t=p,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);case 9:return t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);default:return t=-2,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}},i.prototype.free=function(e){this.reset(e,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(e,t,i){o(e,t,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(e,t){var i,n,a;return n=e.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.len+=c&_[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.dist+=c&_[n],c>>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);e.window[r++]=e.window[d++],l--,d==e.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,e.window[r++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,e.read!=e.write)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);this.mode=8;case 8:return i=p,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 9:return i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);default:return i=-2,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i)}},n.prototype.free=function(e){},n.prototype.inflate_fast=function(e,t,i,n,a,s,r,l){var d,c,u,h,m,g,v,w,b,y,x,k,C,$,S,T;v=l.next_in_index,w=l.avail_in,m=r.bitb,g=r.bitk,b=r.write,y=b<r.read?r.read-b-1:r.end-b,x=_[e],k=_[t];do{for(;g<20;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if(d=m&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(m&_[h]),m>>=h,g-=h;g<15;)w--,m|=(255&l.next_in[v++])<<g,g+=8;for(d=m&k,c=a,u=s,T=3*(u+d),h=c[T];;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if($=c[T+2]+(m&_[h]),m>>=h,g-=h,y-=C,b>=$)S=b-$,r.window[b++]=r.window[S++],r.window[b++]=r.window[S++],C-=2;else{S=b-$;do{S+=r.end}while(S<0);if(h=r.end-S,C>h){if(C-=h,b-S>0&&h>b-S)do{r.window[b++]=r.window[S++]}while(0!=--h);else o(r.window,S,r.window,b,h),b+=h,S+=h,h=0;S=0}}do{r.window[b++]=r.window[S++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3;d+=c[T+2],d+=m&_[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3);if(d+=c[T+2],d+=m&_[h],T=3*(u+d),0==(h=c[T])){m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--;break}}else m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--}while(y>=258&&w>=10);return C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,f},a.prototype.huft_build=function(e,t,i,n,a,s,r,l,d,c,h){var p,_,g,v,w,b,y,x,k,C,$,S,T,M,E;C=0,w=i;do{this.c[e[t+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return r[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(y=b,x<b&&(x=b),w=15;0!=w&&0==this.c[w];w--);for(g=w,x>w&&(x=w),l[0]=x,M=1<<b;b<w;b++,M<<=1)if((M-=this.c[b])<0)return-3;if((M-=this.c[w])<0)return-3;for(this.c[w]+=M,this.x[1]=b=0,C=1,T=2;0!=--w;)this.x[T]=b+=this.c[C],T++,C++;w=0,C=0;do{0!=(b=e[t+C])&&(this.v[this.x[b]++]=w),C++}while(++w<i);for(i=this.x[g],this.x[0]=w=0,C=0,v=-1,S=-x,this.u[0]=0,$=0,E=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>S+x;){if(v++,S+=x,E=g-S,E=E>x?x:E,(_=1<<(b=y-S))>p+1&&(_-=p+1,T=y,b<E))for(;++b<E&&!((_<<=1)<=this.c[++T]);)_-=this.c[T];if(E=1<<b,this.hn[0]+E>u)return-3;this.u[v]=$=this.hn[0],this.hn[0]+=E,0!=v?(this.x[v]=w,this.r[0]=b,this.r[1]=x,b=w>>>S-x,this.r[2]=$-this.u[v-1]-b,o(this.r,0,d,3*(this.u[v-1]+b),3)):r[0]=$}for(this.r[1]=y-S,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=s[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),_=1<<y-S,b=w>>>S;b<E;b+=_)o(this.r,0,d,3*($+b),3);for(b=1<<y-1;0!=(w&b);b>>>=1)w^=b;for(w^=b,k=(1<<S)-1;(w&k)!=this.x[v];)v--,S-=x,k=(1<<S)-1}return 0!=M&&1!=g?m:f},a.prototype.inflate_trees_bits=function(e,t,i,n,a){var s;return this.initWorkArea(19),this.hn[0]=0,s=this.huft_build(e,0,19,19,null,null,i,t,n,this.hn,this.v),-3==s?a.msg="oversubscribed dynamic bit lengths tree":s!=m&&0!=t[0]||(a.msg="incomplete dynamic bit lengths tree",s=-3),s},a.prototype.inflate_trees_dynamic=function(e,t,i,n,a,s,o,r,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,e,257,x,k,s,n,r,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,e,t,0,C,$,o,a,r,this.hn,this.v),d!=f||0==a[0]&&e>257?(-3==d?l.msg="oversubscribed distance tree":d==m?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(e){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(e),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<e&&(this.v=new Int32Array(e));for(var t=0;t<e;t++)this.v[t]=0;for(var t=0;t<16;t++)this.c[t]=0;for(var t=0;t<3;t++)this.r[t]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),E="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(t,n))&&(e.exports=a)},function(e,t,i){(function(n){var a,s,o;!function(n,r){s=[i(0)],a=r,void 0!==(o="function"==typeof a?a.apply(t,s):a)&&(e.exports=o)}(0,function(e){var t=e.ajaxSettings;t.responseFields.native="responseNative",t.converters["* native"]=!0;var i={},a=0,s={0:200,1223:204},o={},r=n.ajaxSettings.xhr();window.ActiveXObject&&e(window).on("unload",function(){for(var e in o)o[e]()}),i.cors=!!r&&"withCredentials"in r,i.ajax=r=!!r,e.ajaxTransport("native",function(e){var t;if(i.cors||r&&!e.crossDomain)return{send:function(i,n){var r,l=e.xhr(),d=++a,c={};if(l.open(e.type,e.url,e.async,e.username,e.password),e.xhrFields)for(r in 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e=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa "+this.model.get("icon")).addClass(this.model.get("toggle")&&"toggle").attr("target",this.model.get("target")).attr("href",this.model.get("url")).attr("title",this.model.get("tooltip")).tooltip("destroy"),this.model.get("tooltip")&&this.$toggle.tooltip({placement:"bottom"}),this.$dropdown.removeClass().addClass("dropdown").addClass(this.model.get("disabled")&&"disabled").addClass(this.model.get("active")&&"active"),this.model.get("menu")&&this.model.get("show_menu")?(this.$menu.show(),n("#dd-helper").show().off().on("click",function(){n("#dd-helper").hide(),e.model.set("show_menu",!1)})):(e.$menu.hide(),n("#dd-helper").hide()),this.$menu.empty().removeClass("dropdown-menu"),this.model.get("menu")&&(s.each(this.model.get("menu"),function(t){e.$menu.append(e._buildMenuItem(t)),t.divider&&e.$menu.append(n("<li/>").addClass("divider"))}),e.$menu.addClass("dropdown-menu"),e.$toggle.append(n("<b/>").addClass("caret"))),this},_buildMenuItem:function(e){var t=this;return 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i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(e){return"string"==typeof e&&-1===e.indexOf("//")&&"/"!=e.charAt(0)?Galaxy.root+e:e},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});t.default={Collection:m,Tab:_}}).call(t,i(1),i(0),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(9),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(e){var t=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),r=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+r,d=t+":"+i+l,c=null,u=null,h='<iframe 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t=this,i=null;if(Galaxy&&Galaxy.currHistoryPanel){var a=Galaxy.currHistoryPanel.collection.historyId;this.history_cache[a]={name:Galaxy.currHistoryPanel.model.get("name"),dataset_ids:[]},Galaxy.currHistoryPanel.collection.each(function(e){!e.get("deleted")&&e.get("visible")&&t.history_cache[a].dataset_ids.push(e.get("id"))})}var s=function(e,i){if(e){var n=t.history_cache[e.get("history_id")];if(n&&n.dataset_ids){var a=n.dataset_ids,s=a.indexOf(e.get("id"));if(-1!==s&&s+i>=0&&s+i<a.length)return a[s+i]}}},o=function(e,n,a){var o=s(e,n);o?t._loadDataset(o,function(e,t){i=e,a.model.set(t)}):a.model.trigger("change")};this._loadDataset(e,function(e,a){i=e,t.add(n.extend({menu:[{icon:"fa fa-chevron-circle-left",tooltip:"Previous in History",onclick:function(e){o(i,-1,e)},disabled:function(){return!s(i,-1)}},{icon:"fa fa-chevron-circle-right",tooltip:"Next in History",onclick:function(e){o(i,1,e)},disabled:function(){return!s(i,1)}}]},a))})},_loadDataset:function(e,t){var i=this,s=new 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i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use 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class="prompt">'+(0,l.default)("Tags")+"</label>",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return'<input class="tags-input" value="'+this.tagsToCSV()+'"/>'},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t='<span class="label label-info">'+e+"</span>";i.push(t)}),0===i.length&&i.push("<img src="+t+' class="add-tag-button" title="Add tags"/>'),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(0),s=n(a),o=i(61),r=n(o),l=i(4),d=n(l),c=s.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),c.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=r.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3);!function(e){e&&e.__esModule}(s);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),a.each(this.options.parameters,function(t){var i=n("<div/>").addClass("upload-"+t.id+" upload-icon-button 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To upload some files, log in to the FTP server at <strong>"+t.ftp_upload_site+"</strong> using your Galaxy credentials.",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}).set(t),this.collection=this.model.get("collection"),this.setElement(this._template()),this.$content=this.$(".upload-ftp-content"),this.$wait=this.$(".upload-ftp-wait"),this.$help=this.$(".upload-ftp-help"),this.$number=this.$(".upload-ftp-number"),this.$disk=this.$(".upload-ftp-disk"),this.$body=this.$(".upload-ftp-body"),this.$warning=this.$(".upload-ftp-warning"),this.$select=this.$(".upload-ftp-select-all"),this.render()},render:function(){var e=this;this.$wait.show(),this.$content.hide(),this.$warning.hide(),this.$help.hide(),n.ajax({url:Galaxy.root+"api/remote_files",method:"GET",success:function(t){e.model.set("ftp_files",t),e._index(),e._renderTable()},error:function(){e._renderTable()}})},_renderTable:function(){var e=this,t=this.model.get("ftp_files");if(this.rows=[],t&&t.length>0){this.$body.empty();var i=0;a.each(t,function(t){e.rows.push(e._renderRow(t)),i+=t.size}),this.$number.html(t.length+" files"),this.$disk.html(o.default.bytesToString(i,!0)),this.collection&&(this.$("._has_collection").show(),this.$select.addClass(this.model.get("class_add")).off().on("click",function(){e._all()}),this._refresh()),this.$content.show()}else this.$warning.show();this.model.get("help_enabled")&&this.$help.show(),this.$wait.hide()},_renderRow:function(e){var t=this,i=this.model.attributes,a=n(this._templateRow(e)),s=a.find(".icon");if(this.$body.append(a),this.collection){var o=this.ftp_index[e.path];s.addClass(void 0===o?i.class_add:i.class_remove),a.on("click",function(){t._switch(s,e),t._refresh()})}else a.on("click",function(){i.onchange(e)});return s},_index:function(){var e=this;this.ftp_index={},this.collection&&this.collection.each(function(t){"ftp"==t.get("file_mode")&&(e.ftp_index[t.get("file_path")]=t.id)})},_all:function(){var e=this.model.attributes,t=this.model.get("ftp_files"),i=this.$select.hasClass(e.class_add);for(var n in t){var a=t[n],s=this.ftp_index[a.path];(void 0===s&&i||void 0!==s&&!i)&&this._switch(this.rows[n],a)}this._refresh()},_switch:function(e,t){e.removeClass();var i=this.model.attributes,n=this.ftp_index[t.path];if(void 0===n){var a=i.onadd(t);e.addClass(i.class_remove),this.ftp_index[t.path]=a}else i.onremove(n),e.addClass(i.class_add),this.ftp_index[t.path]=void 0},_refresh:function(){var e=a.reduce(this.ftp_index,function(e,t){return void 0!==t&&e++,e},0);this.$select.removeClass(),0==e?this.$select.addClass(this.model.get("class_add")):this.$select.addClass(e==this.rows.length?this.model.get("class_remove"):this.model.get("class_partial"))},_templateRow:function(e){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+a.escape(e.path)+'</td><td class="ftp-size">'+o.default.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_template:function(){return'<div class="'+this.model.get("cls")+'"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">'+this.model.get("help_text")+'</div><div class="upload-ftp-content"><span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(165)),r=a(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new r.default.View({placement:e.placement||"bottom",container:e.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."}})}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. 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h=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),f={},p=0,m=0,_=!1,g=!1,v=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:a,start:l,stop:d,reset:r,configure:c,compatible:u}}}(e)}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}function r(e,t){var i=e.toJSON();return C(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var l=i(188),d=o(l),c=i(166),u=o(c),h=i(8),f=o(h),p=i(207),m=o(p),_=i(9),g=o(_),v=i(208),w=(o(v),i(7)),b=o(w);i(209);var y=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['<a class="name" title="',(0,b.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,b.default)("Remove this dataset from the list"),'">',(0,b.default)("Discard"),"</button>"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,b.default)("Enter a new name for the element"),":\n(",(0,b.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,b.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:y,collectionClass:d.default.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;n.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset"!==e.history_content_type?(0,b.default)("is not a dataset"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,b.default)("has been deleted or purged"):null:(0,b.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(a(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content i").hoverhighlight(".collection-creator",this.highlightClr)},_invalidElementsAlert:function(){this._showAlert(this.templates.invalidElements({problems:this.invalidElements}),"alert-warning")},_disableNameAndCreate:function(e){(e=!!n.isUndefined(e)||e)&&(this.$(".collection-name").prop("disabled",!0),this.$(".create-collection").toggleClass("disabled",!0))},$list:function(){return this.$(".collection-elements")},_renderClearSelected:function(){n.size(this.selectedIds)?this.$(".collection-elements-controls > .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,a=s("<div/>"),o=i.$list();n.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);a.append(t.$el)}),i._renderClearSelected(),o.empty().append(a.children()),n.invoke(i.elementViews,"render"),o.height()>o.css("max-height")?o.css("border-width","1px 0px 1px 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";return t+='<a class="cancel-create" href="javascript:void(0);">'+(0,b.default)("Cancel")+"</a> ",t+=(0,b.default)("or"),t+=' <a class="reset" href="javascript:void(0);">'+(0,b.default)("start over")+"</a>.",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:(0,b.default)("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,b.default)("An error occurred");if(e.xhr){var n=e.xhr,a=e.message;0===n.readyState&&0===n.status?i+=": "+(0,b.default)("Galaxy could not be reached and may be updating.")+(0,b.default)(" Try again in a few minutes."):n.responseJSON?i+=":<br /><pre>"+JSON.stringify(n.responseJSON)+"</pre>":i+=": "+a}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart 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i=e.offset(),n=e.scrollTop(),a=t-i.top,s=i.top+e.outerHeight()-t;a>=0&&a<this.autoscrollDist?e.scrollTop(n-2):s>=0&&s<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestElement:function(e){for(var t=this.$(".collection-elements li.collection-element").toArray(),i=0;i<t.length;i++){var n=a(t[i]),s=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(s+o>e&&s-o<e)return n}return a()},_dropElements:function(e){e.originalEvent&&(e=e.originalEvent),e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestElement(e.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".collection-elements .collection-element").last()),this._syncOrderToDom(),!1},_syncOrderToDom:function(){var e=this,t=[];this.$(".collection-elements .collection-element").each(function(){var i=a(this).attr("data-element-id"),s=n.findWhere(e.workingElements,{id:i});s?t.push(s):console.error("missing element: ",i)}),this.workingElements=t,this._renderList()},_elementDragstart:function(e,t){t.select(!0),this.$dragging=this.$(".collection-elements .collection-element.selected")},_elementDragend:function(e,t){a(".element-drop-placeholder").remove(),this.$dragging=null},templates:n.extend({},m.default.CollectionCreatorMixin._creatorTemplates,{header:n.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',(0,b.default)("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',(0,b.default)("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" ','title="',(0,b.default)("Close and show more help"),'" aria-hidden="true">&times;</button>','<span class="alert-message"></span>',"</div>"].join("")),middle:n.template(['<div class="collection-elements-controls">','<a class="reset" href="javascript:void(0);" ','title="',(0,b.default)("Undo all 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class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,b.default)("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',(0,b.default)("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',(0,b.default)("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',(0,b.default)("Create list"),"</button>","</div>","</div>"].join("")),helpContent:n.template(["<p>",(0,b.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"</p>","<ul>","<li>",(0,b.default)(["Rename elements in the list by clicking on ",'<i data-target=".collection-element .name">the existing name</i>.'].join("")),"</li>","<li>",(0,b.default)(["Discard elements from the final created list by clicking on the ",'<i data-target=".collection-element .discard">"Discard"</i> button.'].join("")),"</li>","<li>",(0,b.default)(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'<i data-target=".collection-element">them</i> and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the <i data-target=".clear-selected">"Clear selected"</i> link.'].join("")),"</li>","<li>",(0,b.default)(['Click the <i data-target=".reset">"Start over"</i> link to begin again as if you had just opened ',"the interface."].join("")),"</li>","<li>",(0,b.default)(['Click the <i data-target=".cancel-create">"Cancel"</i> button to exit the interface.'].join("")),"</li>","</ul><br />","<p>",(0,b.default)(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>.'].join("")),"</p>"].join("")),invalidElements:n.template([(0,b.default)("The following selections could not be included due to problems:"),"<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>"].join("")),noElementsLeft:n.template(['<li class="no-elements-left-message">',(0,b.default)("No elements left! "),(0,b.default)("Would you like to "),'<a class="reset" href="javascript:void(0)">',(0,b.default)("start over"),"</a>?","</li>"].join("")),invalidInitial:n.template(['<div class="header flex-row no-flex">','<div class="alert alert-warning" style="display: block">','<span class="alert-message">',"<% if( _.size( problems ) ){ %>",(0,b.default)("The following selections could not be included due to problems"),":","<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>","<% } else if( _.size( elements ) < 1 ){ %>",(0,b.default)("No datasets were selected"),".","<% } %>","<br />",(0,b.default)("At least one element is needed for the collection"),". ",(0,b.default)("You may need to "),'<a class="cancel-create" href="javascript:void(0)">',(0,b.default)("cancel"),"</a> ",(0,b.default)("and reselect new elements"),".","</span>","</div>","</div>",'<div class="footer flex-row no-flex">','<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',(0,b.default)("Cancel"),"</button>","</div>","</div>","</div>"].join(""))}),toString:function(){return"ListCollectionCreator"}}),k=function(e,t,i){var a,o=s.Deferred(),r=Galaxy.modal||new g.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),a=new i(t),r.show({title:t.title||(0,b.default)("Create a collection"),body:a.$el,width:"80%",height:"100%",closing_events:!0}),a.render(),window._collectionCreator=a,o},C=function(e,t){return t=t||{},t.title=(0,b.default)("Create a collection from a list of datasets"),k(e,t,x)};t.default={DatasetCollectionElementView:y,ListCollectionCreator:x,collectionCreatorModal:k,listCollectionCreatorModal:C,createListCollection:r}}).call(t,i(1),i(2),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(189),o=n(s),r=i(206),l=n(r),d=i(7),c=(n(d),l.default.HistoryContentMixin),u=o.default.ListDatasetCollection,h=o.default.PairDatasetCollection,f=o.default.ListPairedDatasetCollection,p=o.default.ListOfListsDatasetCollection,m=u.extend(c).extend({defaults:e.extend(e.clone(u.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:a(u.prototype.save),toString:function(){return"History"+u.prototype.toString.call(this)}}),_=h.extend(c).extend({defaults:e.extend(e.clone(h.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:a(h.prototype.save),toString:function(){return"History"+h.prototype.toString.call(this)}}),g=f.extend(c).extend({defaults:e.extend(e.clone(f.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:a(f.prototype.save),toString:function(){return"History"+f.prototype.toString.call(this)}}),v=p.extend(c).extend({defaults:e.extend(e.clone(p.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:a(p.prototype.save),toString:function(){return"HistoryListOfListsDatasetCollection("+this.get("name")+")"}});t.default={HistoryListDatasetCollection:m,HistoryPairDatasetCollection:_,HistoryListPairedDatasetCollection:g,HistoryListOfListsDatasetCollection:v}}).call(t,i(2))},function(e,t,i){"use 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this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:e.extend({},r.default.DatasetAssociation.prototype.defaults,u.defaults),_downloadQueryParameters:function(){var e=this.get("file_ext"),t=this.get("element_identifier");return"?to_ext="+e+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+t},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),u.constructor.call(this,e,t)},hasDetails:function(){return 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e=n.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=n.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?a.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return 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this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,n.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,g.default)("(empty)")},toJSON:function(){return a.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:s.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,a){var s;try{s=new Date(a.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=s||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var a={history_id:this.id};e&&(a.current=!0),t&&(a.name=t),i||(a.all_datasets=!1),a.view="dev-detailed";var s=this,o=n.post(this.urlRoot,a);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,b=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return a.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),a.defaults(t,i)},fetchFirst:function(e){var t=this,i=s.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:a.extend(a.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,a.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,a){var s=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){s.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:b}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(213),r=s(o),l=i(214),d=s(l),c=i(188),u=s(c),h=i(193),f=s(h),p=i(8),m=s(p),_=i(252),g=s(_),v=r.default.PaginatedCollection,w=v.extend(m.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},v.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},model:function(e,t){if("dataset"===e.history_content_type)return new d.default.HistoryDatasetAssociation(e,t);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new u.default.HistoryListDatasetCollection(e,t);case"paired":return new u.default.HistoryPairDatasetCollection(e,t);case"list:paired":return new u.default.HistoryListPairedDatasetCollection(e,t);case"list:list":return new u.default.HistoryListOfListsDatasetCollection(e,t)}var i="Unknown collection_type: "+e.collection_type;return console.warn(i,e),{validationError:i}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){if(this.historyId)return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(v.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),hid:m.default.buildComparator("hid",{ascending:!1}),"hid-asc":m.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return v.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(v.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:v.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=v.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},fetchCollectionCounts:function(t){return t=t||{},t.keys=["type_id","element_count"].join(","),t.filters=e.extend(t.filters||{},{history_content_type:"dataset_collection"}),t.remove=!1,this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,a=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,a){var s=i.get(t[n]);return s?e.concat(s):e},[]),i.ajaxQueue("save",a,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new g.default.AjaxQueue(n.slice().reverse().map(function(n,a){var s=e.isString(t)?n[t]:t;return function(){return s.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var r=e.extend(e.clone(t),{view:"summary",keys:l,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){s.fetch.call(s,r).fail(a.reject).done(function(e){a.notify(e,o,n),e.length!==o?(s.allFetched=!0,a.resolve(e,o,n)):i(n+o)})})}t=t||{};var a=n.Deferred(),s=this,o=t.limitPerCall||s.limitPerProgressiveFetch,r=d.default.HistoryDatasetAssociation.prototype.searchAttributes,l=r.join(",");return i(),a},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,a,s;e.isString(t)?(i=t,s="hda",a="dataset"):(i=t.id,s={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",a="hdca"===s?"dataset_collection":"dataset");var o=this,r=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:s,type:a})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,r,{},"Error copying contents",{type:a,id:i,source:s})});return r},createHDCA:function(e,t,i,n,a){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(a)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=a.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:w}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(8),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return s.storageKeyPrefix+e},get:function(e){return new s({id:s.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(s.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:s}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(8),l=o(r),d=i(7),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:l.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:l.default.wrapTemplate(['<div class="subtitle"></div>']),details:l.default.wrapTemplate(['<div class="details"></div>'])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['<div class="details">',"</div>"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(194),l=o(r),d=i(166),c=o(d),u=i(175),h=o(u),f=i(8),p=o(f),m=i(7),_=o(m),g=l.default.ListItemView,v=g.extend({_logNamespace:"dataset",className:g.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),g.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return g.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,_.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,_.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,_.default)("This dataset is not yet viewable");else{t.title=(0,_.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return s(this.templates.noAccess(this.model.toJSON(),this));var e=g.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=s('<div class="detail-messages"></div>'),n=t.model.toJSON();return 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o=i(3),r=s(o),l=i(4),d=s(l),c=i(9),u=s(c),h=i(63),f=s(h),p=i(40),m=s(p),_=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(r.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),r.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),r.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("<input/>").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),r.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new m.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var a in t){var s=t[a],o=this.form.data.match(a),r=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&r){if(!l.optional&&null==s)return this.form.highlight(o),!1;if(s&&s.batch){var d=s.values.length,c=d>0&&s.values[0]&&s.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(e.hid+": "+e.name)))}),s.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("<pre/>").text(JSON.stringify(e,null,4)))}});t.default={View:_}}).call(t,i(1),i(0),i(2))},,function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(e){return-1!==i.indexOf(this.attributes.async_ops,e)},add_filter:function(e,t,i){if(i){var n,a=this.attributes.filters[e];if(null===a||void 0===a)n=t;else if("string"==typeof a)if("All"==a||a==t)n=t;else{var s=[];s[0]=a,s[1]=t,n=s}else n=a,-1===n.indexOf(t)&&n.push(t);this.attributes.filters[e]=n}else this.attributes.filters[e]=t},remove_filter:function(e,t){var n=this.attributes.filters[e];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[e]="";else{var a=i.indexOf(n,t);-1!==a&&(n[a]="")}},get_url_data:function(){var e={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(e.operation=this.attributes.operation),this.attributes.item_ids&&(e.id=this.attributes.item_ids);var t=this;return i.each(i.pairs(t.attributes.filters),function(t){e["f-"+t[0]]=t[1]}),e},get_url:function(e){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(e)}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a);t.default={grid:function(e){var t="";return t=e.embedded?this.grid_header(e)+this.grid_table(e):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(e)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(e),e.info_text&&(t+='<br><div class="toolParamHelp" style="clear: both;">'+e.info_text+"</div>"),t},grid_table:function(e){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(e){var t='<div class="grid-header">';if(e.embedded||(t+="<h2>"+e.title+"</h2>"),e.global_actions){t+='<ul class="manage-table-actions">';var i=e.global_actions.length>=3;i&&(t+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in e.global_actions){var a=e.global_actions[n];t+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(t+="</div>"),t+="</ul>"}return e.insert&&(t+=e.insert),t+=this.grid_filters(e),t+="</div>"},header:function(e){var t="<tr>";e.show_item_checkboxes&&(t+="<th>",e.items.length>0&&(t+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),t+="</th>");for(var i in e.columns){var n=e.columns[i];n.visible&&(t+='<th id="'+n.key+'-header">',n.href?t+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":t+=n.label,t+='<span class="sort-arrow">'+n.extra+"</span></th>")}return t+="</tr>"},body:function(t){var i="",n=0;0==t.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in t.items){var s=t.items[a],o=s.encode_id;i+="<tr ",t.current_item_id==s.id&&(i+='class="current"'),i+=">",t.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var r in t.columns){var l=t.columns[r];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=s.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===e.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",m="";l.attach_popup&&(p="grid-"+a+"-popup",m="menubutton",""!=u&&(m+=" split"),m+=" popup"),i+="<td "+d+">",u?(0!=t.operations.length&&(i+='<div id="'+p+'" class="'+m+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=t.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+m+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(e){var t="";if(e.use_paging&&e.num_pages>1){var i=e.num_page_links,n=e.cur_page_num,a=e.num_pages,s=i/2,o=n-s,r=0;o<=0&&(o=1,r=s-(n-o));var l,d=s+r,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),t+='<tr id="page-links-row">',e.show_item_checkboxes&&(t+="<td></td>"),t+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(t+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var u=o;u<c+1;u++)u==e.cur_page_num?t+='<span class="page-link inactive-link" id="page-link-'+u+'">'+u+"</span>":t+='<span class="page-link" id="page-link-'+u+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+u+'">'+u+"</a></span>";c<a&&(t+='...<span class="page-link" id="page-link-'+a+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+a+'">'+a+"</a></span>"),t+="</span>",t+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(e.show_item_checkboxes){t+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var h in e.operations){var f=e.operations[h];f.allow_multiple&&(t+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}t+="</td></tr>"}var p=!1;for(h in e.operations)if(e.operations[h].global_operation){p=!0;break}if(p){t+='<tr><td colspan="100">';for(h in e.operations){var f=e.operations[h];f.global_operation&&(t+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}t+="</td></tr>"}return e.legend&&(t+='<tr><td colspan="100">'+e.legend+"</td></tr>"),t},message:function(e){var t=e.status;return-1!=["success","ok"].indexOf(t)&&(t="done"),'<p><div class="'+t+'message transient-message">'+n.escape(e.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1;for(var s in e.columns){var o=e.columns[s];if("advanced"==o.filterable){var r=o.key,l=i[r],d=t[r];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div id="standard-search" style="display: '+c+';"><table><tr><td style="padding: 0;"><table>';for(var s in e.columns){var o=e.columns[s];"standard"==o.filterable&&(u+=this.grid_column_filter(e,o))}u+="</table></td></tr><tr><td>",a&&(u+='<a href="" class="advanced-search-toggle">Advanced Search</a>'),u+="</td></tr></table></div>",u+='<div id="advanced-search" style="display: '+n+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var s in e.columns){var o=e.columns[s];"advanced"==o.filterable&&(u+=this.grid_column_filter(e,o))}return u+="</table></div>"},grid_column_filter:function(t,i){var n=(t.default_filter_dict,t.filters),a=i.label,s=i.key;"advanced"==i.filterable&&(a=a.toLowerCase());var o="<tr>";if("advanced"==i.filterable&&(o+='<td align="left" style="padding-left: 10px">'+a+":</td>"),o+='<td style="padding-bottom: 1px;">',i.is_text){o+='<form class="text-filter-form" column_key="'+s+'" action="'+t.url+'" method="get" >';for(u in t.columns){var r=t.columns[u],l=n[r.key];l&&"All"!=l&&(r.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+r.key+'" name="f-'+r.key+'" value="'+l+'"/>')}o+='<span id="'+s+'-filtering-criteria">';var d=n[s];if(d){var c=e.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(s,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(s,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var m=p.length;m<20&&(m=20),m+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+s+'-filter" name="f-'+s+'" type="text" placeholder="'+p+'" size="'+m+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+s+'-filtering-criteria">';var _=!1;for(var g in t.categorical_filters[s]){var v=t.categorical_filters[s][g],w="",b="";for(var y in v)w=y,b=v[y];_&&(o+=" | "),_=!0;var h=n[s];h&&v[s]&&h==b?o+='<span class="categorical-filter '+s+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+s+'-filter"><a href="javascript:void(0);" filter_key="'+w+'" filter_val="'+b+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(e,t){return'<span class="text-filter-val">'+(t=s.default.sanitize(t))+'<a href="javascript:void(0);" filter_key="'+e+'" filter_val="'+t+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(146),l=a(r),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),m=i(26),_=a(m),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var w=null,b=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=e.Model.extend;var x=y.extend({initialize:function(e){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=e},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var e=[];n(".bookmark").each(function(){e.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var t=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,i={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:t},bookmarks:e};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(e){Galaxy.modal.hide(),b.vis_id=e.vis_id,b.has_changes=!1,window.history.pushState({},"",e.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var e=this,t=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(e){o.each(e,function(e){b.add_drawable(l.default.object_from_template(e,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=e.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){e.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){e.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=t,t},add_bookmark:function(e,t,i){var a=n("#right .unified-panel-body"),s=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(s),r=(n("<a href=''/>").text(e).appendTo(o).click(function(){return b.go_to(e),!1}),n("<div/>").text(t).appendTo(s));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){return s.slideUp("fast"),s.remove(),b.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);r.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,s},create_visualization:function(e,t,i,a,s){var r=this,d=new l.default.TracksterView(o.extend(e,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(e){if(t){var n=t.chrom,o=t.start,c=t.end,u=t.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(e[0].chrom)}else d.change_chrom(e[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],r.add_bookmark(f.position,f.annotation,s);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(t){new c.default.TrackBrowserRouter(t),e.history.start()},init_keyboard_nav:function(e){n(document).keyup(function(t){if(!n(t.srcElement).is(":input"))switch(t.which){case 37:e.move_fraction(.25);break;case 38:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()-20);break;case 39:e.move_fraction(-.25);break;case 40:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(e){if(e.has_changes){var t=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(t.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=e.View.extend({initialize:function(){w=new x(Galaxy.root),w.createButtonMenu(),w.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(w.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var e=this,t=p.default.get("dbkey"),i={},n={dbkey:t,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(t||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){e.view_in_saved(n)},"View in new visualization":function(){e.view_new()}}})},view_in_saved:function(e){var t=new _.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:t.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){e.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(e)})}}})},view_existing:function(){var e=galaxy_config.app.viz_config;b=w.create_visualization({container:n("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,!0),this.init_editor()},view_new:function(){var e=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(t){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(t),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){e.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=t.map(function(e){return e[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(e){for(var t='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<e.length;i++)t+='<option value="'+e[i][1]+'">'+e[i][0]+"</option>";return t+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(e,t){n(document).trigger("convert_to_values"),b=w.create_visualization({container:n("#center .unified-panel-body"),name:e,dbkey:t},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){b.add_drawable(l.default.object_from_template(e,b,b))}}),n("#add-bookmark-button").click(function(){var e=b.chrom+":"+b.low+"-"+b.high;return w.add_bookmark(e,"Bookmark description",!0)}),w.init_keyboard_nav(b),n(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});t.default={TracksterUI:x,GalaxyApp:k}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function o(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var r=i(2),l=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(r),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),m=i(148),_=a(m),g=i(149),v=a(g),w=i(150),b=a(w),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),S=a($),T=i(151),M=a(T);i(25);var E=l.extend,P={},O=function(e,t){P[e.attr("id")]=t},A=function(t,i,n,a){n=".group",P[t.attr("id")]=a,t.bind("drag",{handle:"."+i,relative:!0},function(t,i){var a,s,o,r,l,d=(e(this),e(this).parent()),c=d.children(".track,.group"),u=P[e(this).attr("id")];if(s=e(this).parents(n),0!==s.length){o=s.position().top,r=o+s.outerHeight();var h=P[s.attr("id")];if(i.offsetY<o)return e(this).insertBefore(s),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>r)return e(this).insertAfter(s),h.remove_drawable(u),void h.container.add_drawable(u)}for(s=null,l=0;l<c.length;l++)if(a=e(c.get(l)),o=a.position().top,r=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=r)return i.offsetY-o<r-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void P[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=e(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),P[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(e(this).insertBefore(c.get(l)),P[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})},D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",I=["Histogram","Line","Filled","Intensity"],z=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};z.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(e){new S.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],E(z.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var j=function(e,t,i){z.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};E(j.prototype,z.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i<e.length;i++)t=ne(e[i],this.view,this),this.add_drawable(t)},init:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].init()},_draw:function(e){for(var t=0;t<this.drawables.length;t++)this.drawables[t]._draw(e)},to_dict:function(){for(var e=[],t=0;t<this.drawables.length;t++)e.push(this.drawables[t].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:e}},add_drawable:function(e){this.drawables.push(e),e.container=this,this.changed()},add_drawable_before:function(e,t){this.changed();var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,0,e),!0)},replace_drawable:function(e,t,i){var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables[n]=t,i&&e.container_div.replaceWith(t.container_div),this.changed()),n},remove_drawable:function(e){var t=this.drawables.indexOf(e);return-1!==t&&(this.drawables.splice(t,1),e.container=null,this.changed(),!0)},move_drawable:function(e,t){var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(t,0,e),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(e){for(var t,i=this.drawables.slice(0),n=[];0!==i.length;)t=i.shift(),t instanceof e?n.push(t):t.drawables&&(i=i.concat(t.drawables));return n}});var L=function(t,i,n){if(E(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),j.call(this,t,i,n),this.content_div=e("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),A(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};E(L.prototype,z.prototype,j.prototype,{action_icons_def:[z.prototype.action_icons_def[0],z.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},z.prototype.action_icons_def[2]],build_container_div:function(){var t=e("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i<t;i++){if(a=this.drawables[i],a.get_type()!==s){can_composite=!1;break}a instanceof Z&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),e(".tooltip").remove()),o>1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],l[r.name]=[r];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],r.name in l&&l[r.name].push(r);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new b.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].filters_manager=this.saved_filters_managers[e];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var e=0;e<this.drawables.length;e++){var t=this.drawables[e];this.saved_filters_managers.push(t.filters_manager),t.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var e=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,e,!0);e.request_draw()},add_drawable:function(e){j.prototype.add_drawable.call(this,e),this.update_icons()},remove_drawable:function(e){j.prototype.remove_drawable.call(this,e),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var e=E(j.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),e},request_draw:function(e){l.each(this.drawables,function(t){t.request_draw(e)})}});var R=n.View.extend({initialize:function(e){E(e,{obj_type:"View"}),j.call(this,"View",e.container,e),this.chrom=null,this.vis_id=e.vis_id,this.dbkey=e.dbkey,this.stand_alone=void 0===e.stand_alone||e.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:e.name})},render:function(){this.requested_redraw=!1;var t=this.container,i=this;this.top_container=e("<div/>").addClass("top-container").appendTo(t),this.browser_content_div=e("<div/>").addClass("content").appendTo(t),this.bottom_container=e("<div/>").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,i),this.intro_div=e("<div/>").addClass("intro").appendTo(this.viewport_container);e("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(e){l.each(e,function(e){i.add_drawable(ne(e,i,i))})})});this.nav_container=e("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(Z),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new W(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});E(R.prototype,j.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500)}else view.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(p.default.commatize(e)+" - "+p.default.commatize(t)),this.nav_input.val(this.chrom+":"+p.default.commatize(e)+"-"+p.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){t.num=100;var i=this,n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new X(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e('<option value="">Select Chrom/Contig</option>'));for(var s=0,o=i.chrom_data.length;s<o;s++){var r=i.chrom_data[s].chrom,l=e("<option>");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('<option value="previous">Previous 100</option>')),t.next_chroms&&i.chrom_select.append(e('<option value="next">Next 100</option>')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;o<r;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(e){e=e.replace(/,/g,""),e=e.replace(/:|\-/g," ");var t=e.split(/\s+/),i=t[0],n=t[1]?parseInt(t[1],10):void 0,a=t[2]?parseInt(t[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(e){var t=this,i=t.high-t.low;this.move_delta(e*i)},move_delta:function(e){var t=this,i=t.high-t.low;t.low-e<t.max_low?(t.low=t.max_low,t.high=t.max_low+i):t.high-e>t.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){j.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(j.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;l.each(n,function(t){var n=l.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;e<this.max_low&&(e=this.max_low),t>this.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(t=e+this.min_separation),this.low=Math.floor(e),this.high=Math.ceil(t),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(e){var t=e[0],i=e[1];t&&t._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(e){e._draw()})},zoom_in:function(e,t){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;e&&(n=e/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var e=this.high-this.low,t=e/2+this.low,i=e*this.zoom_factor/2;this.low=Math.round(t-i),this.high=Math.round(t+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(e){if(this.overview_drawable){if(this.overview_drawable.dataset.id===e.dataset.id)return;this.overview_viewport.find(".track").remove()}var t=e.copy({content_div:this.overview_viewport}),i=this;t.header_div.hide(),t.is_overview=!0,i.overview_drawable=t,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){e(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var N=C.default.Tool.extend({defaults:{track:null},initialize:function(e){C.default.Tool.prototype.initialize.call(this,e);var t=!0;void 0!==e.tool_state&&void 0!==e.tool_state.hidden&&(t=e.tool_state.hidden),this.set("hidden",t),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(e){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),V=n.View.extend({events:{"change :input":"update_value"},render:function(){var t=this.$el.addClass("param-row"),i=this.model;e("<div>").addClass("param-label").text(i.get("label")).appendTo(t);e("<div/>").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("<div style='clear: both;'/>").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),G=n.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()});e("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(e){var t=new V({model:e});t.render(),n.append(t.$el)}),n.find("input").click(function(){e(this).select()});var a=e("<div>").addClass("param-row").appendTo(n),s=e("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);e("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e<this.params.length;e++)this.params[e].update_value()},run_on_dataset:function(){var e=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:e.id},null,function(t){Galaxy.modal.show({title:e.get("name")+" is Running",body:e.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var e,t=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:t.view.chrom,start:t.view.low,end:t.view.high}),a={target_dataset_id:t.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},s=t,o=i.get("name")+s.tool_region_and_parameters_str(n);if(s.container===view){var r=new L(view,view,{name:t.config.get_value("name")}),l=s.container.replace_drawable(s,r,!1);r.container_div.insertBefore(s.view.content_div.children()[l]),r.add_drawable(s),s.container_div.appendTo(r.content_div),e=r}else e=s.container;var d=new s.constructor(view,e,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(s.mode),d.set_filters_manager(s.filters_manager.copy(d)),d.update_icons(),e.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(e){d.set_dataset(new x.default.Dataset(e)),d.tiles_div.text("Running job."),d.init()})},run:function(t,i,n){t.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(t),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});e.when(a.go()).then(function(e){"no converter"===e?(i.container_div.addClass("error"),i.content_div.text(D)):e.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+e.message)):n(e)})}}),U=function(e,t){v.default.Scaler.call(this,t),this.filter=e};U.prototype.gen_val=function(e){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(e[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var H=function(t,i,n,a,s){this.track=t,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=e("<div class='track-tile'/>").append(a),this.data=s,this.stale=!1};H.prototype.predisplay_actions=function(){};var F=function(e,t,i,n,a){H.call(this,e,t,i,n,a)};F.prototype.predisplay_actions=function(){};var B=function(e,t,i,n,a,s,o,r,l,d,c){H.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};E(B.prototype,H.prototype),B.prototype.predisplay_actions=function(){};var q=function(t,i,a){E(a,{drag_handle_class:"draghandle"}),z.call(this,t,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};E(q.prototype,z.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},z.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},z.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(t){var i="<strong>Tool</strong>:"+t.tool.get("name")+"<br/><strong>Dataset</strong>:"+t.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},s=function(){var i,a=e('select[name="regions"] option:selected').val(),s=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(e(".bookmark"),function(t){return new c.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===a?[s]:"bookmarks"===a?o:[s].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:s}})}},z.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&z.prototype.can_draw.call(this)},build_container_div:function(){return e("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("<div class='track-resize'>");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof W?"LabelTrack":this instanceof X?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof te?"ReadTrack":this instanceof ee?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Z?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("<span/>").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(D)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+t.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("<span/>").text(" ")),a.append(e("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(t,i,n){q.call(this,t,i,n);var a=this;if(A(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new b.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new N(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new G({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};E(Y.prototype,z.prototype,q.prototype,{action_icons_def:q.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();E(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){if(this.can_draw()){var i=t&&t.clear_after,n=this.view.low,a=this.view.high,s=this.view.container.width(),o=this.view.resolution_px_b,r=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=s/(view.max_high-view.max_low),r=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*r),f=Math.floor(n/h),p=[],m=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,t),p.push(u),e.when(u).then(function(e){m.push(e)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var _=this;e.when.apply(e,p).then(function(){_.tiles_div.children(".remove").remove(),m=l.filter(m,function(e){return null!==e}),0!==m.length&&_.postdraw_actions(m,s,o,i)})}},_add_yaxis_label:function(t,i){var n=this,a="max"===t?"top":"bottom",o="max"===t?"max":"min",r="max"===t?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=s(n.config.get_value(r),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=e("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),n.config.set_value(r,s(t,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){if(l.filter(e,function(e){return e instanceof F}).length>0){this.max_height_px=0;var a=this;l.each(e,function(e){e instanceof F||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(e,function(e){return e.has_icons})&&l.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)})},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){n||(n={});var a=n.force,s=n.mode||this.mode,o=1/i,r=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,t),u=a?void 0:r.tile_cache.get_elt(c);if(u)return function(e){return e&&"track"in e}(u)&&r.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var e=l.find(I,function(e){return e===s})?"Coverage":s,i=l.map(d,function(i){return i.data_manager.get_data(t,e,o,r.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(t,s,o,view.reference_track.data_url_extra_params)),i},f=e.Deferred();return r.tile_cache.set_elt(c,f),e.when.apply(e,h()).then(function(){var a,s=h(),o=s;if(l.find(s,function(e){return p.default.is_deferred(e)}))return r.tile_cache.set_elt(c,void 0),void e.when(r.draw_helper(t,i,n)).then(function(e){f.resolve(e)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(s.pop(),t));var u=[],m=[];l.each(d,function(e,t){var n=e.mode,a=o[t];"Auto"===n&&(n=e.get_mode(a),e.update_auto_mode(n)),u.push(n),m.push(e.get_canvas_height(a,n,i,b))});var _,g=r.view.canvas_manager.new_canvas(),v=t.get("start"),w=t.get("end"),b=Math.ceil((w-v)*i)+r.left_offset,y=l.max(m);g.width=b,g.height=n.height||y;var x=g.getContext("2d");x.translate(r.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(e,n){_=e.draw_tile(o[n],x,u[n],t,i,a)}),void 0!==_&&(r.tile_cache.set_elt(c,_),r.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new v.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new F(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+l.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var W=function(e,t){q.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};E(W.prototype,q.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("<div/>").addClass("label-container");s<i.high;){var l=Math.floor((s-i.low)/n*o);r.append(e("<div/>").addClass("pos-label").text(p.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var J=function(e,t,i){if(Y.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=ne(n,e,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(e){(e instanceof Z||e instanceof te)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};E(J.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:j.prototype.to_dict,add_drawable:j.prototype.add_drawable,unpack_drawables:j.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;l.each(this.drawables,function(t){t.visible_height_px=e}),q.prototype.on_resize.call(this)},change_mode:function(e){Y.prototype.change_mode.call(this,e);for(var t=0;t<this.drawables.length;t++)this.drawables[t].change_mode(e)},init:function(){for(var t=[],i=0;i<this.drawables.length;i++)t.push(this.drawables[i].init());var n=this;e.when.apply(e,t).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:z.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var e,t=new L(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)e=this.drawables[i],e.update_icons(),t.add_drawable(e),e.container=t,t.content_div.append(e.container_div);this.container.replace_drawable(this,t,!0);t.request_draw({clear_tile_cache:!0})},before_draw:function(){var e=l.min(l.map(this.drawables,function(e){return e.config.get_value("min_value")})),t=l.max(l.map(this.drawables,function(e){return e.config.get_value("max_value")}));this.config.set_value("min_value",e),this.config.set_value("max_value",t),l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)})},update_all_min_max:function(){var e=this.config.get_value("min_value"),t=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(e,t,i,n){var a,s=-1;for(a=0;a<e.length;a++){var o=e[a].html_elt.find("canvas").height();o>s&&(s=o)}for(a=0;a<e.length;a++){var r=e[a];r.html_elt.find("canvas").height()!==s&&(this.draw_helper(r.region,i,{force:!0,height:s}),r.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var X=function(e){Y.call(this,e,{content_div:e.top_labeltrack},{resize:!1,header:!1}),this.left_offset=e.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};E(X.prototype,z.prototype,Y.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:z.prototype.can_draw,draw_helper:function(e,t,i){var n,a=this.tiles_div.is(":visible"),s=null;return t>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=Y.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l<d;l++)t.fillStyle=this.view.get_base_color(o[l]),t.fillText(o[l],Math.floor(l*a),10);return new H(this,n,a,r,s)}});var K=function(t,i,n){this.mode="Histogram",Y.call(this,t,i,n),this.left_offset=30;var a=this;e.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(e){e&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};E(K.prototype,z.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(e,t,i,n,a){return this._draw_line_track_tile(e,t,i,n,a)},can_subset:function(e){return e.data[1][0]-e.data[0][0]==1},postdraw_actions:function(e,t,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Q=function(e,t,i){this.mode="Heatmap",Y.call(this,e,t,i)};E(Q.prototype,z.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){e.data})},draw_tile:function(e,t,i,n,a){var s=t.canvas;return new v.default.DiagonalHeatmapPainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new H(this,n,a,s,e.data)}});var Z=function(e,t,i){Y.call(this,e,t,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};E(Z.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s,o=this;if(0===l.filter(t,function(e){return e instanceof F}).length){var r={};l.each(l.pluck(t,"incomplete_features"),function(e){l.each(e,function(e){r[e[0]]=e})});var d=this;l.each(t,function(t){var i=l.omit(r,l.map(t.incomplete_features,function(e){return e[0]}));if(i=l.omit(i,l.keys(t.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),s=a.getContext("2d");a.height=Math.max(t.canvas.height,d.get_canvas_height(n,t.mode,t.w_scale,100)),a.width=t.canvas.width,s.drawImage(t.canvas,0,0),s.translate(o.left_offset,0);var c=d.draw_tile(n,s,t.mode,t.region,t.w_scale,t.seq_data);e(t.canvas).replaceWith(e(c.canvas)),t.canvas=a,l.extend(t.other_tiles_features_drawn,r)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(s=0;s<t.length;s++)if(t[s].data.length)for(h=t[s].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(t[0]instanceof B){var m=!0;for(s=0;s<t.length;s++)if(!t[s].all_slotted){m=!1;break}this.action_icons.show_more_rows_icon.toggle(!m)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(e){"Auto"===this.mode&&("no_detail"===e&&(e="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+e+")"))},incremental_slots:function(e,t,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[e];return a&&a.mode===i||(a=new _.default.FeatureSlotter(e,i,100,function(e){return n.measureText(e)}),this.slotters[e]=a),a.slot_features(t)},get_mode:function(e){return"no_detail"===e.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var m=this.filters_manager.filters,_=0,g=e.data.length;_<g;_++){for(var v,w=e.data[_],b=!1,y=0,x=m.length;y<x;y++)if(v=m[y],v.update_attrs(w),!v.keep(w)){b=!0;break}b||(h.push(w),w[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new U(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new U(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,s,function(e){return r.view.get_base_color(e)}),S=null;if(t.fillStyle=this.config.get_value("block_color"),t.font=t.canvas.manager.default_font,t.textAlign="right",e.data){var T=$.draw(t,l.width,l.height,a,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-u}return o?void 0:new B(r,n,a,l,e.data,i,e.message,p,S,incomplete_features,s)}});var ee=function(e,t,i){Y.call(this,e,t,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};E(ee.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(e,t,i,n,a){if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,"Histogram",n,a);var s=this.view;return new this.painter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(e){return s.get_base_color(e)}).draw(t,t.canvas.width,t.canvas.height,a),new H(this,n,a,t.canvas,e.data)},get_canvas_height:function(e,t,i,n){if("bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==e.data.length&&(a=e.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),t).get_required_height(a)},predraw_init:function(){var e=[q.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||e.push(this.dataset.fetch()),e},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s=l.filter(t,function(e){return e instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===s.length&&this.config.get_value("show_labels")&&o&&o.length>1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(e("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var te=function(e,t,i){Z.call(this,e,t,i),this.painter=v.default.ReadPainter,this.update_icons()};E(te.prototype,z.prototype,Y.prototype,Z.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var ie={CompositeTrack:J,DrawableGroup:L,DiagonalHeatmapTrack:Q,FeatureTrack:Z,LineTrack:K,ReadTrack:te,VariantTrack:ee,VcfTrack:ee},ne=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new ie[n](t,i,e)};t.default={TracksterView:R,DrawableGroup:L,LineTrack:K,FeatureTrack:Z,DiagonalHeatmapTrack:Q,ReadTrack:te,VariantTrack:ee,CompositeTrack:J,object_from_template:ne}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(a),o=e.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(e){e.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var e=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),s.each(this.model.action_icons_def,function(t){e.add_action_icon(t.name,t.title,t.css_class,t.on_click_fn,t.prepend,t.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,t,i,a,s,o){var r=this;this.action_icons[e]=n("<a/>").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(function(){a(r.model)}).appendTo(this.icons_div),o&&this.action_icons[e].hide()},set_display_modes:function(e,t){if(e){this.model.display_modes=e,this.model.mode=t||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,s=i.display_modes.length;a<s;a++){var o=i.display_modes[a];n[o]=function(e){return function(){i.change_mode(e)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});t.default={TrackHeaderView:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e,t){this.slot=e,this.feature=t},r=function(e,t,i,n){this.slots={},this.start_end_dct={},this.w_scale=e,this.mode=t,this.include_label="Pack"===t,this.max_rows=i,this.measureText=n};s(r.prototype,{_get_draw_coords:function(e){var t=Math.floor(e[1]*this.w_scale),i=Math.ceil(e[2]*this.w_scale),n=e[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;t-a>=0?(t-=a,"left"):(i+=a,"right")}return[t,i]},_find_slot:function(e){for(var t=e[0],i=e[1],n=0;n<=this.max_rows;n++){var a=!1,s=this.start_end_dct[n];if(void 0!==s)for(var o=0,r=s.length;o<r;o++){var l=s[o];if(i>l[0]&&t<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(e){for(var t,i,n=this.start_end_dct,a=[],s=0,r=0,l=e.length;r<l;r++){t=e[r],i=t[0];var d=this.slots[i];if(d){if(t[1]<d.feature[1]||d.feature[2]<t[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(t),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}s=Math.max(s,this.slots[i].slot)}else a.push(r)}for(var r=0,l=a.length;r<l;r++){t=e[a[r]],i=t[0];var m=this._get_draw_coords(t),_=this._find_slot(m);_>=0&&(void 0===n[_]&&(n[_]=[]),n[_].push(m),this.slots[i]=new o(_,t),s=Math.max(s,_))}return s+1}}),t.default={FeatureSlotter:r}},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=function(e,t){var i=e[0],n=e[1],a=t[0],s=t[1];return i<a?n<=a?1001:n<=s?1003:1002:i>s?1006:n<=s?1005:1004},o=function(e,t){var i=s(e,t);return 1001!==i&&1006!==i},r=function(e,t,i,n,a,s){void 0===s&&(s=4);var o,r=n-t,l=a-i,d=Math.floor(Math.sqrt(r*r+l*l)/s),c=r/d,u=l/d;for(o=0;o<d;o++,t+=c,i+=u)o%2==0&&e.fillRect(t,i,s,1)},l=function(e,t,i,n){var a=t-n/2,s=t+n/2,o=i-Math.sqrt(3*n/2);e.beginPath(),e.moveTo(a,o),e.lineTo(s,o),e.lineTo(t,i),e.lineTo(a,o),e.strokeStyle=this.fillStyle,e.fill(),e.stroke(),e.closePath()},d=function(e){this.default_val=e||1};d.prototype.gen_val=function(e){return this.default_val};var c=function(e){this.incomplete_features=e.incomplete_features,this.feature_mapper=e.feature_mapper},u=function(e,t,i,n,s){this.data=e,this.view_start=t,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=s};u.prototype.default_prefs={},u.prototype.draw=function(e,t,i,n){},u.prototype.get_start_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,-.5)},u.prototype.get_end_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,.5)},u.prototype.get_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,0)},u.prototype._chrom_pos_to_draw_pos=function(e,t,i){return Math.floor(t*(Math.max(0,e-this.view_start)+i))};var h=function(e,t,i,n,a){u.call(this,e,t,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(e,t,i,n){var s=!1,o=this.prefs.min_value,r=this.prefs.max_value,l=r-o,d=i,c=this.view_start,u=this.mode,h=this.data;e.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(e.fillStyle="#aaa",e.fillRect(0,f,t,1)),e.beginPath();var p,m,_;_=h.length>1?a.map(h.slice(0,-1),function(e,t){return Math.ceil((h[t+1][0]-h[t][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,w=parseInt(v.slice(1),16),b=(16711680&w)>>16,y=(65280&w)>>8,x=255&w,k=!1,C=!1,$=0,S=h.length;$<S;$++)if(e.fillStyle=e.strokeStyle=v,k=C=!1,g=_[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(m=h[$][1])){if(m<o?(C=!0,m=o):m>r&&(k=!0,m=r),"Histogram"===u)m=Math.round(m/l*d),e.fillRect(p,f,g,-m);else if("Intensity"===u){var T=(m-o)/l,M=Math.round(b+(255-b)*(1-T)),E=Math.round(y+(255-y)*(1-T)),P=Math.round(x+(255-x)*(1-T));e.fillStyle="rgb("+M+","+E+","+P+")",e.fillRect(p,0,g,d)}else m=Math.round(d-(m-o)/l*d),s?e.lineTo(p,m):(s=!0,"Filled"===u?(e.moveTo(p,d),e.lineTo(p,m)):e.moveTo(p,m));if(e.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===u||"Intensity"===u?O=g:(p-=2,O=4),k&&e.fillRect(p,0,O,3),C&&e.fillRect(p,d-3,O,3)}e.fillStyle=v}else s&&"Filled"===u&&e.lineTo(p,d),s=!1;"Filled"===u?(s&&(e.lineTo(p,f),e.lineTo(0,f)),e.fill()):e.stroke(),e.restore()};var f=function(e){this.feature_positions={},this.slot_height=e,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(e,t,i,n){this.feature_positions[t]||(this.feature_positions[t]=[]),this.feature_positions[t].push({data:e,x_start:i,x_end:n})},f.prototype.get_feature_data=function(e,t){var i,n=Math.floor((t-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;e+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],e>=i.x_start&&e<=i.x_end)return i.data};var p=function(e,t,i,n,a,s,o){u.call(this,e,t,i,n,a),this.alpha_scaler=s||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(e,t){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=e*n),i+this.get_top_padding(t)},get_top_padding:function(e){return 0},draw:function(e,t,i,n,a){var s=this.data,o=this.view_start,r=this.view_end;e.save(),e.fillStyle=this.prefs.block_color,e.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,m=s.length;p<m;p++){var _=s[p],g=_[0],v=_[1],w=_[2],b=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==b)&&v<r&&w>o&&(l=this.draw_element(e,this.mode,_,b,o,r,n,d,t),u.map_feature_data(_,b,l[0],l[1]),(v<o||w>r)&&h.push(_))}return e.restore(),u.y_translation=this.get_top_padding(t),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(e,t,i,n,a,s,o,r,l){return[0,0]}});var m=function(e,t,i,n,a,s,o){p.call(this,e,t,i,n,a,s,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(m.prototype,p.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"no_detail"===e?3:"Squish"===e?5:10},draw_element:function(e,t,i,n,a,s,o,r,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),m=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),_=p,g=m,d=("Dense"===t?0:0+n)*r+this.get_top_padding(l),v=null,w=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(e.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===t&&(n=1),"no_detail"===t)e.fillStyle=b,e.fillRect(p,d+5,m-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),w=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var S,T;if("Squish"===t?(S=1,T=3,$=!1):(S=5,T=9),C){var M,E;"Squish"===t||"Dense"===t?(M=d+Math.floor(1.5)+1,E=1):f?(M=d,E=T):(M+=2.5,E=1),this.draw_background_connector&&("Squish"===t||"Dense"===t?e.fillStyle="#ccc":f?"+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand")):e.fillStyle="#ccc",e.fillRect(p,M,m-p,E));for(var P=0,O=C.length;P<O;P++){var A,D,I=C[P],z=Math.floor(Math.max(0,(I[0]-a-.5)*o)),j=Math.ceil(Math.min(l,Math.max((I[1]-a-.5)*o)));if(!(z>j)){if(e.fillStyle=b,e.fillRect(z,d+(T-S)/2+1,j-z,S),void 0!==v&&k>x&&!(z>w||j<v)){var L=Math.max(z,v),R=Math.min(j,w);e.fillRect(L,d+1,R-L,T),1===C.length&&"Pack"===t&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),L+14<R&&(L+=2,R-=2),e.fillRect(L,d+1,R-L,T))}this.draw_individual_connectors&&A&&this.draw_connector(e,A,D,z,j,d),A=z,D=j}}if("Pack"===t){e.globalAlpha=1,e.fillStyle="white";var N=this.height_scaler.gen_val(i),V=Math.ceil(T*N),G=Math.round((T-V)/2);1!==N&&(e.fillRect(p,M+1,m-p,G),e.fillRect(p,M+T-G+1,m-p,G))}}else e.fillStyle=b,e.fillRect(p,d+1,m-p,T),f&&$&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),e.fillRect(p,d+1,m-p,T));e.globalAlpha=1,h&&"Pack"===t&&c>a&&(e.fillStyle=y,0===a&&p-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,m+2,d+8,this.max_label_length),g+=e.measureText(h).width+2):(e.textAlign="right",e.fillText(h,p-2,d+8,this.max_label_length),_-=e.measureText(h).width+2))}return e.globalAlpha=1,[_,g]}});var _=function(e,t,i,n,a,s,o,r,l){p.call(this,e,t,i,n,a,s,o),this.ref_seq=r?r.data:null,this.base_color_fn=l};a.extend(_.prototype,p.prototype,{get_row_height:function(){var e,t=this.mode;return"Dense"===t?e=10:"Squish"===t?e=5:(e=10,this.prefs.show_insertions&&(e*=2)),e},_parse_cigar:function(e){var t="MIDNSHP=X",i=[[0,0]],n=i[0],s=0,o=a.map(e.match(/[0-9]+[MIDNSHP=X]/g),function(e){var a=parseInt(e.slice(0,-1),10),o=e.slice(-1);return"N"===o?0!==n[1]&&(n=[s+a,s+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,s+=a),[t.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(e,t,i,n,a,r,d,c,u,h){var f=function(e){return Math.floor(Math.max(0,(e-a-.5)*i))};e.textAlign="center";var p,m,_=[a,r],g=0,v=0,w=Math.round(i/2),b=e.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===t,C=k?9:3,$=n+1,S=new x(e,C,i,t),T=[],M=[],E=this._parse_cigar(c);c=E.cigar,T=E.blocks;for(var P=0;P<T.length;P++){var O=T[P];o([d+O[0],d+O[1]],_)&&(p=f(d+O[0]),m=f(d+O[1]),p===m&&(m+=1),e.fillStyle=y,e.fillRect(p,$,m-p,C))}for(var A=0,D=c.length;A<D;A++){var I=c[A],z="MIDNSHP=X"[I[0]],j=I[1],L=d+g;if(p=f(L),m=f(L+j),o([L,L+j],_))switch(p===m&&(m+=1),z){case"H":case"S":case"P":break;case"M":g+=j;break;case"=":case"X":var R="";"X"===z?R=h.slice(v,v+j):this.ref_seq&&(R=this.ref_seq.slice(Math.max(0,L-a),Math.min(L-a+j,r-a)));for(var N=Math.max(L,a),V=0;V<R.length;V++)if(R&&!this.prefs.show_differences||"X"===z){var G=Math.floor(Math.max(0,(N+V-a)*i));e.fillStyle=this.base_color_fn(R[V]),k&&i>b?e.fillText(R[V],G,n+9):i>.05&&e.fillRect(G-w,$,Math.max(1,Math.round(i)),C)}"X"===z&&(v+=j),g+=j;break;case"N":e.fillStyle="#ccc",e.fillRect(p,$+(C-1)/2,m-p,1),g+=j;break;case"D":S.draw_deletion(p,$,j),g+=j;break;case"I":var U=p-w;if(o([L,L+j],_)){var H=h.slice(v,v+j);if(this.prefs.show_insertions){var F=p-(m-p)/2;if(("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b){switch(e.fillStyle="yellow",e.fillRect(F-w,n-9,m-p,9),M[M.length]={type:"triangle",data:[U,n+4,5]},e.fillStyle="#ccc",s([L,L+j],_)){case 1003:H=H.slice(a-L);break;case 1004:H=H.slice(0,L-r);break;case 1005:break;case 1002:H=H.slice(a-L,L-r)}for(var V=0,B=H.length;V<B;V++){var G=Math.floor(Math.max(0,(L+V-a)*i));e.fillText(H[V],G-(m-p)/2,n)}}else e.fillStyle="yellow",e.fillRect(F,n+("Dense"!==this.mode?2:5),m-p,"Dense"!==t?3:9)}else("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b&&M.push({type:"text",data:[H.length,U,n+9]})}v+=j}else g=function(e,t,i){return-1!=="M=NXD".indexOf(t)&&(e+=i),e}(g,z,j),v=function(e,t,i){return-1!=="IX".indexOf(t)&&(e+=i),e}(v,z,j)}e.fillStyle="yellow";for(var q,Y,W,P=0;P<M.length;P++)q=M[P],Y=q.type,W=q.data,"text"===Y?(e.save(),e.font="bold "+e.font,e.fillText(W[0],W[1],W[2]),e.restore()):"triangle"===Y&&l(e,W[0],W[1],W[2])},draw_element:function(e,t,i,n,a,s,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),m=("Dense"===t?0:0+n)*l,_="Pack"===t?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=s&&i[4][2]?this.draw_read(e,t,o,m,a,s,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=s&&i[5][2]?this.draw_read(e,t,o,m,a,s,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),w=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&w>v){e.fillStyle="#ccc";var b=m+1+(_-1)/2;r(e,v,b,w,b)}}else this.draw_read(e,t,o,m,a,s,c,i[4],i[5],i[6]);return"Pack"===t&&c>=a&&"."!==h&&(e.fillStyle=this.prefs.label_color,0===a&&f-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,p+2,m+9,this.max_label_length)):(e.textAlign="right",e.fillText(h,f-2,m+9,this.max_label_length))),[0,0]}});var g=function(e,t,i,n,a,s,o){m.call(this,e,t,i,n,a,s,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,m.prototype,{calculate_longest_feature_length:function(){for(var e=0,t=0,i=this.data.length;t<i;t++){var n=this.data[t],a=n[1],s=n[2];e=Math.max(e,s-a)}return e},get_top_padding:function(e){var t=this.view_end-this.view_start,i=e/t;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(e,t,i,n,a,s){var o=(i+n)/2,r=n-o;Math.PI;r>0&&(e.beginPath(),e.arc(o,s,n-o,Math.PI,0),e.stroke())}});var v=function(e,t){Array.isArray(e)?this.rgb=e:6==e.length?this.rgb=e.match(/.{2}/g).map(function(e){return parseInt(e,16)}):7==e.length?this.rgb=e.substring(1,7).match(/.{2}/g).map(function(e){return parseInt(e,16)}):this.rgb=e.split("").map(function(e){return parseInt(e+e,16)}),this.alpha="number"==typeof t?t:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(e){return Math.round(e)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},toHSL:function(){var e,t,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,s=this.alpha,o=Math.max(i,n,a),r=Math.min(i,n,a),l=(o+r)/2,d=o-r;if(o===r)e=t=0;else{switch(t=l>.5?d/(2-o-r):d/(o+r),o){case i:e=(n-a)/d+(n<a?6:0);break;case n:e=(a-i)/d+2;break;case a:e=(i-n)/d+4}e/=6}return{h:360*e,s:t,l:l,a:s}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},mix:function(e,t){var i=this,n=t,a=2*n-1,s=i.toHSL().a-e.toHSL().a,o=((a*s==-1?a:(a+s)/(1+a*s))+1)/2,r=1-o,l=[i.rgb[0]*o+e.rgb[0]*r,i.rgb[1]*o+e.rgb[1]*r,i.rgb[2]*o+e.rgb[2]*r],d=i.alpha*n+e.alpha*(1-n);return new v(l,d)}};var w=function(e,t,i,n){this.start_color=new v(e),this.end_color=new v(t),this.start_value=i,this.end_value=n,this.value_range=n-i};w.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e=(e-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-e).toCSS()};var b=function(e,t,i,n,a){this.positive_ramp=new w(t,i,0,a),this.negative_ramp=new w(t,e,0,-n),this.start_value=n,this.end_value=a};b.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e>=0?this.positive_ramp.map_value(e):this.negative_ramp.map_value(-e)};var y=function(e,t,i,n,a){u.call(this,e,t,i,n,a);var s,o;if(void 0===this.prefs.min_value){var r=1/0;for(s=0,o=this.data.length;s<o;s++)r=Math.min(r,this.data[s][6]);this.prefs.min_value=r}if(void 0===this.prefs.max_value){var l=-1/0;for(s=0,o=this.data.length;s<o;s++)l=Math.max(l,this.data[s][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(e,t,i,n){var a,s,o,r,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),m=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),_=function(e){return(e-h)*n};e.save(),e.rotate(-45*Math.PI/180),e.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],s=_(a[1]),o=_(a[2]),r=_(a[4]),l=_(a[5]),d=a[6],e.fillStyle=m.map_value(d),e.fillRect(s,r,o-s,l-r);e.restore()};var x=function(e,t,i,n){this.ctx=e,this.row_height=t,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=e.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(e,t,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;t+=.5*(this.row_height-n),this.ctx.fillRect(e,t,i*this.px_per_base,n)}});var k=function(e,t,i,n,a,s){u.call(this,e,t,i,n,a),this.base_color_fn=s,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"Squish"===e?5:10},get_required_height:function(e){var t=this.prefs.summary_height;return e>1&&this.prefs.show_sample_data&&(t+=this.divider_height+e*this.get_row_height()),t},draw:function(e,t,i,n){e.save();var s,o,r,l,d,c,u,h,f,p,m,_=function(e,t){var i=e.length,n=t.length,a=0,s=1,o=null;return"-"===t?(o="deletion",s=e.length):0===e.indexOf(t)&&i>n?(o="deletion",s=i-n,a=n):0===t.indexOf(e)&&i<n&&(o="insertion",s=n-i,a=n),null!==o?{type:o,start:a,len:s}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,w="Squish"===this.mode?5:10,b=n<.1?w:"Squish"===this.mode?3:9,y=!0,k=new x(e,w,n,this.mode);1===v&&(w=b=n<e.canvas.manager.char_width_px?this.prefs.summary_height:w,k.row_height=w,y=!1),this.prefs.show_sample_data&&y&&(e.fillStyle="#F3F3F3",e.globalAlpha=1,e.fillRect(0,this.prefs.summary_height-this.divider_height,t,this.divider_height)),e.textAlign="center";for(var C=0;C<this.data.length;C++)if(s=this.data[C],o=s[1],r=s[3],l=[s[4].split(",")],d=s[7].split(","),c=s.slice(8),l=a.map(a.flatten(l),function(e){var t={type:"snp",value:e,start:0},i=_(r,e);return a.extend(t,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(e.fillStyle="#999999",e.globalAlpha=1,m=0;m<l.length;m++)for(h=this.get_start_draw_pos(o+l[m].start,n),e.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,m=0;m<l.length;m++){e.fillStyle="deletion"===l[m].type?"black":this.base_color_fn(l[m].value);var $=c/d.length,S=Math.ceil(this.prefs.summary_height*$);e.fillRect(h,f-S,g,S),f-=S}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,m=0;m<d.length;m++,f+=w)if(p=d[m]?d[m].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],e.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],e.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;e.fillStyle=this.base_color_fn(T),k.draw_details?e.fillText(T,this.get_draw_pos(o,n),f+w):e.fillRect(h,f+1,g,b)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}e.restore()}}),t.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:m,ReadPainter:_,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e){this.manager=null,this.name=e.name,this.index=e.index,this.tool_id=e.tool_id,this.tool_exp_name=e.tool_exp_name};s(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var r=function(t,i,n){return e("<a/>").attr("href","javascript:void(0);").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(t){o.call(this,t),this.low="low"in t?t.low:-Number.MAX_VALUE,this.high="high"in t?t.high:Number.MAX_VALUE,this.min="min"in t?t.min:Number.MAX_VALUE,this.max="max"in t?t.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=e("<div/>").addClass("filter-row slider-row");var n=e("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(e("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),e("<span/>").text(this.low+"-"+this.high)),s=e("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=e("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=e("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(e,t){i.slide(e,t)},change:function(e,t){i.control_element.slider("option","slide").call(i.control_element,e,t)}}),i.slider=i.control_element,i.slider_label=a,function(t,i,n){t.click(function(){var t=i.text(),a=parseFloat(n.slider("option","max")),s=a<=1?4:a<=1e6?a.toString().length:6,o=!1,r=e(this).parents(".slider-row");r.addClass("input"),n.slider("option","values")&&(s=2*s+1,o=!0),i.text(""),e("<input type='text'/>").attr("size",s).attr("maxlength",s).attr("value",t).appendTo(i).focus().select().click(function(e){e.stopPropagation()}).blur(function(){e(this).remove(),i.text(t),r.removeClass("input")}).keyup(function(t){if(27===t.keyCode)e(this).trigger("blur");else if(13===t.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),s=function(e){return isNaN(e)||e>a||e<i},l=e(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],s(l[0])||s(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this)}else if(l=parseFloat(l),s(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this);n.slider(o?"values":"value",l),r.removeClass("input")}})})}(s,a,i.control_element);var d=e("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=r("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=r("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),e("<div style='clear: both;'/>").appendTo(i.parent_div)};s(l.prototype,{to_dict:function(){var e=o.prototype.to_dict.call(this);return s(e,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(e,t){return t-e<=2?.01:1},slide:function(e,t){var i=t.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(e){return e.length>this.index},_keep_val:function(e){return isNaN(e)||e>=this.low&&e<=this.high},keep:function(e){if(!this.applies_to(e))return!0;var t=e[this.index];if(t instanceof Array){for(var i=!0,n=0;n<t.length;n++)if(!this._keep_val(t[n])){i=!1;break}return i}return this._keep_val(e[this.index])},update_attrs:function(e){var t=!1;if(!this.applies_to(e))return t;var i=e[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),t=!0),a>this.max&&(this.max=Math.ceil(a),t=!0)}return t},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var e=this.slider.slider("option","min"),t=this.slider.slider("option","max");(this.min<e||this.max>t)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(t,i){if(this.track=t,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=e("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).bind("keydown",function(e){e.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),s=("height_filter"in i?i.height_filter:null),o=i.filters,r=0;r<o.length;r++)"number"===o[r].type?(n=new l(o[r]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===s&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=e("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;e("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};s(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var e,t={},i=[],n=0;n<this.filters.length;n++)e=this.filters[n],i.push(e.to_dict());return t.filters=i,t.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,t.height_filter=this.height_filter?this.height_filter.name:null,t.visible=this.parent_div.is(":visible"),t},copy:function(e){for(var t=new d(e),i=0;i<this.filters.length;i++)t.add_filter(this.filters[i].copy());return t},add_filter:function(e){e.manager=this,this.parent_div.append(e.parent_div),this.filters.push(e)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var e=0;e<this.filters.length;e++){this.filters[e].update_ui_elt()}},clear_filters:function(){for(var e=0;e<this.filters.length;e++){var t=this.filters[e];t.slider.slider("option","values",[t.min,t.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var t,i,n=(function(e,t,i){return t in e||(e[t]=i),e[t]}),a={},s=0;s<this.filters.length;s++)t=this.filters[s],t.tool_id&&(t.min!==t.low&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" >= "+t.low),t.max!==t.high&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" <= "+t.high));var o=[];for(var r in a)o[o.length]=[r,a[r]];!function t(i,n){var a=n[0],s=a[0],o=a[1],r="("+o.join(") and (")+")",l={cond:r,input:i,target_dataset_id:i,tool_id:s};n=n.slice(1),e.getJSON(run_tool_url,l,function(e){e.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+s,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):t(e.dataset_id,n)})}(this.track.dataset_id,o)}}),t.default={FiltersManager:d,NumberFilter:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(13),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=i(152),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=a.default.GenomeDataManager.extend({load_data:function(t,i,n,a){var s=e.Deferred();this.set_data(t,s);var r=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new e.Deferred;return e.when(o.makeBwg(r)).then(function(i,n){e.when(i.readWigData(t.get("chrom"),t.get("start"),t.get("end"))).then(function(e){var i=[],n={max:Number.MIN_VALUE};e.forEach(function(e){n.max!==e.min-1&&(i.push([n.max+1,0]),i.push([e.min-2,0])),i.push([e.min-1,e.score]),i.push([e.max,e.score]),n=e});var a={data:i,region:t,dataset_type:"bigwig"};l.set_data(t,a),s.resolve(a)})}),s}});t.default={BBIDataManager:r}}).call(t,i(0))},function(e,t,i){(function(n){var a,s;a=[i(153),i(154),i(155)],void 0!==(s=function(e,t){"use strict";function i(){}function a(e){e&&(this.id=e)}function s(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function o(e,t,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:e,timeout:5e3,beforeSend:function(e){e.setRequestHeader("Range","bytes="+t+"-"+(t+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function r(e,t){return e[t]+e[t+1]*y+e[t+2]*x+e[t+3]*k+e[t+4]*C}function l(){}function d(e,t,i,n){this.bwg=e,this.cirTreeOffset=t,this.cirTreeLength=i,this.isSummary=n}function c(e){var t=n.Deferred(),i=new l;return i.url=e,n.when(o(i.url,0,512)).then(function(e){if(!e)return t.resolve(null,"Couldn't fetch file");var a=e,s=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=s[0]+y*s[1]+x*s[2]+k*s[3];if(d==g)i.type="bigwig";else{if(d!=w)return d==v||d==b?t.resolve(null,"Currently don't support big-endian BBI files"):t.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=r(s,8),i.unzoomedDataOffset=r(s,16),i.unzoomedIndexOffset=r(s,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=r(s,36),i.totalSummaryOffset=r(s,44),i.uncompressBufSize=l[13],i.extHeaderOffset=r(s,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=r(s,24*c+72),f=r(s,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(e){return i.schema=e,t.resolve(i)})})}),t}function u(e,t,i,n,a){this.bbi=e,this.type=t,this.fieldCount=i,this.offset=n,this.field=a}var h=e.Range,f=e.union,p=e.intersection,m=t.inflateBuffer,_=t.arrayCopy,g=2291137574,v=654086024,w=2273964779,b=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var e=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var t=this.unzoomedDataOffset;return t=t+4-(t-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,t-this.chromTreeOffset)).then(function(t){var i=new Uint8Array(t),n=new Int16Array(t),a=new Int32Array(t),s=(a[0],a[1],a[2]),o=(a[3],r(i,16),function(t){var a=i[t],l=n[t/2+1];t+=4;for(var d=0;d<l;++d)if(0===a){t+=s;var c=r(i,t);t+=8,c-=e.chromTreeOffset,o(c)}else{for(var u="",h=0;h<s;++h){var f=i[t++];0!==f&&(u+=String.fromCharCode(f))}var p=i[t+3]<<24|i[t+2]<<16|i[t+1]<<8|i[t+0];i[t+7],i[t+6],i[t+5],i[t+4],t+=8,e.chromsToIDs[u]=p,0===u.indexOf("chr")&&(e.chromsToIDs[u.substr(3)]=p),e.idsToChroms[p]=u,e.maxID=Math.max(e.maxID,p)}});o(32)})},d.prototype.readWigData=function(e,t,i){var n=this.bwg.chromsToIDs[e];return void 0===n?[]:this.readWigDataById(n,t,i)},d.prototype.readWigDataById=function(e,t,i){var a=this,s=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var r=new Int32Array(a.cirHeader);a.cirBlockSize=r[1],n.when(a.readWigDataById(e,t,i)).then(function(e){s.resolve(e)})}),s;var l=[],d=0,c=(Date.now(),function(n,a,s,o){return(e<0||n==e)&&a<=i&&s>=t}),u=function(e,t){if(a.bwg.instrument&&console.log("level="+t+"; offset="+e+"; time="+(0|Date.now())),d+=e.length,1==e.length&&e[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return m(a.cachedCirRoot,0,t),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}));for(var i,o=4+32*a.cirBlockSize,r=0;r<e.length;++r){var u=new h(e[r],e[r]+o);i=i?f(i,u):u}for(var _=i.ranges(),g=0;g<_.length;++g){var v=_[g];p(e,v,t)}},p=function(e,t,i,r){t.max(),t.min();n.when(o(a.bwg.url,t.min(),t.max()-t.min())).then(function(o){for(var r=0;r<e.length;++r)t.contains(e[r])&&(m(o,e[r]-t.min(),i),e[r]-a.cirTreeOffset==48&&e[r]-t.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}))})},m=function(n,a,s){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16),y=r(o,a+24);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&l.push({offset:b,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&x.push(b),a+=24}x.length>0&&u(x,s+1)}};return u([a.cirTreeOffset+48],1),s},d.prototype.fetchFeatures=function(e,t){var a=this,s=n.Deferred();if(t.sort(function(e,t){return(0|e.offset)-(0|t.offset)}),0===t.length)return[];var r=[],l=function(e,t,n,s){s||(s={});var o=new i;o._chromId=e,o.segment=a.bwg.idsToChroms[e],o.min=t,o.max=n,o.type=a.bwg.type;for(var l in s)o[l]=s[l];r.push(o)},d=function(){if(0===t.length){Date.now();return s.resolve(r)}var i=t[0];if(i.data)a.parseFeatures(i.data,l,e),t.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<t.length&&t[h].offset==c+u;)u+=t[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(e){for(var i=0,n=0;i<u;){var s,o=t[n];if(a.bwg.uncompressBufSize>0)s=m(e,i+2,o.size-2);else{var r=new Uint8Array(o.size);_(new Uint8Array(e,i,o.size),0,r,0,o.size),s=r.buffer}o.data=s,i+=o.size,++n}d()})}};return d(),s},d.prototype.parseFeatures=function(e,t,i){var s=new Uint8Array(e);if(this.isSummary)for(var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),d=e.byteLength/32,c=0;c<d;++c){var u=r[8*c],m=r[8*c+1],_=r[8*c+2],g=r[8*c+3],v=(l[8*c+4],l[8*c+5]),w=l[8*c+6];l[8*c+7];if(i(u,m+1,_)){var b={type:"bigwig",score:w/g,maxScore:v};"bigbed"==this.bwg.type&&(b.type="density"),t(u,m+1,_,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),u=r[0],y=r[1],x=(r[2],r[3]),k=r[4],C=s[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var S=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&t(u,T,M,{score:S})}else if(2==C)for(var c=0;c<d;++c){var m=r[2*c+6]+1,_=m+k-1,S=l[2*c+7];i(u,m,_)&&t(u,m,_,{score:S})}else if(1==C)for(var c=0;c<d;++c){var m=r[3*c+6]+1,_=r[3*c+7],S=l[3*c+8];m>_&&(m=_),i(u,m,_)&&t(u,m,_,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var E=0,P=this.bwg.definedFieldCount,O=this.bwg.schema;E<s.length;){var u=s[E+3]<<24|s[E+2]<<16|s[E+1]<<8|s[E+0],m=s[E+7]<<24|s[E+6]<<16|s[E+5]<<8|s[E+4],_=s[E+11]<<24|s[E+10]<<16|s[E+9]<<8|s[E+8];E+=12;for(var A="";;){var D=s[E++];if(0==D)break;A+=String.fromCharCode(D)}var I,z={};if(I=A.length>0?A.split("\t"):[],I.length>0&&P>3&&(z.label=I[0]),I.length>1&&P>4){var S=parseInt(I[1]);isNaN(S)||(z.score=S)}if(I.length>2&&P>5&&(z.orientation=I[2]),I.length>5&&P>8){var j=I[5];$.test(j)&&(z.itemRgb="rgb("+j+")")}if(I.length>P-3&&O)for(var L=P-3;L<I.length;++L)z[O.fields[L+3].name]=I[L];if(i(u,m+1,_,I))if(P<12)t(u,m+1,_,z);else{var R=0|I[3],N=0|I[4],V=0|I[6],G=I[7].split(","),U=I[8].split(",");if(z.exonFrames){var H=z.exonFrames.split(",");z.exonFrames=void 0}z.type="transcript";var F=new a;for(var B in z)F[B]=z[B];if(F.id=I[0],F.segment=this.bwg.idsToChroms[u],F.min=m+1,F.max=_,F.notes=[],z.groups=[F],I.length>9){var q=z.geneName||I[9],Y=q;I.length>10&&(Y=I[10]),z.geneName2&&(Y=z.geneName2);var W=n.extend({},F);W.id=q,W.label=Y,W.type="gene",z.groups.push(W)}for(var J=[],X=0;X<V;++X){var K=(0|U[X])+m,Q=K+(0|G[X]),Z=new h(K,Q);J.push(Z)}for(var ee=f(J),te=ee.ranges(),ie=0;ie<te.length;++ie){var ne=te[ie];t(u,ne.min()+1,ne.max(),z)}if(N>R){var ae="+"==z.orientation?new h(R,N+3):new h(R-3,N),se=p(ee,ae);if(se){z.type="translation";for(var oe=se.ranges(),re=0,le=0;oe[0].min()>te[le].max();)le++;for(var ie=0;ie<oe.length;++ie){var de=ie;"-"==z.orientation&&(de=oe.length-ie-1);var ne=oe[de];if(z.readframe=re,H){var ce=parseInt(H[de+le]);"number"==typeof ce&&ce>=0&&ce<=2&&(z.readframe=ce,z.readframeExplicit=!0)}var ue=ne.max()-ne.min();re=(re+ue)%3,t(u,ne.min()+1,ne.max(),z)}}}}}}},d.prototype.getFirstAdjacent=function(e,t,i,n){var a=this.bwg.chromsToIDs[e];if(void 0===a)return n([]);this.getFirstAdjacentById(a,t,i,n)},d.prototype.getFirstAdjacentById=function(e,t,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(e,t,i,n)});var s=null,o=-1,l=-1,d=0,c=(Date.now(),function(e,t){d+=e.length;for(var i,n=4+32*a.cirBlockSize,s=0;s<e.length;++s){var o=new h(e[s],e[s]+n);i=i?f(i,o):o}for(var r=i.ranges(),l=0;l<r.length;++l){var c=r[l];u(e,c,t)}}),u=function(o,r,l,c){r.max(),r.min();a.bwg.data.slice(r.min(),r.max()-r.min()).fetch(function(c){for(var 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v=d/4,w=p[v],b=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(w<e||w==e&&b<=t)&&y>=e||i>0&&(y>e||y==e&&x>=t)&&w<=e)&&($<0||x>S)&&($=k,S=i<0?x:b,i<0?y:w),d+=24}$>=0&&c([$],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(e,t,i){var n,a=i-t;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var s=0;s<this.zoomLevels.length;s++)if(a/this.zoomLevels[s].reduction<25e3){n=this.getZoomedView(s);break}return n.readWigData(e,t,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var e=4e3;this.zoomLevels[0]&&(e=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,e,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(e){var t=this.zoomLevels[e];return t.view||(t.view=new d(this,t.indexOffset,4e3,!0)),t.view},l.prototype._tsFetch=function(e,t,i,n,a){var s=this;if(!(e>=this.zoomLevels.length-1)){var o;return 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e||(e=c),i&&(i=!1),this.istate=new t,this.istate.inflateInit(this,i?-e:e)},e.prototype.inflate=function(e){return null==this.istate?-2:this.istate.inflate(this,e)},e.prototype.inflateEnd=function(){if(null==this.istate)return-2;var e=istate.inflateEnd(this);return this.istate=null,e},e.prototype.inflateSync=function(){return istate.inflateSync(this)},e.prototype.inflateSetDictionary=function(e,t){return istate.inflateSetDictionary(this,e,t)},t.prototype.inflateReset=function(e){return null==e||null==e.istate?-2:(e.total_in=e.total_out=0,e.msg=null,e.istate.mode=0!=e.istate.nowrap?7:0,e.istate.blocks.reset(e,null),f)},t.prototype.inflateEnd=function(e){return null!=this.blocks&&this.blocks.free(e),this.blocks=null,f},t.prototype.inflateInit=function(e,t){return e.msg=null,this.blocks=null,nowrap=0,t<0&&(t=-t,nowrap=1),t<8||t>15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<<t),this.inflateReset(e),f)},t.prototype.inflate=function(e,t){var i,n;if(null==e||null==e.istate||null==e.next_in)return-2;for(t=4==t?m:f,i=m;;)switch(e.istate.mode){case 0:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,8!=(15&(e.istate.method=e.next_in[e.next_in_index++]))){e.istate.mode=13,e.msg="unknown compression method",e.istate.marker=5;break}if(8+(e.istate.method>>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<<e.istate.wbits&&(a=(1<<e.istate.wbits)-1,n=i-a),e.istate.blocks.set_dictionary(t,n,a),e.istate.mode=7,f)};var S=[0,0,255,255];t.prototype.inflateSync=function(e){var t,i,n,a,s;if(null==e||null==e.istate)return-2;if(13!=e.istate.mode&&(e.istate.mode=13,e.istate.marker=0),0==(t=e.avail_in))return m;for(i=e.next_in_index,n=e.istate.marker;0!=t&&n<4;)e.next_in[i]==S[n]?n++:n=0!=e.next_in[i]?0:4-n,i++,t--;return e.total_in+=i-e.next_in_index,e.next_in_index=i,e.avail_in=t,e.istate.marker=n,4!=n?-3:(a=e.total_in,s=e.total_out,this.inflateReset(e),e.total_in=a,e.total_out=s,e.istate.mode=7,f)},t.prototype.inflateSyncPoint=function(e){return null==e||null==e.istate||null==e.istate.blocks?-2:e.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(e,t){t&&(t[0]=this.check),6==this.mode&&this.codes.free(e),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(e.adler=this.check=e._adler.adler32(0,null,0,0))},i.prototype.proc=function(e,t){var i,n,a,r,l,d,c;for(r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),m=[],v=[];s(u,h,m,v,e),this.codes.init(u[0],h[0],m[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(t=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var w=0;w<i;w++)this.blens[w]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,b,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&_[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&_[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(w=18==y?7:y-14,b=18==y?11:3;a<i+w;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(n>>>=i,a-=i,b+=n&_[w],n>>>=w,a-=w,w=this.index,i=this.table,w+b>258+(31&i)+(i>>5&31)||16==y&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);y=16==y?this.blens[w-1]:0;do{this.blens[w++]=y}while(0!=--b);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),m=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,m,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,m[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);mode=12;case 8:return t=p,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);case 9:return t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);default:return t=-2,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}},i.prototype.free=function(e){this.reset(e,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(e,t,i){o(e,t,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(e,t){var i,n,a;return n=e.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.len+=c&_[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.dist+=c&_[n],c>>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);e.window[r++]=e.window[d++],l--,d==e.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,e.window[r++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,e.read!=e.write)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);this.mode=8;case 8:return i=p,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 9:return i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);default:return i=-2,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i)}},n.prototype.free=function(e){},n.prototype.inflate_fast=function(e,t,i,n,a,s,r,l){var d,c,u,h,m,g,v,w,b,y,x,k,C,$,S,T;v=l.next_in_index,w=l.avail_in,m=r.bitb,g=r.bitk,b=r.write,y=b<r.read?r.read-b-1:r.end-b,x=_[e],k=_[t];do{for(;g<20;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if(d=m&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(m&_[h]),m>>=h,g-=h;g<15;)w--,m|=(255&l.next_in[v++])<<g,g+=8;for(d=m&k,c=a,u=s,T=3*(u+d),h=c[T];;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if($=c[T+2]+(m&_[h]),m>>=h,g-=h,y-=C,b>=$)S=b-$,r.window[b++]=r.window[S++],r.window[b++]=r.window[S++],C-=2;else{S=b-$;do{S+=r.end}while(S<0);if(h=r.end-S,C>h){if(C-=h,b-S>0&&h>b-S)do{r.window[b++]=r.window[S++]}while(0!=--h);else o(r.window,S,r.window,b,h),b+=h,S+=h,h=0;S=0}}do{r.window[b++]=r.window[S++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3;d+=c[T+2],d+=m&_[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3);if(d+=c[T+2],d+=m&_[h],T=3*(u+d),0==(h=c[T])){m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--;break}}else m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--}while(y>=258&&w>=10);return C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,f},a.prototype.huft_build=function(e,t,i,n,a,s,r,l,d,c,h){var p,_,g,v,w,b,y,x,k,C,$,S,T,M,E;C=0,w=i;do{this.c[e[t+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return r[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(y=b,x<b&&(x=b),w=15;0!=w&&0==this.c[w];w--);for(g=w,x>w&&(x=w),l[0]=x,M=1<<b;b<w;b++,M<<=1)if((M-=this.c[b])<0)return-3;if((M-=this.c[w])<0)return-3;for(this.c[w]+=M,this.x[1]=b=0,C=1,T=2;0!=--w;)this.x[T]=b+=this.c[C],T++,C++;w=0,C=0;do{0!=(b=e[t+C])&&(this.v[this.x[b]++]=w),C++}while(++w<i);for(i=this.x[g],this.x[0]=w=0,C=0,v=-1,S=-x,this.u[0]=0,$=0,E=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>S+x;){if(v++,S+=x,E=g-S,E=E>x?x:E,(_=1<<(b=y-S))>p+1&&(_-=p+1,T=y,b<E))for(;++b<E&&!((_<<=1)<=this.c[++T]);)_-=this.c[T];if(E=1<<b,this.hn[0]+E>u)return-3;this.u[v]=$=this.hn[0],this.hn[0]+=E,0!=v?(this.x[v]=w,this.r[0]=b,this.r[1]=x,b=w>>>S-x,this.r[2]=$-this.u[v-1]-b,o(this.r,0,d,3*(this.u[v-1]+b),3)):r[0]=$}for(this.r[1]=y-S,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=s[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),_=1<<y-S,b=w>>>S;b<E;b+=_)o(this.r,0,d,3*($+b),3);for(b=1<<y-1;0!=(w&b);b>>>=1)w^=b;for(w^=b,k=(1<<S)-1;(w&k)!=this.x[v];)v--,S-=x,k=(1<<S)-1}return 0!=M&&1!=g?m:f},a.prototype.inflate_trees_bits=function(e,t,i,n,a){var s;return this.initWorkArea(19),this.hn[0]=0,s=this.huft_build(e,0,19,19,null,null,i,t,n,this.hn,this.v),-3==s?a.msg="oversubscribed dynamic bit lengths tree":s!=m&&0!=t[0]||(a.msg="incomplete dynamic bit lengths tree",s=-3),s},a.prototype.inflate_trees_dynamic=function(e,t,i,n,a,s,o,r,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,e,257,x,k,s,n,r,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,e,t,0,C,$,o,a,r,this.hn,this.v),d!=f||0==a[0]&&e>257?(-3==d?l.msg="oversubscribed distance tree":d==m?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(e){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(e),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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n={id:i.name,icon:i.config.icon,url:i.config.url,tooltip:i.config.tooltip,onclick:i.config.function&&new Function(i.config.function)};Galaxy.page?Galaxy.page.masthead.collection.add(n):Galaxy.masthead&&Galaxy.masthead.collection.add(n),p.default.appendScriptStyle(i)}})})}}),Galaxy.user.get("is_admin")&&this.add({id:"admin",title:(0,h.default)("Admin"),url:"admin",tooltip:(0,h.default)("Administer this Galaxy"),cls:"admin-only"});var i={id:"help",title:(0,h.default)("Help"),tooltip:(0,h.default)("Support, contact, and community"),menu:[{title:(0,h.default)("Support"),url:e.support_url,target:"_blank"},{title:(0,h.default)("Search"),url:e.search_url,target:"_blank"},{title:(0,h.default)("Mailing Lists"),url:e.mailing_lists,target:"_blank"},{title:(0,h.default)("Videos"),url:e.screencasts_url,target:"_blank"},{title:(0,h.default)("Wiki"),url:e.wiki_url,target:"_blank"},{title:(0,h.default)("How to Cite Galaxy"),url:e.citation_url,target:"_blank"},{title:(0,h.default)("Interactive 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e=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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e=s.defaults(e||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),e.url=t._formatUrl(e.url),n("<li/>").append(n("<a/>").attr("href",e.url).attr("target",e.target).html(e.title).on("click",function(i){i.preventDefault(),t.model.set("show_menu",!1),e.onclick?e.onclick():Galaxy.frame.add(e)}))},_toggleClick:function(e){var t=this,i=this.model;if(e.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(e){i.id!==e.id&&e.get("menu")&&e.set("show_menu",!1)}),i.get("disabled")){var a=function(e,t){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+t).html(e)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){t.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(e){return"string"==typeof e&&-1===e.indexOf("//")&&"/"!=e.charAt(0)?Galaxy.root+e:e},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});t.default={Collection:m,Tab:_}}).call(t,i(1),i(0),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(9),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(e){var t=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),r=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+r,d=t+":"+i+l,c=null,u=null,h='<iframe 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r.default.View({visible:!1}),this.setElement(this.frames.$el),this.buttonActive=e.collection.add({id:"enable-scratchbook",icon:"fa-th",tooltip:(0,m.default)("Enable/Disable Scratchbook"),onclick:function(){t.active=!t.active,t.buttonActive.set({toggle:t.active,show_note:t.active,note_cls:t.active&&"fa fa-check"}),!t.active&&t.frames.hide()},onbeforeunload:function(){if(t.frames.length()>0)return"You opened "+t.frames.length()+" frame(s) which will be lost."}}),this.buttonLoad=e.collection.add({id:"show-scratchbook",icon:"fa-eye",tooltip:(0,m.default)("Show/Hide Scratchbook"),show_note:!0,visible:!1,onclick:function(e){t.frames.visible?t.frames.hide():t.frames.show()}}),this.frames.on("add remove",function(){this.visible&&0==this.length()&&this.hide(),t.buttonLoad.set({note:this.length(),visible:this.length()>0})}).on("show hide ",function(){t.buttonLoad.set({toggle:this.visible,icon:this.visible&&"fa-eye"||"fa-eye-slash"})}),this.history_cache={}},addDataset:function(e){var 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t=this;if(t.options.patchExisting&&e)for(var i in e)e.hasOwnProperty(i)&&(t[i]=e[i])},s.prototype._initLogger=function(e){var t=this;if(t.config.debug){e.consoleLogger=e.consoleLogger||console,e.consoleLevel=e.consoleLevel||m.default.MetricsLogger.ALL;try{e.consoleNamespaceWhitelist=localStorage.getItem(b).split(",")}catch(e){}try{e.consoleFlattenMessages="true"==localStorage.getItem("galaxy:debug:flatten")}catch(e){}console.log(e.consoleFlattenMessages)}return t.logger=new m.default.MetricsLogger(e),t.emit={},["log","debug","info","warn","error","metric"].map(function(e){t.emit[e]=function(i){t.logger.emit(e,arguments[0],Array.prototype.slice.call(arguments,1))}}),t.config.debug&&(u.default.LoggableMixin.logger=t.logger),t},s.prototype._initLocale=function(e){var t=this;return t.debug("_initLocale:",e),t.localize=w.default,window._l=t.localize,t},s.prototype._initUser=function(e){var t=this;return t.debug("_initUser:",e),t.user=new 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u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new r.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),a=t[n];if(a){var s=new a(i,t);i[s.toString()]=s,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:s})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='<label class="prompt">'+(0,l.default)("Tags")+"</label>",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return'<input class="tags-input" value="'+this.tagsToCSV()+'"/>'},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t='<span class="label label-info">'+e+"</span>";i.push(t)}),0===i.length&&i.push("<img src="+t+' class="add-tag-button" title="Add tags"/>'),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(0),s=n(a),o=i(61),r=n(o),l=i(4),d=n(l),c=s.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),c.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=r.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3);!function(e){e&&e.__esModule}(s);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),a.each(this.options.parameters,function(t){var i=n("<div/>").addClass("upload-"+t.id+" upload-icon-button fa").addClass(e.model.get(t.id)&&e.options.class_check||e.options.class_uncheck).on("click",function(){e.model.get("enabled")&&e.model.set(t.id,!e.model.get(t.id))});e.$table.append(n("<tr/>").append(n("<td/>").append(i)).append(n("<td/>").append(t.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=function(e){return e&&e.__esModule?e:{default:e}}(s);t.default=e.View.extend({initialize:function(t){this.model=new e.Model({cls:"upload-ftp",class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",help_enabled:!0,help_text:"This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>"+t.ftp_upload_site+"</strong> using your Galaxy credentials.",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}).set(t),this.collection=this.model.get("collection"),this.setElement(this._template()),this.$content=this.$(".upload-ftp-content"),this.$wait=this.$(".upload-ftp-wait"),this.$help=this.$(".upload-ftp-help"),this.$number=this.$(".upload-ftp-number"),this.$disk=this.$(".upload-ftp-disk"),this.$body=this.$(".upload-ftp-body"),this.$warning=this.$(".upload-ftp-warning"),this.$select=this.$(".upload-ftp-select-all"),this.render()},render:function(){var e=this;this.$wait.show(),this.$content.hide(),this.$warning.hide(),this.$help.hide(),n.ajax({url:Galaxy.root+"api/remote_files",method:"GET",success:function(t){e.model.set("ftp_files",t),e._index(),e._renderTable()},error:function(){e._renderTable()}})},_renderTable:function(){var e=this,t=this.model.get("ftp_files");if(this.rows=[],t&&t.length>0){this.$body.empty();var i=0;a.each(t,function(t){e.rows.push(e._renderRow(t)),i+=t.size}),this.$number.html(t.length+" files"),this.$disk.html(o.default.bytesToString(i,!0)),this.collection&&(this.$("._has_collection").show(),this.$select.addClass(this.model.get("class_add")).off().on("click",function(){e._all()}),this._refresh()),this.$content.show()}else this.$warning.show();this.model.get("help_enabled")&&this.$help.show(),this.$wait.hide()},_renderRow:function(e){var t=this,i=this.model.attributes,a=n(this._templateRow(e)),s=a.find(".icon");if(this.$body.append(a),this.collection){var o=this.ftp_index[e.path];s.addClass(void 0===o?i.class_add:i.class_remove),a.on("click",function(){t._switch(s,e),t._refresh()})}else a.on("click",function(){i.onchange(e)});return s},_index:function(){var e=this;this.ftp_index={},this.collection&&this.collection.each(function(t){"ftp"==t.get("file_mode")&&(e.ftp_index[t.get("file_path")]=t.id)})},_all:function(){var e=this.model.attributes,t=this.model.get("ftp_files"),i=this.$select.hasClass(e.class_add);for(var n in t){var a=t[n],s=this.ftp_index[a.path];(void 0===s&&i||void 0!==s&&!i)&&this._switch(this.rows[n],a)}this._refresh()},_switch:function(e,t){e.removeClass();var i=this.model.attributes,n=this.ftp_index[t.path];if(void 0===n){var a=i.onadd(t);e.addClass(i.class_remove),this.ftp_index[t.path]=a}else i.onremove(n),e.addClass(i.class_add),this.ftp_index[t.path]=void 0},_refresh:function(){var e=a.reduce(this.ftp_index,function(e,t){return void 0!==t&&e++,e},0);this.$select.removeClass(),0==e?this.$select.addClass(this.model.get("class_add")):this.$select.addClass(e==this.rows.length?this.model.get("class_remove"):this.model.get("class_partial"))},_templateRow:function(e){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+a.escape(e.path)+'</td><td class="ftp-size">'+o.default.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_template:function(){return'<div class="'+this.model.get("cls")+'"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">'+this.model.get("help_text")+'</div><div class="upload-ftp-content"><span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(165)),r=a(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new r.default.View({placement:e.placement||"bottom",container:e.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."}})}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},t),a=n.data;if(a.error_message)return void n.error(a.error_message);var s=new FormData;for(var o in a.payload)s.append(o,a.payload[o]);var r=0;for(var o in a.files){var l=a.files[o];s.append(l.name,l.file,l.file.name),r+=l.file.size}if(r>1048576*n.maxfilesize)return void n.error(n.error_filesize);var d=new XMLHttpRequest;d.open("POST",n.url,!0),d.setRequestHeader("Accept","application/json"),d.setRequestHeader("Cache-Control","no-cache"),d.setRequestHeader("X-Requested-With","XMLHttpRequest"),d.onreadystatechange=function(){if(d.readyState==d.DONE){var t=null,i="";if(d.responseText)try{t=e.parseJSON(d.responseText),i=t.err_msg}catch(e){t=d.responseText,i=t}if(d.status<200||d.status>299){var a=d.statusText;403==d.status?a=n.error_login:0==d.status?a=n.error_server:a||(a=n.error_default),n.error(a+" ("+d.status+"). 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t.name===e.name&&t.size===e.size}).length&&(e.duplicate=!0)}),t.each(e,function(e){e.duplicate||(i=String(p++),f[i]=e,h.announce(i,f[i]),m++)}),i}}function a(e){f[e]&&(delete f[e],m--)}function s(){if(0==m||g)return g=!1,_=!1,void h.complete();_=!0;var e=-1;for(var t in f){e=t;break}f[e];a(e),i.uploadpost({url:h.url,data:h.initialize(e),success:function(t){h.success(e,t),s()},error:function(t){h.error(e,t),s()},progress:function(t){h.progress(e,t)}})}function o(){v.dialog()}function r(e){for(e in f)a(e)}function l(){_||(_=!0,s())}function d(){g=!0}function c(e){return h=i.extend({},h,e)}function u(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var h=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),f={},p=0,m=0,_=!1,g=!1,v=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:a,start:l,stop:d,reset:r,configure:c,compatible:u}}}(e)}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}function r(e,t){var i=e.toJSON();return C(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var l=i(188),d=o(l),c=i(166),u=o(c),h=i(8),f=o(h),p=i(207),m=o(p),_=i(9),g=o(_),v=i(208),w=(o(v),i(7)),b=o(w);i(209);var y=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['<a class="name" title="',(0,b.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,b.default)("Remove this dataset from the list"),'">',(0,b.default)("Discard"),"</button>"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,b.default)("Enter a new name for the element"),":\n(",(0,b.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,b.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:y,collectionClass:d.default.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;n.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset"!==e.history_content_type?(0,b.default)("is not a dataset"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,b.default)("has been deleted or purged"):null:(0,b.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(a(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content 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t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,b.default)("An error occurred");if(e.xhr){var n=e.xhr,a=e.message;0===n.readyState&&0===n.status?i+=": "+(0,b.default)("Galaxy could not be reached and may be updating.")+(0,b.default)(" Try again in a few minutes."):n.responseJSON?i+=":<br /><pre>"+JSON.stringify(n.responseJSON)+"</pre>":i+=": "+a}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart 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i=e.offset(),n=e.scrollTop(),a=t-i.top,s=i.top+e.outerHeight()-t;a>=0&&a<this.autoscrollDist?e.scrollTop(n-2):s>=0&&s<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestElement:function(e){for(var t=this.$(".collection-elements li.collection-element").toArray(),i=0;i<t.length;i++){var n=a(t[i]),s=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(s+o>e&&s-o<e)return n}return a()},_dropElements:function(e){e.originalEvent&&(e=e.originalEvent),e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestElement(e.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".collection-elements .collection-element").last()),this._syncOrderToDom(),!1},_syncOrderToDom:function(){var e=this,t=[];this.$(".collection-elements .collection-element").each(function(){var i=a(this).attr("data-element-id"),s=n.findWhere(e.workingElements,{id:i});s?t.push(s):console.error("missing element: 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class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,b.default)("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',(0,b.default)("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',(0,b.default)("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',(0,b.default)("Create list"),"</button>","</div>","</div>"].join("")),helpContent:n.template(["<p>",(0,b.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. 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",(0,b.default)("You may need to "),'<a class="cancel-create" href="javascript:void(0)">',(0,b.default)("cancel"),"</a> ",(0,b.default)("and reselect new elements"),".","</span>","</div>","</div>",'<div class="footer flex-row no-flex">','<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',(0,b.default)("Cancel"),"</button>","</div>","</div>","</div>"].join(""))}),toString:function(){return"ListCollectionCreator"}}),k=function(e,t,i){var a,o=s.Deferred(),r=Galaxy.modal||new g.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),a=new i(t),r.show({title:t.title||(0,b.default)("Create a collection"),body:a.$el,width:"80%",height:"100%",closing_events:!0}),a.render(),window._collectionCreator=a,o},C=function(e,t){return t=t||{},t.title=(0,b.default)("Create a collection from a list of 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r=i(192),l=o(r),d=i(193),c=(o(d),i(213)),u=o(c),h=i(3),f=o(h),p=i(8),m=o(p),_=i(7),g=o(_),v=e.Model.extend(m.default.LoggableMixin).extend(m.default.mixin(m.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:l.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,a){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,n.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,g.default)("(empty)")},toJSON:function(){return a.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:s.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,a){var s;try{s=new Date(a.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=s||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var a={history_id:this.id};e&&(a.current=!0),t&&(a.name=t),i||(a.all_datasets=!1),a.view="dev-detailed";var s=this,o=n.post(this.urlRoot,a);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,b=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return a.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),a.defaults(t,i)},fetchFirst:function(e){var t=this,i=s.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:a.extend(a.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,a.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,a){var s=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){s.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:b}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(213),r=s(o),l=i(214),d=s(l),c=i(188),u=s(c),h=i(193),f=s(h),p=i(253),m=s(p),_=i(8),g=s(_),v=i(215),w=s(v),b=r.default.PaginatedCollection,y=b.extend(g.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync add":this.trackJobStates}),t=t||{},b.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var e=this;this.each(function(t){if(!t.has("job_states_summary")&&"dataset_collection"===t.attributes.history_content_type){var i=t.attributes.job_source_type,n=t.attributes.job_source_id;if(i){e.jobStateSummariesCollection.add({id:n,model:i,history_id:e.history_id,collection_id:t.attributes.id});var a=e.jobStateSummariesCollection.get(n);t.jobStatesSummary=a}}})},model:function(e,t){if("dataset"===e.history_content_type)return new d.default.HistoryDatasetAssociation(e,t);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new u.default.HistoryListDatasetCollection(e,t);case"paired":return new u.default.HistoryPairDatasetCollection(e,t);case"list:paired":return new u.default.HistoryListPairedDatasetCollection(e,t);case"list:list":return new u.default.HistoryListOfListsDatasetCollection(e,t)}var i="Unknown collection_type: "+e.collection_type;return console.warn(i,e),{validationError:i}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(e){this.stopPolling(),this.historyId=e,e&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new m.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=e,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(e){return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(b.prototype.comparators),{name:g.default.buildComparator("name",{ascending:!0}),"name-dsc":g.default.buildComparator("name",{ascending:!1}),hid:g.default.buildComparator("hid",{ascending:!1}),"hid-asc":g.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,a=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,a){var s=i.get(t[n]);return s?e.concat(s):e},[]),i.ajaxQueue("save",a,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new w.default.AjaxQueue(n.slice().reverse().map(function(n,a){var s=e.isString(t)?n[t]:t;return function(){return s.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var r=e.extend(e.clone(t),{view:"summary",keys:l,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){s.fetch.call(s,r).fail(a.reject).done(function(e){a.notify(e,o,n),e.length!==o?(s.allFetched=!0,a.resolve(e,o,n)):i(n+o)})})}t=t||{};var a=n.Deferred(),s=this,o=t.limitPerCall||s.limitPerProgressiveFetch,r=d.default.HistoryDatasetAssociation.prototype.searchAttributes,l=r.join(",");return i(),a},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,a,s;e.isString(t)?(i=t,s="hda",a="dataset"):(i=t.id,s={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",a="hdca"===s?"dataset_collection":"dataset");var o=this,r=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:s,type:a})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,r,{},"Error copying contents",{type:a,id:i,source:s})});return r},createHDCA:function(e,t,i,n,a){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(a)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=a.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:y}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(8),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return s.storageKeyPrefix+e},get:function(e){return new s({id:s.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(s.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:s}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(8),l=o(r),d=i(7),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:l.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:l.default.wrapTemplate(['<div class="subtitle"></div>']),details:l.default.wrapTemplate(['<div class="details"></div>'])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['<div class="details">',"</div>"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(194),l=o(r),d=i(166),c=o(d),u=i(175),h=o(u),f=i(8),p=o(f),m=i(7),_=o(m),g=l.default.ListItemView,v=g.extend({_logNamespace:"dataset",className:g.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),g.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return g.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,_.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,_.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,_.default)("This dataset is not yet viewable");else{t.title=(0,_.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return s(this.templates.noAccess(this.model.toJSON(),this));var e=g.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=s('<div class="detail-messages"></div>'),n=t.model.toJSON();return e.each(t.templates.detailMessages,function(e){i.append(s(e(n,t)))}),i},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case c.default.NOT_VIEWABLE:return[];case c.default.OK:case c.default.FAILED_METADATA:case c.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,h.default)({title:(0,_.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:e.isEmpty(this.model.get("meta_files"))?s(['<a class="download-btn icon-btn" ','href="',this.model.urls.download,'" title="'+(0,_.default)("Download")+'" download>','<span class="fa fa-floppy-o"></span>',"</a>"].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return s(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+(0,_.default)("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+t.download+'" download>',(0,_.default)("Download dataset"),"</a></li>",e.map(this.model.get("meta_files"),function(e){return['<li><a href="',t.meta_download+e.file_type,'">',(0,_.default)("Download")," ",e.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:e.extend(e.clone(g.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){return"DatasetListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=e.extend({},g.prototype.templates.warnings,{failed_metadata:p.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',(0,_.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,_.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,_.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,_.default)("This dataset has been deleted"),"</div>","<% } %>"])}),i=p.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),n=p.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,_.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),a={};a[c.default.OK]=a[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,_.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,_.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),a[c.default.NEW]=p.default.wrapTemplate(["<div>",(0,_.default)("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset"),a[c.default.NOT_VIEWABLE]=p.default.wrapTemplate(["<div>",(0,_.default)("You do not have permission to view this dataset"),"</div>"],"dataset"),a[c.default.DISCARDED]=p.default.wrapTemplate(["<div>",(0,_.default)("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),a[c.default.QUEUED]=p.default.wrapTemplate(["<div>",(0,_.default)("This job is waiting to run"),"</div>"],"dataset"),a[c.default.RUNNING]=p.default.wrapTemplate(["<div>",(0,_.default)("This job is currently running"),"</div>"],"dataset"),a[c.default.UPLOAD]=p.default.wrapTemplate(["<div>",(0,_.default)("This dataset is currently uploading"),"</div>"],"dataset"),a[c.default.SETTING_METADATA]=p.default.wrapTemplate(["<div>",(0,_.default)("Metadata is being auto-detected"),"</div>"],"dataset"),a[c.default.PAUSED]=p.default.wrapTemplate(["<div>",(0,_.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),a[c.default.ERROR]=p.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',(0,_.default)("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),a[c.default.EMPTY]=p.default.wrapTemplate(["<div>",(0,_.default)("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),a.unknown=p.default.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var s={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',(0,_.default)("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},o=p.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return e.extend({},g.prototype.templates,{warnings:t,details:i,noAccess:n,summaries:a,detailMessages:s,displayApplications:o})}(),t.default={DatasetListItemView:v}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(194),r=s(o),l=i(195),d=s(l),c=i(8),u=s(c),h=i(7),f=s(h),p=r.default.FoldoutListItemView,m=r.default.ListItemView,_=p.extend({className:p.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,p.prototype.initialize.call(this,e)},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,i){e.has(t.changed,"deleted")?this.render():e.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=e.extend({},p.prototype.templates.warnings,{error:u.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","</div>","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,f.default)("This collection has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,f.default)("This collection has been deleted"),"</div>","<% } %>"])}),i=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection"),n=u.default.wrapTemplate(['<div class="subtitle">','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<%        if( collection.collection_type === "list" ){ %>',(0,f.default)("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,f.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,f.default)("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,f.default)("a list of <%- countText %>dataset lists"),"<% } %>","</div>"],"collection");return e.extend({},p.prototype.templates,{warnings:t,titleBar:i,subtitle:n})}();var g=m.extend({className:m.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),m.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return e.extend({},m.prototype.templates,{titleBar:t})}();var v=d.default.DatasetListItemView.extend({className:d.default.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),d.default.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):a.when()},toString:function(){return"DatasetDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var w=_.extend({className:_.prototype.className+" dataset-collection-element",_swapNewRender:function(e){_.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:_,DCEListItemView:g,DatasetDCEListItemView:v,NestedDCDCEListItemView:w}}).call(t,i(2),i(0),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(20),o=a(s),r=i(4),l=a(r),d=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.url=this.model.get("url"),this.redirect=this.model.get("redirect"),this.setElement("<div/>"),this.render()},render:function(){var e=this;n.ajax({url:Galaxy.root+this.url,type:"GET"}).done(function(t){var i=n.extend({},e.model.attributes,t),a=new o.default({title:i.title,message:i.message,status:i.status||"warning",icon:i.icon,inputs:i.inputs,buttons:{submit:new l.default.Button({tooltip:i.submit_tooltip,title:i.submit_title||"Save",icon:i.submit_icon||"fa-save",cls:"btn btn-primary ui-clear-float",onclick:function(){e._submit(a)}})}});e.$el.empty().append(a.$el)}).fail(function(t){e.$el.empty().append(new l.default.Message({message:"Failed to load resource "+e.url+".",status:"danger",persistent:!0}).$el)})},_submit:function(e){var t=this;n.ajax({url:Galaxy.root+t.url,data:JSON.stringify(e.data.create()),type:"PUT",contentType:"application/json"}).done(function(i){var a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},t.redirect?window.location=Galaxy.root+t.redirect+"?"+n.param(a):(e.data.matchModel(i,function(t,i){e.field_list[i].value(t.value)}),t._showMessage(e,success_message))}).fail(function(i){t._showMessage(e,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(e,t){e.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),e.message.update(t)}});t.default={View:d}}).call(t,i(1),i(0))},,,,,,,,function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(166),r=s(o),l=i(8),d=s(l),c=i(7),u=s(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:r.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
 //!! this state is not in trans.app.model.Dataset.states - set it here -
-this.get("accessible")||this.set("state",r.default.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/edit?dataset_id="+e,download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return n.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return n.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=n.contains(r.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var i=this;return e.Model.prototype.fetch.call(this,t).always(function(){i._generateUrls()})},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},save:function(t,i){return i=i||{},i.wait=!!n.isUndefined(i.wait)||i.wait,e.Model.prototype.save.call(this,t,i)},delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?a.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return a.when();e=e||{},e.url=this.urls.purge;var t=this,i=a.ajax(e);return i.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),i.fail(function(i,n,a){var s=(0,u.default)("Unable to purge dataset");i.responseJSON&&i.responseJSON.error?s=i.responseJSON.error:-1!==i.responseText.indexOf("Removal of datasets by users is not allowed in this Galaxy instance")&&(s="Removal of datasets by users is not allowed in this Galaxy instance"),i.responseText=s,t.trigger("error",t,i,e,(0,u.default)(s),{error:s})}),i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=a.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=e.call(a,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:a})}),l.always(function(e){s.push(e),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return 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.search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:n.bind(this._firstSearch,this),onsearch:n.bind(this.searchItems,this),onclear:n.bind(this.clearSearch,this)}),e},_firstSearch:function(e){return this.log("onFirstSearch",e),this.searchItems(e)},searchItems:function(e,t){if(this.log("searchItems",e,this.searchFor,t),!t&&this.searchFor===e)return this;this.searchFor=e,this.renderItems(),this.trigger("search:searching",e,this);var i=this.$("> .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]),controls:u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- view.title %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=a(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- model.name %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function a(){return['<input type="text" name="',t.name,'" placeholder="',t.placeholder,'" ','class="search-query ',t.classes,'" ',"/>"].join("")}var l=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===s.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===s.default.type(t)&&(t=s.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(a()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===l&&t.escWillClear)i.call(this,e);else{var a=o(this).val();(e.which===d||t.minSearchLen&&a.length>=t.minSearchLen)&&n.call(this,e,a)}}).val(t.initialVal)}(),function(){return o(['<span class="search-clear fa fa-times-circle" ','title="',r("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o(['<span class="search-loading fa fa-spinner fa-spin" ','title="',r("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}()]))}var a=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=s.default,r=window._l||function(e){return e};s.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(195),s=n(a),o=i(8),r=n(o),l=i(218),d=n(l),c=i(7),u=n(c),h=s.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+"</span>\n            </div>\n            </br>\n            "+d.default.nametagTemplate(t)+"\n        </div>\n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:r.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,u.default)("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function i(t){return 0==t.indexOf("name:")?'<span class="label label-info">'+e.escape(t.slice(5))+"</span>":""}function n(t){return'<span class="nametags">'+e.sortBy(e.uniq(t.tags)).map(i).join("")+"</span>"}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(166),s=n(a),o=i(196),r=n(o),l=i(220),d=n(l),c=i(8),u=(n(c),i(218)),h=n(u),f=i(7),p=n(f),m=r.default.DCListItemView,_=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){m.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:tags change:populated change:visible":function(e,t){this.render()}})},_getFoldoutPanelClass:function(){var e=this.model.get("collection_type");switch(e){case"list":return d.default.ListCollectionView;case"paired":return d.default.PairCollectionView;case"list:paired":return d.default.ListOfPairsCollectionView;case"list:list":return d.default.ListOfListsCollectionView}throw new TypeError("Unknown collection_type: "+e)},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t=this.model.get("populated")?s.default.OK:s.default.RUNNING;return this.$el.addClass("state-"+t),this.$el},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+'</span>\n            </div>\n            <div class="subtitle"></div>\n            '+h.default.nametagTemplate(t)+"\n        </div>\n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:_}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(215),s=n(a),o=i(189),r=(n(o),i(196)),l=n(r),d=i(8),c=n(d),u=i(7),h=n(u),f=s.default.ModelListPanel,p=f.extend({_logNamespace:"collections",className:f.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:l.default.DatasetDCEListItemView,NestedDCDCEViewClass:l.default.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(e){f.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=f.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return f.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});p.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',(0,h.default)("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',(0,h.default)("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,h.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,h.default)("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,h.default)("a list of dataset lists"),"<% } %>","</div>","</div>",'<div class="tags-display"></div>','<div class="actions">','<a class="download-btn icon-btn" ','href="<%- view.downloadUrl %>','" title="" download="" data-original-title="Download Collection">','<span class="fa fa-floppy-o"></span>',"</a>","</div>","</div>"],"collection");return e.extend(e.clone(f.prototype.templates),{controls:t})}();var m=p.extend({DatasetDCEViewClass:l.default.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),_=m.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),g=p.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemView.extend({foldoutPanelClass:_}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),v=p.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemView.extend({foldoutPanelClass:_}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionView:p,ListCollectionView:m,PairCollectionView:_,ListOfPairsCollectionView:g,ListOfListsCollectionView:v}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(166),o=a(s),r=i(195),l=a(r),d=i(181),c=a(d),u=i(222),h=a(u),f=i(175),p=a(f),m=i(8),_=a(m),g=i(7),v=a(g),w=l.default.DatasetListItemView,b=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),a={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(a.disabled=!0,i?a.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(a.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(a.disabled=!0,a.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(a)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,a=function(t){var a='<div id="thdiv-'+e+'" class="toolhelp">';t.name&&t.help?(a+="<strong>Tool help for "+t.name+"</strong><hr/>",a+=t.help):a+="<strong>Tool help is unavailable for this dataset.</strong><hr/>",a+="</div>",i.$el.find(".details").append(n.parseHTML(a))},s=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){a(e)}).fail(function(){a({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){s(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});b.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:_.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',(0,v.default)("An error occurred setting the metadata for this dataset"),'<br /><a href="<%- dataset.urls.edit %>" target="_top">',(0,v.default)("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:_.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,v.default)("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',(0,v.default)("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',(0,v.default)("Permanently remove it from 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e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:b}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r);i(25);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var 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n=l.default.extend({routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)user(/)":"show_user","(/)user(/)(:form_id)":"show_user_form","(/)pages(/)create(/)":"show_pages_create","(/)pages(/)edit(/)":"show_pages_edit","(/)pages(/)(:action_id)":"show_pages","(/)visualizations(/)edit(/)":"show_visualizations_edit","(/)visualizations/(:action_id)":"show_visualizations","(/)workflows/import_workflow":"show_import_workflow","(/)workflows/run(/)":"show_run","(/)workflows(/)list":"show_workflows","(/)workflows/list_published(/)":"show_workflows_published","(/)workflows/create(/)":"show_workflows_create","(/)histories(/)citations(/)":"show_history_citations","(/)histories(/)rename(/)":"show_histories_rename","(/)histories(/)import(/)":"show_histories_import","(/)histories(/)permissions(/)":"show_histories_permissions","(/)histories(/)(:action_id)":"show_histories","(/)datasets(/)list(/)":"show_datasets","(/)custom_builds":"show_custom_builds","(/)datasets/edit":"show_dataset_edit_attributes","(/)datasets/error":"show_dataset_error"},require_login:["show_user","show_user_form","show_workflows"],authenticate:function(e,t){return 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F.default.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new _.default.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#galaxy_main").prop("src",e)},_loadWorkflow:function(){var e=this;V.default.get({url:Galaxy.root+"api/workflows/"+V.default.getQueryString("id")+"/download?style=run",success:function(t){e.page.display(new L.default.View(t))},error:function(t){var i=t.err_msg||"Error occurred while loading the resource.",n={message:i,status:"danger",persistent:!0};e.page.display(new U.default.Message(n))}})}});K(function(){Galaxy.page=new p.default.View(e.extend(t,{Left:c.default,Right:h.default,Router:n}))})}}).call(t,i(2))},function(e,t,i){"use 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e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:(0,c.default)("All workflows"),href:"workflow"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflows/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['<div class="toolTitle">','<a href="',this.root,e.href,'" target="galaxy_main">',e.title,"</a>","</div>"].join("")},_templateAllWorkflow:function(e){return['<div class="toolTitle">','<a href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_templateWorkflowLink:function(e){return['<div class="toolTitle">','<a class="'+e.cls+' " href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_template:function(){return['<div class="toolMenuContainer">','<div class="toolMenu" style="display: none">','<div 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try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=s.default.merge(e,this.options),this.ui_button=new u.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;s.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:i<n?-1:0}),t.options.datatypes_disable_auto||t.list_extensions.unshift(t.options.auto)}}),s.default.get({url:Galaxy.root+"api/genomes",success:function(e){for(var i in e)t.list_genomes.push({id:e[i][1],text:e[i][0]});t.list_genomes.sort(function(e,i){return e.id==t.options.default_genome?-1:i.id==t.options.default_genome?1:e.text>i.text?1:e.text<i.text?-1:0})}})},show:function(){var e=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model)return void window.setTimeout(function(){e.show()},500);this.current_user=Galaxy.user.id,this.modal||(this.tabs=new d.default.View,this.default_view=new f.default(this),this.tabs.add({id:"regular",title:"Regular",$el:this.default_view.$el}),this.composite_view=new m.default(this),this.tabs.add({id:"composite",title:"Composite",$el:this.composite_view.$el}),this.collection_view=new g.default(this),this.tabs.add({id:"collection",title:"Collection",$el:this.collection_view.$el}),this.modal=new r.default.View({title:"Download from web or upload from disk",body:this.tabs.$el,height:this.options.height,width:this.options.width,closing_events:!0,title_separator:!1})),this.modal.show()},currentHistory:function(){return this.current_user&&Galaxy.currHistoryPanel.model.get("id")},currentFtp:function(){return this.current_user&&this.options.ftp_upload_site},toData:function(e,t){var i={payload:{tool_id:"upload1",history_id:t||this.currentHistory(),inputs:{}},files:[],error_message:null};if(e&&e.length>0){var n={file_count:e.length,dbkey:e[0].get("genome","?"),file_type:e[0].get("extension","auto")};for(var a in e){var s=e[a];if(s.set("status","running"),!(s.get("file_size")>0)){i.error_message="Upload content incomplete.",s.set("status","error"),s.set("info",i.error_message);break}var o="files_"+a+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=s.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=s.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=s.get("genome",null),n[o+"file_type"]=s.get("extension",null),s.get("file_mode")){case"new":n[o+"url_paste"]=s.get("url_paste");break;case"ftp":n[o+"ftp_files"]=s.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:s.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(1))},function(e,t,i){"use strict";(function(e,i){Object.defineProperty(t,"__esModule",{value:!0});var n=e.View.extend({initialize:function(t){var n=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load 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e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(243),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(244),x=s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local file",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new x.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new c.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&a.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Type (set all):</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139),p=s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});var a=this.app.select_genome.value(),s=this.app.select_extension.value();this.select_genome=new p.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:a,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new p.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:s,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:a,extension:s}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-extension" style="float: left;"/>&nbsp;&nbsp<div class="upload-extension-info upload-icon-button fa fa-search"/></td><td><div class="upload-genome"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(e){this.$container=e.$container,this.collection=e.collection,this.new_content=e.new_content,this.max=e.max||50,this.content_list={},this.$message=i("<div/>").addClass("ui-limitloader").append("...only the first "+this.max+" entries are visible."),this.$container.append(this.$message),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add",this._refresh,this),this.listenTo(this.collection,"remove",this._remove,this)},_done:function(){var e=n.size(this.content_list)>this.max;return this.$message[e?"show":"hide"](),e},_reset:function(){n.each(this.content_list,function(e){e.remove()}),this.content_list={},this.$message.hide()},_remove:function(e){var t=e.id,i=this.content_list[t];i&&(i.remove(),delete this.content_list[t]),this._refresh()},_refresh:function(){if(!this._done())for(var e in this.collection.models){var t=this.collection.models[e];this.content_list[t.id];if(!this.content_list[t.id]){var i=this.new_content(t);if(this.content_list[t.id]=i,this._done())break}}}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(246),c=s(d),u=i(185),h=s(u),f=i(165),p=(s(f),i(139)),m=s(p),_=i(4),g=s(_);t.default=e.View.extend({collection:new l.default.Collection,initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new g.default.Button({title:"Start",onclick:function(){t._eventStart()}}),this.btnClose=new g.default.Button({title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=n.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&n.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){new h.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new c.default(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),a.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_template:function(){return'<div class="upload-view-composite"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th/><th/><th>Description</th><th>Name</th><th>Size</th><th>Settings</th><th>Status</th></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Composite Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome/Build:</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(183),d=s(l),c=i(184),u=s(c),h=i(165),f=s(h),p=i(4),m=s(p),_=i(139);s(_);i(186),t.default=e.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new m.default.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new f.default.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new f.default.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(a.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(r.default.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){e.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){"new"==this.model.get("file_mode")?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(r.default.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new u.default({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new d.default(this).$el),this.settings.show())},_template:function(){return'<tr class="upload-row"><td><div class="upload-source"/><div class="upload-text-column"><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-status"/></td><td><div class="upload-file-desc upload-title"/></td><td><div class="upload-file-name upload-title"/></td><td><div class="upload-file-size upload-size"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(248),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(187);s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local files",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP files",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnBuild=new b.default.Button({id:"btn-build",title:"Build",onclick:function(){t._eventBuild()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(i);var n=new c.default(this,{model:i});this.$(".upload-table > tbody:first").append(n.$el),this._updateScreen(),n.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=n.pluck(t.outputs,"hid"),a=this.collection.get(e);a.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,a.get("file_size"))),this.upload_completed+=100*a.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];n.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=n.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,a=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[a?"enable":"disable"](),this.btnFtp[a?"enable":"disable"](),this.btnCreate[a?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title-compressed">Collection Type:</span><span class="upload-footer-collection-type"/><span class="upload-footer-title-compressed">File Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title-compressed">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139);s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title-extended"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),s=n(a),o=i(250),r=n(o),l=i(251),d=n(l),c=i(7),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return['<div id="current-history-panel" class="history-panel middle"/>'].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t,i){return n.clone(m).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),r=a(o),l=i(211),d=a(l),c=i(8),u=(a(c),i(7)),h=a(u),f=i(40),p=a(f),m=[{html:(0,h.default)("History Lists"),header:!0},{html:(0,h.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,h.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,h.default)("Current History"),header:!0,anon:!0},{html:(0,h.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,h.default)("Copy History"),func:function(){(0,d.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Share or Publish"),href:"history/sharing"},{html:(0,h.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,h.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,h.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,h.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,h.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,h.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,h.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Purge Deleted Datasets"),confirm:(0,h.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,h.default)("Downloads"),header:!0},{html:(0,h.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,h.default)("Other Actions"),header:!0},{html:(0,h.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(t){var i=[];e.each(t.models,function(e,t){var n=t.toJSON();n.activate&&i.push({html:(0,h.default)(n.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,h.default)("Webhooks"),header:!0}),e.merge(m,i))}});var _=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,a=s(i,n,Galaxy.root);return new r.default(e,a)};t.default=_}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(191),r=(s(o),i(253)),l=s(r),d=i(8),c=s(d),u=i(7),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,m=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'<a class="uploader-link" href="javascript:void(0)">',(0,h.default)("load your own data"),"</a>",(0,h.default)(" or "),'<a class="get-data-link" href="javascript:void(0)">',(0,h.default)("get data from an external source"),"</a>"].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):a.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):a.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="quota-message errormessage">',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:m}}).call(t,i(2),i(0),i(0))},function(e,t,i){"use strict";(function(e){function i(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function n(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof t);e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,enumerable:!1,writable:!0,configurable:!0}}),t&&(Object.setPrototypeOf?Object.setPrototypeOf(e,t):e.__proto__=t)}function a(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}Object.defineProperty(t,"__esModule",{value:!0});var s=function e(t,i,n){null===t&&(t=Function.prototype);var a=Object.getOwnPropertyDescriptor(t,i);if(void 0===a){var s=Object.getPrototypeOf(t);return null===s?void 0:e(s,i,n)}if("value"in a)return a.value;var o=a.get;if(void 0!==o)return o.call(n)},o=function(){function e(e,t){for(var i=0;i<t.length;i++){var n=t[i];n.enumerable=n.enumerable||!1,n.configurable=!0,"value"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}return function(t,i,n){return i&&e(t.prototype,i),n&&e(t,n),t}}(),r=function(){function t(i){a(this,t),this.deferred=e.Deferred(),this.queue=[],this.responses=[],this.numToProcess=0,this.running=!1,this.init(i||[]),this.start()}return o(t,[{key:"init",value:function(e){var t=this;e.forEach(function(e){t.add(e)})}},{key:"add",value:function(e){var t=this,i=this.queue.length;return this.numToProcess+=1,this.queue.push(function(){var n=i,a=e();a.done(function(e){t.deferred.notify({curr:n,total:t.numToProcess,response:e})}),a.always(function(e){t.responses.push(e),t.queue.length?t.queue.shift()():t.stop()})}),this}},{key:"start",value:function(){return this.queue.length&&(this.running=!0,this.queue.shift()()),this}},{key:"stop",value:function(t,i){return this.running=!1,this.queue=[],t?this.deferred.reject(i):this.deferred.resolve(this.responses),this.numToProcess=0,this.deferred=e.Deferred(),this}},{key:"done",value:function(e){return this.deferred.done(e)}},{key:"fail",value:function(e){return this.deferred.fail(e)}},{key:"always",value:function(e){return this.deferred.always(e)}},{key:"progress",value:function(e){return this.deferred.progress(e)}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(),l=function(e){function t(e){a(this,t);var n=i(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e));return n.names={},n}return n(t,e),o(t,[{key:"add",value:function(e){if(!e.hasOwnProperty("name")||!e.hasOwnProperty("fn"))throw new Error('NamedAjaxQueue.add requires an object with both "name" and "fn": '+JSON.stringify(e));if(!this.names.hasOwnProperty(e.name))return this.names[e.name]=!0,s(t.prototype.__proto__||Object.getPrototypeOf(t.prototype),"add",this).call(this,e.fn)}},{key:"clear",value:function(){return this.names={},this}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(r);t.default={AjaxQueue:r,NamedAjaxQueue:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(254),r=s(o),l=i(192),d=(s(l),i(166)),c=(s(d),i(214)),u=s(c),h=i(256),f=s(h),p=i(257),m=s(p),_=i(181),g=s(_),v=i(222),w=s(v),b=i(187),y=s(b),x=i(260),k=s(x),C=i(261),$=s(C),S=i(175),T=s(S),M=i(67),E=(s(M),i(8)),P=s(E),O=i(7),A=s(O);i(25);var D=r.default.HistoryView,I=D.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},D.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return D.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return D.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return D.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=D.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=D.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new g.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,D.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,A.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,A.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,A.default)("Permanently delete datasets"),func:function(){if(confirm((0,A.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,A.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,A.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,A.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,a=this,t=t||a.getSelectedModels(),i=i||!1;"list"==e?n=y.default.createListCollection:"paired"==e?n=k.default.createPairCollection:"list:paired"==e?n=$.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){a.model.refresh()})},_getItemViewOptions:function(e){var t=D.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(D.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["<i>",(0,A.default)("Searching "),i,"/",this.model.contentsShown(),"</i>"].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),a("<div/>").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),a("<div/>").addClass("history-drop-target-help").text((0,A.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});I.prototype.templates=function(){var e=P.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'<span class="shown-count">',"<%- shown %> ",(0,A.default)("shown"),"</span>","<% } %>","<% if( history.contents_active.deleted ){ %>",'<span class="deleted-count">',"<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>","<% } else { %>","<%- history.contents_active.deleted %> ",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("deleted"),"</a>","<% } %>","</span>","<% } %>","<% if( history.contents_active.hidden ){ %>",'<span class="hidden-count">',"<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>","<%- history.contents_active.hidden %> ",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hidden"),"</a>","<% } %>","</span>","<% } %>"],"history"),t=P.default.wrapTemplate([(0,A.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>, ","<% } else { %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("show deleted"),"</a>, ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("show hidden"),"</a>","<% } %>","<% } %>"],"history");return n.extend(n.clone(D.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:I}}).call(t,i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(215),o=a(s),r=i(191),l=a(r),d=i(192),c=a(d),u=i(193),h=(a(u),i(217)),f=a(h),p=i(219),m=a(p),_=i(158),g=(a(_),i(212)),v=a(g),w=i(175),b=a(w),y=i(8),x=a(y),k=i(7),C=a(k);i(216);var $=o.default.ModelListPanel,S=$.extend({_logNamespace:"history",HDAViewClass:f.default.HDAListItemView,HDCAViewClass:m.default.HDCAListItemView,collectionClass:c.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:$.prototype.className+" history-panel",emptyMsg:(0,C.default)("This history is empty"),noneFoundMsg:(0,C.default)("No matching datasets found"),searchPlaceholder:(0,C.default)("search datasets"),FETCH_COLLECTION_COUNTS_DELAY:2e3,initialize:function(e){$.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.detailedFetchTimeoutId=null},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return $.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this._clearDetailedFetchTimeout(),this},_clearDetailedFetchTimeout:function(){this.detailedFetchTimeoutId&&(clearTimeout(this.detailedFetchTimeoutId),this.detailedFetchTimeoutId=null)},_setUpListeners:function(){var t=this;$.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,a){this.errorHandler(e,t,i,n,a)},"loading-done":function(){t.detailedFetchTimeoutId=e.delay(function(){t.detailedFetchTimeoutId=null,t.model.contents.fetchCollectionCounts()},t.FETCH_COLLECTION_COUNTS_DELAY)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(t,i,n){var a=this;return n=e.extend(n||{silent:!0}),this.info("loadHistory:",t,i,n),this.setModel(new l.default.History({id:t})),n.silent=!0,this.trigger("loading"),this.model.fetchWithContents(i,n).always(function(){a.render(),a.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):n.when()},_setUpCollectionListeners:function(){return $.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(t,i,a){var s=n('<div 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RegExp(this.filters[1])]),i}e=e||{},e.createPair=e.createPair||function(e){e=e||{};var t=e.listA.splice(e.indexA,1)[0],i=e.listB.splice(e.indexB,1)[0],n=e.listB.indexOf(t),a=e.listA.indexOf(i);return-1!==n&&e.listB.splice(n,1),-1!==a&&e.listA.splice(a,1),this._pair(t,i,{silent:!0})};var i=[];return e.preprocessMatch=e.preprocessMatch||function(e){var i=t.call(this);return n.extend(e,{matchTo:e.matchTo.name.replace(i[0],""),possible:e.possible.name.replace(i[1],"")})},function(t){this.debug("autopair _strategy ---------------------------"),t=t||{};var i,n=t.listA,a=t.listB,s=0,o={score:0,index:null},r=[];for(this.debug("starting list lens:",n.length,a.length),this.debug("bestMatch (starting):",JSON.stringify(o,null,"  "));s<n.length;){var l=n[s];for(o.score=0,i=0;i<a.length;i++){var d=a[i];if(this.debug(s+":"+l.name),this.debug(i+":"+d.name),n[s]!==a[i]&&(o=e.match.call(this,e.preprocessMatch.call(this,{matchTo:l,possible:d,index:i,bestMatch:o})),this.debug("bestMatch:",JSON.stringify(o,null,"  ")),1===o.score)){this.debug("breaking early due to perfect match");break}}var c=e.scoreThreshold.call(this);if(this.debug("scoreThreshold:",c),this.debug("bestMatch.score:",o.score),o.score>=c?r.push(e.createPair.call(this,{listA:n,indexA:s,listB:a,indexB:o.index})):s+=1,!n.length||!a.length)return r}return this.debug("paired:",JSON.stringify(r,null,"  ")),this.debug("autopair _strategy ---------------------------"),r}}function l(e,t){var i=e.toJSON();return y(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(262),c=o(d),u=i(208),h=o(u),f=i(207),p=o(f),m=i(8),_=o(m),g=i(7),v=o(g);i(209);var w=e.View.extend(_.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset 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e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),b=e.View.extend(_.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator 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e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,a){e(n,t)&&i[a].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,a){if(n===a)return n;var s=Math.floor((a-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[s].name);if(o<0)return i(n,s);if(o>0)return i(s+1,a);for(;t.unpaired[s]&&t.unpaired[s].name===e.name;)s++;return s}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:r({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var 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t.blocking=!0,a.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(s)}).always(function(){t.blocking=!1}).fail(function(e,i,n){t._ajaxErrHandler(e,i,n)}).done(function(e,i,n){t.trigger("collection:created",e,i,n),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,i,n)})},_ajaxErrHandler:function(e,t,i){this.error(e,t,i);var n=this,a=(0,v.default)("An error occurred while creating this collection");e&&(0===e.readyState&&0===e.status?a+=": "+(0,v.default)("Galaxy could not be reached and may be updating.")+(0,v.default)(" Try again in a few minutes."):e.responseJSON?a+="<br /><pre>"+JSON.stringify(e.responseJSON)+"</pre>":a+=": "+i),n._showAlert(a,"alert-danger")},render:function(e,t){return this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var 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.unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-o[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=o[1].map(function(e,t){return void 0!==o[0][t]&&o[0][t]!==e&&s.push(a._renderPairButton()),a._renderUnpairedDataset(e)}),i=o[0].map(function(e){return a._renderUnpairedDataset(e)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(s)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(e){return["(",e," ",(0,v.default)("filtered out"),")"].join("")},_renderUnpairedDataset:function(e){return s("<li/>").attr("id","dataset-"+e.id).addClass("dataset 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i=e.offset().left+e.outerWidth(),n=t.offset().left+t.outerWidth(),a=Math.floor(i)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",a>0?a:0)}},_renderPaired:function(e,t){if(this.$(".paired-column-title .title").text([this.paired.length,(0,v.default)("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(e,t){var n=new w({pair:e});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',(0,v.default)("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var e=s('<div class="empty-message"></div>').text("("+(0,v.default)("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(e),e},footerSettings:{".hide-originals":"hideOriginals",".remove-extensions":"removeExtensions"},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(e){function t(e,t){return['<button class="filter-choice btn" ','data-forward="',e,'" data-reverse="',t,'">',(0,v.default)("Forward"),": ",e,", ",(0,v.default)("Reverse"),": ",t,"</button>"].join("")}var i=s(n.template(['<div class="choose-filters">','<div class="help">',(0,v.default)("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",n.values(this.commonFilters).map(function(e){return t(e[0],e[1])}).join(""),"</div>"].join(""))({}));return this.$(e).popover({container:".collection-creator",placement:"bottom",html:!0,content:i})},_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_setUpBehaviors:function(){return this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("pair:new",function(){this._renderUnpaired(),this._renderPaired(),this.$(".paired-columns").scrollTop(8e6)}),this.on("pair:unpair",function(e){this._renderUnpaired(),this._renderPaired(),this.splitView()}),this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()],this.metric("filter-change",this.filters),this._renderFilters(),this._renderUnpaired()}),this.on("autopair",function(){this._renderUnpaired(),this._renderPaired();var e,t=null;this.paired.length?(t="alert-success",e=this.paired.length+" "+(0,v.default)("pairs created"),this.unpaired.length||(e+=": "+(0,v.default)("all datasets have been successfully paired"),this.hideUnpaired(),this.$(".collection-name").focus())):e=(0,v.default)(["Could not automatically create any pairs from the given dataset names.","You may want to choose or enter different filters and try auto-pairing again.","Close this message using the X on the right to view more help."].join(" ")),this._showAlert(e,t)}),this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(e){this.trigger("filter-change")},"focus .forward-unpaired-filter 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this.unpairedPanelHidden=this.pairedPanelHidden=!1,this._renderMiddle(e,t),this},_clickUnpairAll:function(e){this.metric("unpairAll"),this.unpairAll()},_clickAutopair:function(e){var t=this.autoPair();this.metric("autopair",t.length,this.unpaired.length),this.trigger("autopair")},_clickFilterChoice:function(e){var t=s(e.currentTarget);this.$(".forward-unpaired-filter input").val(t.data("forward")),this.$(".reverse-unpaired-filter input").val(t.data("reverse")),this._hideChooseFilters(),this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide"),this.$(".popover").css("display","none")},_clearFilters:function(e){this.$(".forward-unpaired-filter input").val(""),this.$(".reverse-unpaired-filter input").val(""),this.trigger("filter-change")},_clickUnpairedDataset:function(e){return e.stopPropagation(),this.toggleSelectUnpaired(s(e.currentTarget))},toggleSelectUnpaired:function(e,t){t=t||{};var i=e.data("dataset"),n=void 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this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=a.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=e.call(a,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:a})}),l.always(function(e){s.push(e),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(166),s=(n(a),i(8)),o=(n(s),i(7)),r=(n(o),{defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id");return""+this.urlRoot+t+"/contents/"+e+"s/"+i},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}});t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i={_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_changeHideOriginals:function(e){this.hideOriginals=this.$(".hide-originals").prop("checked")},_changeName:function(e){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(e){13!==e.keyCode||this.blocking||this._clickCreate()},_getName:function(){return 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n=this,a=this.$(".footer").empty().html(this.templates.footer());return e.each(this.footerSettings,function(e,t){n.$(t).prop("checked",n[e])}),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),a},_creatorTemplates:{main:e.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex"></div>'].join(""))}};t.default={CollectionCreatorMixin:i}}).call(t,i(2))},function(e,t,i){"use strict";function n(e,t){var i=/(-?[0-9\.]+)/g,n=e.toString().toLowerCase()||"",a=t.toString().toLowerCase()||"",s=String.fromCharCode(0),o=n.replace(i,s+"$1"+s).split(s),r=a.replace(i,s+"$1"+s).split(s),l=new Date(n).getTime(),d=l?new Date(a).getTime():null;if(d){if(l<d)return-1;if(l>d)return 1}for(var c,u,h=0,f=Math.max(o.length,r.length);h<f;h++){if(c=parseFloat(o[h])||o[h],u=parseFloat(r[h])||r[h],c<u)return-1;if(c>u)return 1}return 0}Object.defineProperty(t,"__esModule",{value:!0}),t.default=n},function(e,t,i){"use strict";var n=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default;a.default.fn.extend({hoverhighlight:function(e,t){return e=e||"body",this.length?(s(this).each(function(){var i=s(this),n=i.data("target");n&&i.mouseover(function(i){s(n,e).css({background:t})}).mouseout(function(e){s(n).css({background:""})})}),this):this}})},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(64),d=s(l),c=i(4),u=s(c),h=i(20),f=s(h),p=i(44),m=s(p),_=i(63),g=s(_),v=i(9),w=s(v),b=i(40),y=s(b),x=i(190),k=s(x),C=e.View.extend({initialize:function(t){var i=this;this.modal=parent.Galaxy.modal||new w.default.View,this.model=t&&t.model||new e.Model(t),this.deferred=new 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"+e.annotation),e.step_version&&(s+=" (Galaxy Version "+e.step_version+")"),e=r.default.merge({index:i,fixed_title:a.escape(s),icon:n||"",help:null,citations:null,collapsible:!0,collapsed:i>0&&!t._isDataStep(e),sustain_version:!0,sustain_repeats:!0,sustain_conditionals:!0,narrow:!0,text_enable:"Edit",text_disable:"Undo",cls_enable:"fa fa-edit",cls_disable:"fa fa-undo",errors:e.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=e.step_type},e),t.steps[i]=e,t.links[i]=[],t.parms[i]={}}),a.each(this.steps,function(e,i){m.default.visitInputs(e.inputs,function(e,n){t.parms[i][n]=e})}),a.each(this.steps,function(e,i){a.each(e.output_connections,function(e){a.each(t.steps,function(n,a){n.step_index===e.input_step_index&&t.links[i].push(n)})})}),a.each(this.steps,function(e,i){a.each(t.steps,function(n,s){var o={};a.each(e.output_connections,function(e){n.step_index===e.input_step_index&&(o[e.input_name]=e)}),a.each(t.parms[s],function(t,n){var a=o[n];a&&(t.type="hidden",t.help=t.step_linked?t.help+", ":"",t.help+="Output dataset '"+a.output_name+"' from step "+(parseInt(i)+1),t.step_linked=t.step_linked||[],t.step_linked.push(e))})})});var i=0;this.wp_inputs={},a.each(this.steps,function(i,n){a.each(t.parms[n],function(t,n){e(t.value,function(e){e.links.push(i),t.wp_linked=!0,t.type="text",t.backdrop=!0,t.style="ui-form-wp-target"})}),a.each(i.post_job_actions,function(t){a.each(t.action_arguments,function(t){e(t,function(){})})})}),a.each(this.steps,function(e,i){if("tool"==e.step_type){var n=!0;m.default.visitInputs(e.inputs,function(i,a,s){var o=i.value&&"RuntimeValue"==i.value.__class__,l=-1!=["data","data_collection"].indexOf(i.type),d=s[i.data_ref];i.step_linked&&!t._isDataStep(i.step_linked)&&(n=!1),i.options&&(0==i.options.length&&!n||i.wp_linked)&&(i.is_workflow=!0),d&&(i.is_workflow=d.step_linked&&!t._isDataStep(d.step_linked)||i.wp_linked),(l||i.value&&"RuntimeValue"==i.value.__class__&&!i.step_linked)&&(e.collapsed=!1),o&&(i.value=i.default_value),i.flavor="workflow",o||l||"hidden"===i.type||i.wp_linked||(i.optional||!r.default.isEmpty(i.value)&&""!==i.value)&&(i.collapsible_value=i.value,i.collapsible_preview=!0)})}})},render:function(){var e=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),a.each(this.steps,function(t){e._renderStep(t)})},_renderHeader:function(){var e=this;this.execute_btn=new u.default.Button({icon:"fa-check",title:"Run workflow",cls:"btn 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The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var e=this.model.get("step_version_changes");e&&e.length>0&&this.$message.append(new u.default.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var e=this;this.wp_form=null,a.isEmpty(this.wp_inputs)||(this.wp_form=new f.default({title:"<b>Workflow Parameters</b>",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){a.each(e.wp_form.input_list,function(t,i){a.each(t.links,function(t){e._refreshStep(t)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new f.default({cls:"ui-portlet-narrow",title:"<b>History Options</b>",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(e){var t=this,i=null;this.deferred.execute(function(s){if(t.$steps.addClass("ui-steps"),"tool"==e.step_type)e.postchange=function(t,i){var a={tool_id:e.id,tool_version:e.version,inputs:n.extend(!0,{},i.data.create())};i.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",a),r.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.id+"/build",data:a,success:function(e){i.update(e),i.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",e),t.reject()}})},i=new g.default(e),e.post_job_actions&&e.post_job_actions.length&&i.portlet.append(n("<div/>").addClass("ui-form-element-disabled").append(n("<div/>").addClass("ui-form-title").html("<b>Job Post Actions</b>")).append(n("<div/>").addClass("ui-form-preview").html(a.reduce(e.post_job_actions,function(e,t){return e+" "+t.short_str},""))));else{var 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0;if(e.step_linked)o={values:[]},a.each(e.step_linked,function(e){if(t._isDataStep(e)){var i=t.forms[e.index].data.create().input;i&&a.each(i.values,function(e){o.values.push(e)})}}),!e.multiple&&o.values.length>0&&(o={values:[o.values[0]]});else if(e.wp_linked){o=e.value;for(var r,l=/\$\{(.+?)\}/g;r=l.exec(e.value);){var d=t.wp_form.field_list[t.wp_form.data.match(r[1])],c=d&&d.value();c&&(o=o.split(r[0]).join(c))}}void 0!==o&&s.value(o)}}}),i.trigger("change")):e.needs_refresh=!0},_refreshHistory:function(){var e=this,t=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),t&&t.refresh().success(function(){0===t.numOfUnfinishedShownContents()&&(e._refresh_history=setTimeout(function(){e._refreshHistory()},t.UPDATE_DELAY))})},_execute:function(){var e=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(t){setTimeout(function(){t.resolve(),e._submit()},0)})},_submit:function(){var e=this,t=this.history_form.data.create(),i={new_history_name:t["new_history|name"]?t["new_history|name"]:null,history_id:t["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},a=!0;for(var s in this.forms){var o=this.forms[s],l=o.data.create(),d=e.steps[s],c=d.step_index;o.trigger("reset");for(var u in l){var h=l[u],f=o.data.match(u),p=(o.field_list[f],o.input_list[f]);if(!p.step_linked){if(!(a=this._isDataStep(d)?h&&h.values&&h.values.length>0:p.optional||p.is_workflow&&""!==h||!p.is_workflow&&null!==h)){o.highlight(f);break}i.parameters[c]=i.parameters[c]||{},i.parameters[c][u]=l[u]}}if(!a)break}a?(Galaxy.emit.debug("tool-form-composite::submit()","Validation 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times</b>":"")+".")).append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. 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this._setUpItemViewListeners(a),a},_destroyItemView:function(e){this.stopListening(e),this.views=n.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:n.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){n.each(this.views,function(e){e.expand()})},collapseAll:function(){n.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(-1!==s){var o=n._createItemView(e);return a(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,s),e()}]),o}},_attachView:function(e,t,i){i=!!n.isUndefined(i)||i,t=t||0;var a=this;return a.views.splice(t,0,e),a._insertIntoListAt(t,a._renderItemView$el(e).hide()),a.trigger("view:attached",e),i?e.$el.slideDown(a.fxSpeed,function(){a.trigger("view:attached:rendered")}):(e.$el.show(),a.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var s=this,o=n.find(s.views,function(t){return t.model===e});if(o)return s.views=n.without(s.views,o),s.trigger("view:removed",o),a({}).queue("fx",[function(e){o.$el.fadeOut(s.fxSpeed,e)},function(e){o.remove(),s.trigger("view:removed:rendered"),s.views.length?e():s._renderEmptyMessage().fadeIn(s.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i<n?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(e){return e.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:n.bind(this._firstSearch,this),onsearch:n.bind(this.searchItems,this),onclear:n.bind(this.clearSearch,this)}),e},_firstSearch:function(e){return this.log("onFirstSearch",e),this.searchItems(e)},searchItems:function(e,t){if(this.log("searchItems",e,this.searchFor,t),!t&&this.searchFor===e)return this;this.searchFor=e,this.renderItems(),this.trigger("search:searching",e,this);var i=this.$("> .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]),controls:u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- view.title %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=a(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- model.name %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function a(){return['<input type="text" name="',t.name,'" placeholder="',t.placeholder,'" ','class="search-query ',t.classes,'" ',"/>"].join("")}var l=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===s.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===s.default.type(t)&&(t=s.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(a()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===l&&t.escWillClear)i.call(this,e);else{var a=o(this).val();(e.which===d||t.minSearchLen&&a.length>=t.minSearchLen)&&n.call(this,e,a)}}).val(t.initialVal)}(),function(){return o(['<span class="search-clear fa fa-times-circle" ','title="',r("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o(['<span class="search-loading fa fa-spinner fa-spin" ','title="',r("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}()]))}var a=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=s.default,r=window._l||function(e){return e};s.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(195),s=n(a),o=i(8),r=n(o),l=i(219),d=n(l),c=i(7),u=n(c),h=s.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+"</span>\n            </div>\n            </br>\n            "+d.default.nametagTemplate(t)+"\n        </div>\n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:r.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,u.default)("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function i(t){return 0==t.indexOf("name:")?'<span class="label label-info">'+e.escape(t.slice(5))+"</span>":""}function n(t){return'<span class="nametags">'+e.sortBy(e.uniq(t.tags)).map(i).join("")+"</span>"}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(166),s=n(a),o=i(196),r=n(o),l=i(221),d=n(l),c=i(8),u=(n(c),i(219)),h=n(u),f=i(7),p=n(f),m=r.default.DCListItemView,_=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){var e=this.model.get("collection_type");switch(e){case"list":return d.default.ListCollectionView;case"paired":return d.default.PairCollectionView;case"list:paired":return d.default.ListOfPairsCollectionView;case"list:list":return d.default.ListOfListsCollectionView}throw new TypeError("Unknown collection_type: "+e)},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?s.default.OK:s.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e,t=this.model,i=t.get("element_count"),n=t.get("job_source_type"),a=this.model.get("collection_type");e="list"==a?"list":"paired"==a?"dataset pair":"list:paired"==a?"list of pairs":"nested list";var s="";1==i?s=" with 1 item":i&&(s=" with "+i+" items");var o=t.jobStatesSummary,r=""+e+s;if(n&&"Job"!=n){if(o&&o.hasDetails()){var l=o.new(),d=l?null:o.jobCount();if(l)return'\n                        <div class="progress state-progress">\n                            <span class="note">Creating jobs.<span class="blinking">..</span></span>\n                            <div class="progress-bar info" style="width:100%">\n                        </div>';if(o.errored()){return"a "+e+" with "+o.numInError()+" / "+d+" jobs in error"}if(o.terminal())return"a "+r;var c=o.states().running||0,u=o.states().ok||0,h=u/(1*d),f=c/(1*d),p=1-h-f;return'\n                        <div class="progress state-progress">\n                            <span class="note">'+(d&&d>1?d+" jobs":"a job")+" generating a "+e+'</span>\n                            <div class="progress-bar ok" style="width:'+100*h+'%"></div>\n                            <div class="progress-bar running" style="width:'+100*f+'%"></div>\n                            <div class="progress-bar new" style="width:'+100*p+'%">\n                        </div>'}return'\n                    <div class="progress state-progress">\n                        <span class="note">Loading job data for '+e+'.<span class="blinking">..</span></span>\n                        <div class="progress-bar info" style="width:100%">\n                    </div>'}return"a "+r},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+'</span>\n            </div>\n            <div class="state-description">\n            </div>\n            '+h.default.nametagTemplate(t)+"\n        </div>\n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:_}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(216),s=n(a),o=i(189),r=(n(o),i(196)),l=n(r),d=i(8),c=n(d),u=i(7),h=n(u),f=s.default.ModelListPanel,p=f.extend({_logNamespace:"collections",className:f.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:l.default.DatasetDCEListItemView,NestedDCDCEViewClass:l.default.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(e){f.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=f.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return f.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});p.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',(0,h.default)("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',(0,h.default)("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,h.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,h.default)("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,h.default)("a list of dataset lists"),"<% } %>","</div>","</div>",'<div class="tags-display"></div>','<div class="actions">','<a class="download-btn icon-btn" ','href="<%- view.downloadUrl %>','" title="" download="" data-original-title="Download Collection">','<span class="fa fa-floppy-o"></span>',"</a>","</div>","</div>"],"collection");return e.extend(e.clone(f.prototype.templates),{controls:t})}();var m=p.extend({DatasetDCEViewClass:l.default.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),_=m.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),g=p.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemView.extend({foldoutPanelClass:_}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),v=p.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemView.extend({foldoutPanelClass:_}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionView:p,ListCollectionView:m,PairCollectionView:_,ListOfPairsCollectionView:g,ListOfListsCollectionView:v}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(166),o=a(s),r=i(195),l=a(r),d=i(181),c=a(d),u=i(223),h=a(u),f=i(175),p=a(f),m=i(8),_=a(m),g=i(7),v=a(g),w=l.default.DatasetListItemView,b=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),a={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(a.disabled=!0,i?a.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(a.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(a.disabled=!0,a.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(a)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,a=function(t){var a='<div id="thdiv-'+e+'" class="toolhelp">';t.name&&t.help?(a+="<strong>Tool help for "+t.name+"</strong><hr/>",a+=t.help):a+="<strong>Tool help is unavailable for this dataset.</strong><hr/>",a+="</div>",i.$el.find(".details").append(n.parseHTML(a))},s=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){a(e)}).fail(function(){a({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){s(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});b.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:_.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',(0,v.default)("An error occurred setting the metadata for this dataset"),'<br /><a href="<%- dataset.urls.edit %>" target="_top">',(0,v.default)("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:_.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,v.default)("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',(0,v.default)("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',(0,v.default)("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")}),i=_.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-link icon-btn" href="<%- visualizations[0].href %>"',' target="<%- visualizations[0].target %>" title="',(0,v.default)("Visualize in"),' <%- visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown icon-btn">','<a data-toggle="dropdown" title="',(0,v.default)("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%- visualization.href %>"',' target="<%- visualization.target %>">',"<%- visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:b}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r);i(25);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['<label class="prompt">',(0,l.default)("Annotation"),"</label>",'<div class="annotation">',n.escape(e),"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",""+this.model,")"].join("")}});t.default={AnnotationEditor:d}}).call(t,i(1),i(2))},,,,,,,,,,,,,,,,function(e,t,i){"use strict";(function(e){function t(e){return e&&e.__esModule?e:{default:e}}var n=i(0),a=t(n),s=i(177),o=t(s),r=i(182),l=t(r),d=i(240),c=t(d),u=i(250),h=t(u),f=i(179),p=t(f),m=i(141),_=t(m),g=i(197),v=t(g),w=i(264),b=t(w),y=i(265),x=t(y),k=i(204),C=t(k),$=i(26),S=t($),T=i(266),M=t(T),E=i(267),P=t(E),O=i(269),A=t(O),D=i(274),I=t(D),z=i(210),j=t(z),L=i(61),R=t(L),N=i(3),V=t(N),G=i(4),U=t(G),H=i(275),F=t(H),B=i(276),q=t(B),Y=i(65),W=t(Y),J=i(142),X=t(J),K=a.default;window.app=function(t,i){window.Galaxy=new o.default.GalaxyApp(t,i),Galaxy.debug("analysis app");var n=l.default.extend({routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)user(/)":"show_user","(/)user(/)(:form_id)":"show_user_form","(/)pages(/)create(/)":"show_pages_create","(/)pages(/)edit(/)":"show_pages_edit","(/)pages(/)(:action_id)":"show_pages","(/)visualizations(/)edit(/)":"show_visualizations_edit","(/)visualizations/(:action_id)":"show_visualizations","(/)workflows/import_workflow":"show_import_workflow","(/)workflows/run(/)":"show_run","(/)workflows(/)list":"show_workflows","(/)workflows/list_published(/)":"show_workflows_published","(/)workflows/create(/)":"show_workflows_create","(/)histories(/)citations(/)":"show_history_citations","(/)histories(/)rename(/)":"show_histories_rename","(/)histories(/)import(/)":"show_histories_import","(/)histories(/)permissions(/)":"show_histories_permissions","(/)histories(/)(:action_id)":"show_histories","(/)datasets(/)list(/)":"show_datasets","(/)custom_builds":"show_custom_builds","(/)datasets/edit":"show_dataset_edit_attributes","(/)datasets/error":"show_dataset_error"},require_login:["show_user","show_user_form","show_workflows"],authenticate:function(e,t){return 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F.default.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new _.default.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#galaxy_main").prop("src",e)},_loadWorkflow:function(){var e=this;V.default.get({url:Galaxy.root+"api/workflows/"+V.default.getQueryString("id")+"/download?style=run",success:function(t){e.page.display(new j.default.View(t))},error:function(t){var i=t.err_msg||"Error occurred while loading the resource.",n={message:i,status:"danger",persistent:!0};e.page.display(new U.default.Message(n))}})}});K(function(){Galaxy.page=new p.default.View(e.extend(t,{Left:c.default,Right:h.default,Router:n}))})}}).call(t,i(2))},function(e,t,i){"use 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e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:(0,c.default)("All workflows"),href:"workflow"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflows/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['<div class="toolTitle">','<a href="',this.root,e.href,'" target="galaxy_main">',e.title,"</a>","</div>"].join("")},_templateAllWorkflow:function(e){return['<div class="toolTitle">','<a href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_templateWorkflowLink:function(e){return['<div class="toolTitle">','<a class="'+e.cls+' " href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_template:function(){return['<div class="toolMenuContainer">','<div class="toolMenu" style="display: none">','<div 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If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=s.default.merge(e,this.options),this.ui_button=new u.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;s.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:i<n?-1:0}),t.options.datatypes_disable_auto||t.list_extensions.unshift(t.options.auto)}}),s.default.get({url:Galaxy.root+"api/genomes",success:function(e){for(var i in e)t.list_genomes.push({id:e[i][1],text:e[i][0]});t.list_genomes.sort(function(e,i){return e.id==t.options.default_genome?-1:i.id==t.options.default_genome?1:e.text>i.text?1:e.text<i.text?-1:0})}})},show:function(){var e=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model)return void window.setTimeout(function(){e.show()},500);this.current_user=Galaxy.user.id,this.modal||(this.tabs=new d.default.View,this.default_view=new f.default(this),this.tabs.add({id:"regular",title:"Regular",$el:this.default_view.$el}),this.composite_view=new m.default(this),this.tabs.add({id:"composite",title:"Composite",$el:this.composite_view.$el}),this.collection_view=new g.default(this),this.tabs.add({id:"collection",title:"Collection",$el:this.collection_view.$el}),this.modal=new r.default.View({title:"Download from web or upload from disk",body:this.tabs.$el,height:this.options.height,width:this.options.width,closing_events:!0,title_separator:!1})),this.modal.show()},currentHistory:function(){return this.current_user&&Galaxy.currHistoryPanel.model.get("id")},currentFtp:function(){return this.current_user&&this.options.ftp_upload_site},toData:function(e,t){var i={payload:{tool_id:"upload1",history_id:t||this.currentHistory(),inputs:{}},files:[],error_message:null};if(e&&e.length>0){var n={file_count:e.length,dbkey:e[0].get("genome","?"),file_type:e[0].get("extension","auto")};for(var a in e){var s=e[a];if(s.set("status","running"),!(s.get("file_size")>0)){i.error_message="Upload content incomplete.",s.set("status","error"),s.set("info",i.error_message);break}var o="files_"+a+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=s.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=s.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=s.get("genome",null),n[o+"file_type"]=s.get("extension",null),s.get("file_mode")){case"new":n[o+"url_paste"]=s.get("url_paste");break;case"ftp":n[o+"ftp_files"]=s.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:s.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(1))},function(e,t,i){"use strict";(function(e,i){Object.defineProperty(t,"__esModule",{value:!0});var n=e.View.extend({initialize:function(t){var n=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:"",onunload:function(){},onclick:function(){}}).set(t),this.setElement(this._template()),this.$progress=this.$(".progress-bar"),this.listenTo(this.model,"change",this.render,this),this.render(),i(window).on("beforeunload",function(){return n.model.get("onunload")()})},render:function(){var e=this.model.attributes;this.$el.off("click").on("click",function(t){e.onclick(t)}).tooltip({title:this.model.get("tooltip"),placement:"bottom"}),this.$progress.removeClass().addClass("progress-bar").addClass("progress-bar-notransition").addClass(""!=e.status&&"progress-bar-"+e.status).css({width:e.percentage+"%"})},_template:function(){return'<div class="upload-button"><div class="progress"><div class="progress-bar"/><a class="panel-header-button" href="javascript:void(0)" id="tool-panel-upload-button"><span class="fa fa-upload"/></a></div></div>'}});t.default={View:n}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(244),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(245),x=s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local file",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new x.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new c.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&a.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Type (set all):</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139),p=s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});var a=this.app.select_genome.value(),s=this.app.select_extension.value();this.select_genome=new p.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:a,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new p.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:s,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:a,extension:s}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-extension" style="float: left;"/>&nbsp;&nbsp<div class="upload-extension-info upload-icon-button fa fa-search"/></td><td><div class="upload-genome"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(e){this.$container=e.$container,this.collection=e.collection,this.new_content=e.new_content,this.max=e.max||50,this.content_list={},this.$message=i("<div/>").addClass("ui-limitloader").append("...only the first "+this.max+" entries are visible."),this.$container.append(this.$message),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add",this._refresh,this),this.listenTo(this.collection,"remove",this._remove,this)},_done:function(){var e=n.size(this.content_list)>this.max;return this.$message[e?"show":"hide"](),e},_reset:function(){n.each(this.content_list,function(e){e.remove()}),this.content_list={},this.$message.hide()},_remove:function(e){var t=e.id,i=this.content_list[t];i&&(i.remove(),delete this.content_list[t]),this._refresh()},_refresh:function(){if(!this._done())for(var e in this.collection.models){var t=this.collection.models[e];this.content_list[t.id];if(!this.content_list[t.id]){var i=this.new_content(t);if(this.content_list[t.id]=i,this._done())break}}}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(247),c=s(d),u=i(185),h=s(u),f=i(165),p=(s(f),i(139)),m=s(p),_=i(4),g=s(_);t.default=e.View.extend({collection:new l.default.Collection,initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new g.default.Button({title:"Start",onclick:function(){t._eventStart()}}),this.btnClose=new g.default.Button({title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=n.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&n.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){new h.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new c.default(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),a.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_template:function(){return'<div class="upload-view-composite"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th/><th/><th>Description</th><th>Name</th><th>Size</th><th>Settings</th><th>Status</th></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Composite Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome/Build:</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(183),d=s(l),c=i(184),u=s(c),h=i(165),f=s(h),p=i(4),m=s(p),_=i(139);s(_);i(186),t.default=e.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new m.default.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new f.default.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new f.default.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(a.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(r.default.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){e.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){"new"==this.model.get("file_mode")?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(r.default.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new u.default({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new d.default(this).$el),this.settings.show())},_template:function(){return'<tr class="upload-row"><td><div class="upload-source"/><div class="upload-text-column"><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-status"/></td><td><div class="upload-file-desc upload-title"/></td><td><div class="upload-file-name upload-title"/></td><td><div class="upload-file-size upload-size"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(249),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(187);s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local files",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP files",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnBuild=new b.default.Button({id:"btn-build",title:"Build",onclick:function(){t._eventBuild()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(i);var n=new c.default(this,{model:i});this.$(".upload-table > tbody:first").append(n.$el),this._updateScreen(),n.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=n.pluck(t.outputs,"hid"),a=this.collection.get(e);a.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,a.get("file_size"))),this.upload_completed+=100*a.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];n.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=n.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,a=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[a?"enable":"disable"](),this.btnFtp[a?"enable":"disable"](),this.btnCreate[a?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title-compressed">Collection Type:</span><span class="upload-footer-collection-type"/><span class="upload-footer-title-compressed">File Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title-compressed">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139);s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title-extended"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),s=n(a),o=i(251),r=n(o),l=i(252),d=n(l),c=i(7),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return['<div id="current-history-panel" class="history-panel middle"/>'].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t,i){return n.clone(m).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),r=a(o),l=i(211),d=a(l),c=i(8),u=(a(c),i(7)),h=a(u),f=i(40),p=a(f),m=[{html:(0,h.default)("History Lists"),header:!0},{html:(0,h.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,h.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,h.default)("Current History"),header:!0,anon:!0},{html:(0,h.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,h.default)("Copy History"),func:function(){(0,d.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Share or Publish"),href:"history/sharing"},{html:(0,h.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,h.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,h.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,h.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,h.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,h.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,h.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Purge Deleted Datasets"),confirm:(0,h.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,h.default)("Downloads"),header:!0},{html:(0,h.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,h.default)("Other Actions"),header:!0},{html:(0,h.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(t){var i=[];e.each(t.models,function(e,t){var n=t.toJSON();n.activate&&i.push({html:(0,h.default)(n.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,h.default)("Webhooks"),header:!0}),e.merge(m,i))}});var _=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,a=s(i,n,Galaxy.root);return new r.default(e,a)};t.default=_}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(191),r=(s(o),i(254)),l=s(r),d=i(8),c=s(d),u=i(7),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,m=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'<a class="uploader-link" href="javascript:void(0)">',(0,h.default)("load your own data"),"</a>",(0,h.default)(" or "),'<a class="get-data-link" href="javascript:void(0)">',(0,h.default)("get data from an external source"),"</a>"].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):a.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):a.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="quota-message errormessage">',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:m}}).call(t,i(2),i(0),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(1),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=i(215),o=function(e){return e&&e.__esModule?e:{default:e}}(s),r=["new","queued","running"],l=["error","deleted"],d=a.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(l)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var i in e)if((t[e[i]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),i=0;for(var n in e)i+=t[e[n]]||0;return i},numInError:function(){return this.numWithStates(l)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(r)},jobCount:function(){var e=this.states(),t=0;for(var i in e)t+=e[i];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),c=a.Collection.extend({model:d,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var e=this.models.filter(function(e){return!e.terminal()}),t=e.map(function(e){return e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(255),r=s(o),l=i(192),d=(s(l),i(166)),c=(s(d),i(214)),u=s(c),h=i(257),f=s(h),p=i(258),m=s(p),_=i(181),g=s(_),v=i(223),w=s(v),b=i(187),y=s(b),x=i(261),k=s(x),C=i(262),$=s(C),S=i(175),T=s(S),M=i(67),E=(s(M),i(8)),P=s(E),O=i(7),A=s(O);i(25);var D=r.default.HistoryView,I=D.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},D.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return D.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return D.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return D.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=D.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=D.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new g.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,D.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,A.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,A.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,A.default)("Permanently delete datasets"),func:function(){if(confirm((0,A.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,A.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,A.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,A.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,a=this,t=t||a.getSelectedModels(),i=i||!1;"list"==e?n=y.default.createListCollection:"paired"==e?n=k.default.createPairCollection:"list:paired"==e?n=$.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){a.model.refresh()})},_getItemViewOptions:function(e){var t=D.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(D.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["<i>",(0,A.default)("Searching "),i,"/",this.model.contentsShown(),"</i>"].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),a("<div/>").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),a("<div/>").addClass("history-drop-target-help").text((0,A.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});I.prototype.templates=function(){var e=P.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'<span class="shown-count">',"<%- shown %> ",(0,A.default)("shown"),"</span>","<% } %>","<% if( history.contents_active.deleted ){ %>",'<span class="deleted-count">',"<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>","<% } else { %>","<%- history.contents_active.deleted %> ",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("deleted"),"</a>","<% } %>","</span>","<% } %>","<% if( history.contents_active.hidden ){ %>",'<span class="hidden-count">',"<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>","<%- history.contents_active.hidden %> ",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hidden"),"</a>","<% } %>","</span>","<% } %>"],"history"),t=P.default.wrapTemplate([(0,A.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>, ","<% } else { %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("show deleted"),"</a>, ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("show hidden"),"</a>","<% } %>","<% } %>"],"history");return n.extend(n.clone(D.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:I}}).call(t,i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(216),o=a(s),r=i(191),l=a(r),d=i(192),c=a(d),u=i(193),h=(a(u),i(218)),f=a(h),p=i(220),m=a(p),_=i(158),g=(a(_),i(212)),v=a(g),w=i(175),b=a(w),y=i(8),x=a(y),k=i(7),C=a(k);i(217);var $=o.default.ModelListPanel,S=$.extend({_logNamespace:"history",HDAViewClass:f.default.HDAListItemView,HDCAViewClass:m.default.HDCAListItemView,collectionClass:c.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:$.prototype.className+" history-panel",emptyMsg:(0,C.default)("This history is empty"),noneFoundMsg:(0,C.default)("No matching datasets found"),searchPlaceholder:(0,C.default)("search datasets"),initialize:function(e){$.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return $.prototype.freeModel.call(this),this.model&&this.model.stopPolling(),this},_setUpListeners:function(){$.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,a){this.errorHandler(e,t,i,n,a)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(t,i,n){var a=this;return n=e.extend(n||{silent:!0}),this.info("loadHistory:",t,i,n),this.setModel(new l.default.History({id:t})),n.silent=!0,this.trigger("loading"),this.model.fetchWithContents(i,n).always(function(){a.render(),a.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):n.when()},_setUpCollectionListeners:function(){return $.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(t,i,a){var s=n('<div class="loading-indicator"/>');this.$el.html(s.text(t).slideDown(e.isUndefined(i)?this.fxSpeed:i))},_hideLoadingIndicator:function(t){this.$(".loading-indicator").slideUp(e.isUndefined(t)?this.fxSpeed+200:t,function(){n(this).remove()})},_buildNewRender:function(){var e=$.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,b.default)({title:(0,C.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),n())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('<div class="contents-loading-indicator"><span class="fa fa-2x fa-spinner fa-spin"/></div>'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!i.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&$.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var i=$.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return $.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),$.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=$.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone($.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=n(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(t,i,n){if(!i||0!==i.status||0!==i.readyState){if(this.error(t,i,n),e.isString(t)&&e.isString(i)){var a=t,s=i;return v.default.errorModal(a,s,n)}return i&&502===i.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,i,n)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget)).fadeOut(this.fxSpeed,function(){n(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(e.first(this.viewsWhereModel({hid:t})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});S.prototype.templates=function(){var t=function(){return'<div>\n            <div class="controls"></div>\n            <ul class="list-items"></ul>\n            <div class="empty-message infomessagesmall"></div>\',\n        </div>'},i=x.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%- history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,C.default)("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,C.default)("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,C.default)("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,C.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,C.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>",'<div class="list-pagination form-inline"></div>',"</div>"],"history"),n=x.default.wrapTemplate(['<button class="prev" <%- pages.current === 1 ? "disabled" : "" %>>previous</button>','<select class="pages form-control" ','title="',(0,C.default)("Click to open and select a page. Begin typing a page number to select it"),'">',"<% _.range( 1, pages.last + 1 ).forEach( function( i ){ %>",'<option value="<%- i - 1 %>" <%- i === pages.current ? "selected" : "" %>>',"<%- view.ordinalIndicator( i ) %> of <%- pages.last %> pages","</option>","<% }); %>","</select>",'<button class="next" <%- pages.current === pages.last ? "disabled" : "" %>>next</button>'],"pages");return e.extend(e.clone($.prototype.templates),{el:t,controls:i,pagination:n})}(),t.default={HistoryView:S}}).call(t,i(2),i(0))},function(e,t,i){"use strict";function n(e,t){function i(){var i=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n"),n=o(i).hide().css(t.css||{position:"fixed"}),a=n.children(".loading-indicator-text");return t.cover?(n.css({"z-index":2,top:e.css("top"),bottom:e.css("bottom"),left:e.css("left"),right:e.css("right"),opacity:.5,"background-color":"white","text-align":"center"}),a=n.children(".loading-indicator-text").css({"margin-top":"20px"})):(a=n.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"}),a.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})),n}var n=this;return t=s.default.extend({cover:!1},t||{}),n.show=function(t,a,s){return t=t||"loading...",a=a||"fast",e.parent().find(".loading-indicator").remove(),n.$indicator=i().insertBefore(e),n.message(t),n.$indicator.fadeIn(a,s),n},n.message=function(e){n.$indicator.find("i").text(e)},n.hide=function(e,t){return e=e||"fast",n.$indicator&&n.$indicator.length?n.$indicator.fadeOut(e,function(){n.$indicator.remove(),t&&t()}):t&&t(),n},n}Object.defineProperty(t,"__esModule",{value:!0});var a=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=s.default;t.default=n},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(222),o=a(s),r=i(218),l=a(r),d=i(8),c=a(d),u=i(7),h=a(u),f=o.default.DatasetListItemEdit,p=f.extend({className:f.prototype.className+" history-content",_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):t.model.has("rerunnable")?e.when():t.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:n.extend(n.clone(f.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){return"HDAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});p.prototype.templates=function(){var e=n.extend({},f.prototype.templates.warnings,{hidden:c.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,h.default)("This dataset has been hidden"),'<br /><a class="unhide-link" a href="javascript:void(0);">',(0,h.default)("Unhide it"),"</a>","</div>","<% } %>"],"dataset")});return n.extend({},f.prototype.templates,{titleBar:l.default.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),t.default={HDAListItemEdit:p}}).call(t,i(0),i(2))},function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(220),s=n(a),o=i(259),r=n(o),l=i(175),d=n(l),c=i(7),u=n(c),h=s.default.HDCAListItemView,f=h.extend({_getFoldoutPanelClass:function(){var e=this.model.get("collection_type");switch(e){case"list":return r.default.ListCollectionViewEdit;case"paired":return r.default.PairCollectionViewEdit;case"list:paired":return r.default.ListOfPairsCollectionViewEdit;case"list:list":return r.default.ListOfListsCollectionViewEdit}throw new TypeError("Unknown collection_type: "+e)},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),h.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var e=this,t=this.model.get("deleted");return(0,d.default)({title:t?(0,u.default)("Dataset collection is already deleted"):(0,u.default)("Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:t,onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},toString:function(){return"HDCAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});t.default={HDCAListItemEdit:f}},function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(221),s=n(a),o=i(189),r=(n(o),i(260)),l=n(r),d=i(8),c=(n(d),i(181)),u=n(c),h=i(175),f=(n(h),i(7)),p=n(f);i(25);var m=s.default.CollectionView,_=m.extend({DatasetDCEViewClass:l.default.DatasetDCEListItemEdit,NestedDCDCEViewClass:l.default.NestedDCDCEListItemEdit,initialize:function(e){m.prototype.initialize.call(this,e)},_setUpBehaviors:function(e){if(e=e||this.$el,m.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){this.tagsEditorShown=!0;var t=this;e.find("> .controls .name").attr("title",(0,p.default)("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}}),this.tagsEditor=new u.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},usePrompt:!1}),this.tagsEditor.toggle(!0)}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),g=_.extend({DatasetDCEViewClass:l.default.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),v=g.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),w=v.extend({_setUpBehaviors:function(e){m.prototype._setUpBehaviors.call(this,e)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),b=_.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemEdit.extend({foldoutPanelClass:w}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),y=_.extend({NestedDCDCEViewClass:l.default.NestedDCDCEListItemEdit.extend({foldoutPanelClass:w}),toString:function(){return"ListOfListsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionViewEdit:_,ListCollectionViewEdit:g,PairCollectionViewEdit:v,ListOfPairsCollectionViewEdit:b,ListOfListsCollectionViewEdit:y}},function(e,t,i){"use 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See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.</p>'}});t.default={View:h,Model:u}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(4)),r=a(o),l=i(20),d=a(l),c=i(43),u=a(c),h=e.Collection.extend({comparator:function(e,t){return e=e.get("name"),t=t.get("name"),e>t?1:e<t?-1:0}}),f=e.View.extend({initialize:function(t){var i=this,a=Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.model.id;this.model=new e.Model,this.model.url=Galaxy.root+"api/histories/"+a+"/custom_builds_metadata",this.collection=new h,this.collection.url=Galaxy.root+"api/users/"+Galaxy.user.id+"/custom_builds",this.message=new r.default.Message({}),this.installed_builds=new r.default.Select.View({optional:!0,onchange:function(){i.installed_builds.value(null)},empty_text:"List of available builds:",error_text:"No system installed builds available."}),this.table=new u.default.View({cls:"grid",selectable:!1}),this.table.addHeader("Name"),this.table.addHeader("Key"),this.table.addHeader("Number of chroms/contigs"),this.table.addHeader(""),this.table.appendHeader(),this.setElement(n("<div/>").append(n("<h4/>").text("Current Custom Builds")).append(this.table.$el).append(this.$installed=n("<div/>").append(n("<h4/>").text("System Installed Builds").addClass("ui-margin-top")).append(this.installed_builds.$el)).append(n("<h4/>").text("Add a Custom Build").addClass("ui-margin-top")).append(n("<span/>").addClass("ui-column").append(n("<div/>").addClass("ui-column-left").append(this.message.$el).append(this.$form=n("<div/>").addClass("ui-margin-top"))).append(this.$help=n("<div/>").addClass("ui-column-right")))),this.listenTo(this.collection,"add remove reset",function(){i._renderTable()}),this.listenTo(this.model,"change",function(){i._renderForm()}),this.collection.fetch(),this.model.fetch()},render:function(){this._renderTable(),this._renderForm()},_renderTable:function(){var e=this;this.table.delAll(),this.collection.sort(),this.collection.each(function(t){e.table.add(t.get("name")),e.table.add(t.id),e.table.add(void 0!==t.get("count")?t.get("count"):"Processing..."),e.table.add(new r.default.ButtonIcon({icon:"fa-trash-o",cls:"ui-button-icon-plain",tooltip:"Delete custom build.",onclick:function(){t.destroy()}}).$el),e.table.append(t.id)})},_renderForm:function(){var e=this,t=new d.default({inputs:[{type:"text",name:"name",label:"Name",help:"Specify a build name e.g. Hamster."},{type:"text",name:"id",label:"Key",help:"Specify a build key e.g. hamster_v1."},{name:"len",type:"conditional",test_param:{name:"type",label:"Definition",help:"Provide the data source.",type:"select",value:"fasta",data:[{value:"fasta",label:"FASTA-file from history"},{value:"file",label:"Len-file from disk"},{value:"text",label:"Len-file by copy/paste"}]},cases:[{value:"fasta",inputs:[{type:"select",name:"value",label:"FASTA-file",data:this.model.get("fasta_hdas")}]},{value:"file",inputs:[{type:"upload",name:"value",label:"Len-file",data:this.model.get("len_hdas")}]},{value:"text",inputs:[{type:"text",area:!0,name:"value",label:"Edit/Paste"}]}]}],buttons:{save:new r.default.Button({icon:"fa-save",tooltip:"Create new Build",title:"Save",cls:"btn btn-primary ui-clear-float",onclick:function(){var i=t.data.create();i.id&&i.name?e.collection.create(i,{wait:!0,success:function(t){t.get("message")?e.message.update({message:t.get("message"),status:"warning"}):e.message.update({message:"Successfully added a new custom build.",status:"success"})},error:function(t,i){var n=i&&i.responseJSON&&i.responseJSON.err_msg;e.message.update({message:n||"Failed to create custom build.",status:"danger"})}}):e.message.update({message:"All inputs are required.",status:"danger"})}})},onchange:function(){var i=t.data.match("len|type");if(i){var n=t.field_list[i];e._renderHelp(n.value())}}});this.$form.empty().append(t.$el);var i=this.model.get("installed_builds");i&&i.length?(this.$installed.show(),this.installed_builds.update(this.model.get("installed_builds"))):this.$installed.hide(),this._renderHelp("fasta")},_renderHelp:function(e){this.$help.empty().addClass("alert alert-info").html("fasta"==e?this._templateFasta():this._templateLen())},_templateLen:function(){return"<h4>Length Format</h4><p>The length format is two-column, separated by whitespace, of the form:<pre>chrom/contig   length of chrom/contig</pre></p><p>For example, the first few entries of <em>mm9.len</em> are as follows:<pre>chr1    197195432\nchr2    181748087\nchr3    159599783\nchr4    155630120\nchr5    152537259</pre></p><p>Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. 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\ No newline at end of file
diff --git a/static/scripts/bundled/library.bundled.js b/static/scripts/bundled/library.bundled.js
index d40b9fd535d..54232da2d83 100644
--- a/static/scripts/bundled/library.bundled.js
+++ b/static/scripts/bundled/library.bundled.js
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.sort-folder-state":"sortColumnClicked"},collection:null,defaults:{include_deleted:!1,page_count:null,show_page:null},initialize:function(e){this.options=s.defaults(this.options||{},this.defaults,e),this.modal=null,this.rowViews={},this.collection=new d.default.Folder,this.listenTo(this.collection,"add",this.renderOne),this.listenTo(this.collection,"remove",this.removeOne),this.listenTo(this.collection,"sort",this.rePaint),this.listenTo(this.collection,"reset",this.rePaint),this.fetchFolder()},fetchFolder:function(e){var e=e||{};this.options.include_deleted=e.include_deleted;var t=this;this.folderContainer=new d.default.FolderContainer({id:this.options.id}),this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents",this.options.include_deleted&&(this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"),this.folderContainer.fetch({success:function(e){t.folder_container=e,t.render()},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):n.default.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=s.extend(this.options,e);var t=this.templateFolder();a(".tooltip").hide();var i,r=this.folderContainer.attributes.metadata.full_path;if(i=1===r.length?0:r[r.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:i,order:this.current_sort_order})),this.options.dataset_id){var o=s.findWhere(self.rowViews,{id:this.options.dataset_id});o?o.showDatasetDetails():n.default.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();a("#center [data-toggle]").tooltip(),a("#center").css("overflow","auto")},paginate:function(e){this.options=s.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),i=null;i=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=i.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(i=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(i)},rePaint:function(e){this.options=s.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){s.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{current_sort_order:!1})}),a("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;s.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new h.default.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return a(this).data("id")&&a(this).data("id")===e.id}).remove()},removeAllRows:function(){a(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),this.current_sort_order="asc"===this.current_sort_order?"desc":"asc",this.current_sort_key=e.currentTarget.className.replace("sort-folder-",""),this.collection.sortFolder(this.current_sort_key,this.current_sort_order),this.renderSortIcon()},selectAll:function(e){var t=e.target.checked,i=this;a(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=a(this).closest("tr");t?i.makeDarkRow(e):i.makeWhiteRow(e)})},selectClickedRow:function(e){var t,i,s="";t=a(e.target).closest("tr"),"input"===e.target.localName?(s=e.target,i="input"):"td"===e.target.localName&&(s=t.find(":checkbox")[0],i="td"),s.checked?"td"===i?(s.checked="",this.makeWhiteRow(t)):"input"===i&&this.makeDarkRow(t):"td"===i?(s.checked="selected",this.makeDarkRow(t)):"input"===i&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.current_sort_order?(a('[class*="sort-icon"]').removeClass("fa-sort-alpha-desc").removeClass("fa-sort-alpha-asc"),a(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-asc")):a(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-desc")},templateFolder:function(){return s.template(['<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>',"<% _.each(path, function(path_item) { %>","<% if (path_item[0] != id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<table data-library-id="<%- parent_library_id  %>" class="grid table table-condensed">',"<thead>",'<th class="button_heading"></th>','<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>','<th><a class="sort-folder-name" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon-name fa fa-sort-alpha-<%- order %>"></span></th>','<th style="width:20%;"><a class="sort-folder-description" title="Click to reverse order" href="#">description</a> <span title="Sorted alphabetically" class="sort-icon-description fa"></span></th>','<th style="width:5%;"><a class="sort-folder-file_ext" title="Click to reverse order" href="#">data type</a> <span title="Sorted alphabetically" class="sort-icon-file_ext fa"></span></th>','<th style="width:10%;">size</th>','<th style="width:160px;">time updated (UTC)</th>','<th style="width:5%;"><a class="sort-folder-state" title="Click to reverse order" href="#">state</a> <span title="Sorted alphabetically" class="sort-icon-state fa"></span></th>','<th style="width:150px;"></th> ',"</thead>",'<tbody id="folder_list_body">','<tr id="first_folder_item">',"<td>",'<a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a>',"</td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","</tr>","</tbody>","</table>",'<div class="empty-folder-message" style="display:none;">',"This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up",' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>"].join(""))}});t.default={FolderListView:_}}).call(t,i(1),i(2),i(0))},301:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=i(224),h=r(c),_=e.View.extend({events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder","click .edit_folder_btn":"startModifications","click .cancel_folder_btn":"cancelModifications","click .save_folder_btn":"saveModifications"},defaults:{type:null,visibility_config:{edit_folder_btn:!1,save_folder_btn:!1,cancel_folder_btn:!1,permission_folder_btn:!1},edit_mode:!1},initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.render(this.options)},render:function(e){this.options=s.extend(this.options,e);var t=this.options.model,i=null;return"folder"===t.get("type")||"LibraryFolder"===t.get("model_class")?(this.options.type="folder",this.prepareButtons(t),i=t.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===t.get("type")||"LibraryDatasetDatasetAssociation"===t.get("model_class")||"LibraryDataset"===t.get("model_class")?(this.options.type="file",i=t.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(Galaxy.emit.error("Unknown library item type found."),Galaxy.emit.error(t.get("type")||t.get("model_class"))),this.setElement(i({content_item:t,edit_mode:this.options.edit_mode,button_config:this.options.visibility_config})),this.$el.show(),this},prepareButtons:function(e){var t=this.options.visibility_config;!1===this.options.edit_mode?(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("deleted")?(t.edit_folder_btn=!1,t.permission_folder_btn=!1):!1===e.get("deleted")&&(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("can_modify")&&(t.edit_folder_btn=!0),!0===e.get("can_manage")&&(t.permission_folder_btn=!0))):!0===this.options.edit_mode&&(t.edit_folder_btn=!1,t.permission_folder_btn=!1,t.save_folder_btn=!0,t.cancel_folder_btn=!0),this.options.visibility_config=t},showDatasetDetails:function(){Galaxy.libraries.datasetView=new h.default.LibraryDatasetView({id:this.id})},undeleteDataset:function(e){a(".tooltip").hide();var t=this,i=a(e.target).closest("tr").data("id"),s=Galaxy.libraries.folderListView.collection.get(i);s.url=s.urlRoot+s.id+"?undelete=true",s.destroy({success:function(e,s){Galaxy.libraries.folderListView.collection.remove(i);var a=new d.default.Item(s);Galaxy.libraries.folderListView.collection.add(a),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var e=t.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+e+"/datasets/"+t.id}})},error:function(e,t){void 0!==t.responseJSON?n.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){a(".tooltip").hide();var t=a(e.target).closest("tr").data("id"),i=Galaxy.libraries.folderListView.collection.get(t);i.url=i.urlRoot+i.id+"?undelete=true",i.destroy({success:function(e,i){Galaxy.libraries.folderListView.collection.remove(t);var s=new d.default.FolderAsModel(i);Galaxy.libraries.folderListView.collection.add(s),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?n.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_folder_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void n.default.warning("Folder name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_folder_description").val();if(void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.options.edit_mode=!1,a.repaint(e),n.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),n.default.info("Nothing has changed.")},repaint:function(){a(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return s.template(['<tr class="folder_row light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Folder" class="fa fa-folder-o"/>',"</td>",'<td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>',"<% if(!edit_mode) { %>","<td>",'<a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>',"</td>","<td>",'<%- content_item.get("description") %>',"</td>","<% } else if(edit_mode){ %>",'<td><textarea rows="4" class="form-control input_folder_name" placeholder="name" ><%- content_item.get("name") %></textarea></td>','<td><textarea rows="4" class="form-control input_folder_description" placeholder="description" ><%- content_item.get("description") %></textarea></td>',"<% } %>","<td>folder</td>","<td></td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td></td>","<td>","<% if(edit_mode) { %>",'<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-floppy-o"/> Save',"</button>",'<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-times"/> Cancel',"</button>","<% } else if (!edit_mode){%>",'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- content_item.get("name") %>\'" class="primary-button btn-xs edit_folder_btn" type="button" style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-pencil"/> Edit',"</button>",'<a href="#/folders/<%- content_item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permission_folder_btn" title="Permissions of \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-group"/> Manage',"</button>","</a>","<% } %>","</td>","</tr>"].join(""))},templateRowFile:function(){return s.template(['<tr class="dataset_row light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Dataset" class="fa fa-file-o"/>',"</td>",'<td style="text-align: center; ">','<input style="margin: 0;" type="checkbox">',"</td>","<td>",'<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"<a>","</td>",'<td><%- content_item.get("message") %></td>','<td><%= _.escape(content_item.get("file_ext")) %></td>','<td><%= _.escape(content_item.get("file_size")) %></td>','<td><%= _.escape(content_item.get("update_time")) %></td>',"<td>",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","</td>","<td>",'<% if (content_item.get("is_unrestricted")) { %>','<span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"/>',"<% } %>",'<% if (content_item.get("is_private")) { %>','<span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"/>',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','<span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"/>',"<% } %>",'<% if (content_item.get("can_manage")) { %>','<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Permissions of \'<%- content_item.get("name") %>\'">','<span class="fa fa-group"/> Manage',"</button>","</a>","<% } %>","</td>","</tr>"].join(""))},templateRowDeletedFile:function(){return s.template(['<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Dataset" class="fa fa-file-o"/>',"</td>","<td></td>",'<td style="color:grey;">','<%- content_item.get("name") %>',"</td>","<td>",'<%- content_item.get("message") %>',"</td>","<td>",'<%= _.escape(content_item.get("file_ext")) %>',"</td>","<td>",'<%= _.escape(content_item.get("file_size")) %>',"</td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td>",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","</td>","<td>",'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;">','<span class="fa fa-unlock"/> Undelete',"</button>","</td>","</tr>"].join(""))},templateRowDeletedFolder:function(){return s.template(['<tr class="active deleted_folder light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Folder" class="fa fa-folder-o"/>',"</td>","<td></td>",'<td style="color:grey;">','<%- content_item.get("name") %>',"</td>","<td>",'<%- content_item.get("description") %>',"</td>","<td>","folder","</td>","<td></td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td></td>","<td>",'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;">','<span class="fa fa-unlock"/> Undelete',"</button>","</td>","</tr>"].join(""))}});t.default={FolderRowView:_}}).call(t,i(1),i(2),i(0))},302:function(e,t,i){"use strict";(function(e,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=a(r),n=i(156),l=a(n),d=i(303),c=a(d),h=i(2),_=a(h),p=e.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(e){this.options=_.default.defaults(this.options||{},e,this.defaults);var t=this;this.modal=null,this.collection=new l.default.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){t.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})},render:function(e){this.options=_.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),i=null,a=null,r=function(e){return!0===e.get("public")};if(s(".tooltip").hide(),void 0!==e&&(a=void 0!==e.models?e.models:null),null!==this.collection&&null===a)this.sortLibraries(),i=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r));else if(null!==a){if(Galaxy.libraries.preferences.get("with_deleted"))i=a;else{var o=function(e){return!1===e.get("deleted")};i=_.default.filter(a,o)}Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r))}else i=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=i.length;var n=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&n<this.options.total_libraries_count?(i=i.slice(n,n+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=i.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(i=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(i)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),s("#center [data-toggle]").tooltip(),s("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t<e.length;t++){var i=e[t];this.renderOne({library:i})}},renderOne:function(e){var t=e.library,i=new c.default.LibraryRowView(t);this.$el.find("#library_list_body").append(i.el)},sort_clicked:function(){"asc"===Galaxy.libraries.preferences.get("sort_order")?Galaxy.libraries.preferences.set({sort_order:"desc"}):Galaxy.libraries.preferences.set({sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortLibraries("name","asc"):"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortLibraries("name","desc"))},searchLibraries:function(e){if(""!==s.trim(e)){var t=null;t=this.collection.search(e),this.options.searching=!0,this.render({models:t,show_page:1})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return _.default.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});t.default={LibraryListView:p}}).call(t,i(1),i(0))},303:function(e,t,i){"use strict";(function(e,s,a){Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=function(e){return e&&e.__esModule?e:{default:e}}(r),n=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){s(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_library_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_library_description").val();void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0);var a=this.$el.find(".input_library_synopsis").val();if(void 0!==a&&a!==e.get("synopsis")&&(e.set("synopsis",a),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.edit_mode=!1,r.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(s(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return a.template(['<tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<td style="color:grey;"><%- library.get("name") %></td>',"<% } else { %>",'<td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>',"<% } else { %>",'<td><%= _.escape(library.get("description"))%></td>',"<% } %>","<% } else { %>","<td></td>","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>',"<% } else { %>",'<td><%= _.escape(library.get("synopsis"))%></td>',"<% } %>","<% } else { %>","<td></td>","<% } %>","<% } else if(edit_mode){ %>",'<td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>','<td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>','<td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>',"<% } %>",'<td class="right-center">','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>','<span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg"> </span>',"<% }%>",'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- library.get("name") %>\'" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span> Edit</button>','<a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Permissions of \'<%- library.get("name") %>\'" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span> Manage</button></a>','<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"></span> Save</button>','<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"></span> Cancel</button>','<button data-toggle="tooltip" data-placement="top" title="Delete \'<%- library.get("name") %>\'" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"></span> Delete</button>','<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey; <% if(button_config.undelete_library_btn === false) { print("display:none;") } %>" class="fa fa-ban fa-lg"></span>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- library.get("name") %>\' " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"></span> Undelete</button>',"</td>","</tr>"].join(""))}});t.default={LibraryRowView:n}}).call(t,i(1),i(0),i(2))},304:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=e.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click .page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=s.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),t=!1,i=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:i})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){t.createNewLibrary()},Close:function(){t.modal.hide()}}})},createNewLibrary:function(){var e=this.serializeNewLibrary();if(this.validateNewLibrary(e)){var t=new d.default.Library,i=this;t.save(e,{success:function(e){Galaxy.libraries.libraryListView.collection.add(e),i.modal.hide(),i.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),n.default.success("Library created.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured.")}})}else n.default.error("Library's name is missing.");return!1},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(t)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){a("input[name='Name']").val(""),a("input[name='Description']").val(""),a("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val(),synopsis:a("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var t=a(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return s.template(['<div class="library_style_container">','<div id="toolbar_form">','<div id="library_toolbar">','<form class="form-inline" role="form">','<span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>','<span id="library_paginator" class="library-paginator">',"</span>",'<div class="form-group toolbar-item">','<input type="text" class="form-control library-search-input" placeholder="Search" size="30">',"</div>","<% if(admin_user === true) { %>",'<div class="checkbox toolbar-item" style="height: 20px;">',"<label>",'<input id="include_deleted_chk" type="checkbox">',"include deleted ","</input>","</label>","<label>",'<input id="exclude_restricted_chk" type="checkbox">',"exclude restricted","</input>","</label>","</div>",'<span class="toolbar-item" data-toggle="tooltip" data-placement="top" title="Create New Library">','<button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button>',"</span>","<% } %>",'<span class="help-button" data-toggle="tooltip" data-placement="top" title="See this screen annotated">','<a href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">','<button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button>',"</a>","</span>","</form>","</div>","</div>",'<div id="libraries_element">',"</div>","</div>"].join(""))},templatePaginator:function(){return s.template(['<ul class="pagination pagination-sm">',"<% if ( ( show_page - 1 ) > 0 ) { %>","<% if ( ( show_page - 1 ) > page_count ) { %>",'<li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',"<% } else { %>",'<li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>',"<% } %>","<% } else { %>",'<li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',"<% } %>",'<li class="active">','<a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>',"</li>","<% if ( ( show_page ) < page_count ) { %>",'<li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>','<li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',"<% } else { %>",'<li class="disabled"><a href="#page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>','<li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',"<% } %>","</ul>","<span>",' <%- libraries_shown %> libraries shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- library_page_size %> per page" class="page_size_prompt">(change)</a>',"</span>","<span>"," <%- total_libraries_count %> total","</span>"].join(""))},templateNewLibraryInModal:function(){return s.template(['<div id="new_library_modal">',"<form>",'<input type="text" name="Name" value="" placeholder="Name" autofocus>','<input type="text" name="Description" value="" placeholder="Description">','<input type="text" name="Synopsis" value="" placeholder="Synopsis">',"</form>","</div>"].join(""))}});t.default={LibraryToolbarView:c}}).call(t,i(1),i(2),i(0))},305:function(e,t,i){"use strict";(function(e,s,a,r){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),l=o(n),d=i(42),c=o(d),h=i(156),_=o(h),p=i(139),u=o(p);i(198);var f=e.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=s.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();a("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=s.extend(this.options,e),!0===this.options.can_add_library_item?a(".add-library-items").show():a(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(a(".dataset-manipulation").show(),a(".logged-dataset-manipulation").hide()):(a(".logged-dataset-manipulation").show(),a(".dataset-manipulation").show()):(a(".logged-dataset-manipulation").hide(),a(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var t=this.serialize_new_folder();if(this.validate_new_folder(t)){var i,s=new _.default.FolderAsModel,a=e.history.fragment.split("/");i=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],s.url=s.urlRoot+i,s.save(t,{success:function(e){Galaxy.modal.hide(),c.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})}else c.default.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)c.default.info("You must select some datasets first.");else{var e=this;this.histories=new _.default.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)a.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,i){c.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var i=a("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=i;var s=a("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(i,s),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=a(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});for(var o=[],n=i.length-1;n>=0;n--){var l=i[n],d=new _.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=l,d.source="library",o.push(d)}for(var n=s.length-1;n>=0;n--){var c=s[n],d=new _.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=c,d.source="library_folder",o.push(d)}this.initChainCallControl({length:o.length,action:"to_history",history_name:t}),r.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(o,t)},updateProgress:function(){this.progress+=this.progressStep,a(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";a(".completion_span").text(e)},download:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=a(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});var r=Galaxy.root+"api/libraries/datasets/download/"+t,o={ld_ids:i,folder_ids:s};this.processDownload(r,o,"get")},processDownload:function(e,t,i){if(e&&t){t="string"==typeof t?t:a.param(t);var s="";a.each(t.split("&"),function(){var e=this.split("=");s+='<input type="hidden" name="'+e[0]+'" value="'+e[1]+'" />'}),a('<form action="'+e+'" method="'+(i||"post")+'">'+s+"</form>").appendTo("body").submit().remove(),c.default.info("Your download will begin soon.")}else c.default.error("An error occurred.")},addFilesFromHistoryModal:function(){this.histories=new _.default.GalaxyHistories;var e=this;this.histories.fetch().done(function(){e.modal=Galaxy.modal;var t=e.templateAddFilesFromHistory();e.modal.show({closing_events:!0,title:"Adding datasets from your history",body:t({histories:e.histories.models}),buttons:{Add:function(){e.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),e.fetchAndDisplayHistoryContents(e.histories.models[0].id),a("#dataset_add_bulk").change(function(t){e.fetchAndDisplayHistoryContents(t.target.value)})}).fail(function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")})},importFilesFromPathModal:function(){var e=this;this.modal=Galaxy.modal;var t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.id<t.id?-1:0}),e.list_extensions.unshift(e.auto)},cache:!0}),l.default.get({url:Galaxy.root+"api/genomes",success:function(t){e.list_genomes=[];for(var i in t)e.list_genomes.push({id:t[i][1],text:t[i][0]});e.list_genomes.sort(function(e,t){return e.id>t.id?1:e.id<t.id?-1:0})},cache:!0})},renderSelectBoxes:function(){var e=this;this.select_genome=new u.default.View({css:"library-genome-select",data:e.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"}),this.select_extension=new u.default.View({css:"library-extension-select",data:e.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(e){var t=this,i=this.templateBrowserModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Please select folders or files",body:i({}),buttons:{Import:function(){t.importFromJstreePath(t,e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+t.id,{trigger:!0})}}),a(".libimport-select-all").bind("click",function(){a("#jstree_browser").jstree("check_all")}),a(".libimport-select-none").bind("click",function(){a("#jstree_browser").jstree("uncheck_all")}),this.renderSelectBoxes(),e.disabled_jstree_element="folders",this.renderJstree(e),a("input[type=radio]").change(function(i){"jstree-disable-folders"===i.target.value?(e.disabled_jstree_element="folders",t.renderJstree(e),a(".jstree-folders-message").hide(),a(".jstree-preserve-structure").hide(),a(".jstree-files-message").show()):"jstree-disable-files"===i.target.value&&(a(".jstree-files-message").hide(),a(".jstree-folders-message").show(),a(".jstree-preserve-structure").show(),e.disabled_jstree_element="files",t.renderJstree(e))})},renderJstree:function(e){this.options=s.extend(this.options,e);var t=e.source||"userdir",i=this.options.disabled_jstree_element;this.jstree=new _.default.Jstree,this.jstree.url=this.jstree.urlRoot+"?target="+t+"&format=jstree&disable="+i,this.jstree.fetch({success:function(e,t){a("#jstree_browser").jstree("destroy"),a("#jstree_browser").jstree({core:{data:e},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:!1}})},error:function(e,t){void 0!==t.responseJSON?404001===t.responseJSON.err_code?c.default.warning(t.responseJSON.err_msg):c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})},importFromPathsClicked:function(){var e=this.modal.$el.find(".preserve-checkbox").is(":checked"),t=this.modal.$el.find(".link-checkbox").is(":checked"),i=this.modal.$el.find(".spacetab-checkbox").is(":checked"),s=this.modal.$el.find(".posix-checkbox").is(":checked"),r=this.modal.$el.find(".tag-files").is(":checked"),o=this.select_extension.value(),n=this.select_genome.value(),l=a("textarea#import_paths").val(),d=[];if(l){this.modal.disableButton("Import"),l=l.split("\n");for(var h=l.length-1;h>=0;h--){var _=l[h].trim();0!==_.length&&d.push(_)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:i,to_posix_lines:s,source:"admin_path",file_type:o,tag_using_filenames:r,dbkey:n})}else c.default.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var i=a("#jstree_browser").jstree().get_selected(!0),r=s.filter(i,function(e){return 0==e.state.disabled}),o=this.modal.$el.find(".preserve-checkbox").is(":checked"),n=this.modal.$el.find(".link-checkbox").is(":checked"),l=this.modal.$el.find(".spacetab-checkbox").is(":checked"),d=this.modal.$el.find(".posix-checkbox").is(":checked"),h=this.select_extension.value(),_=this.select_genome.value(),p=this.modal.$el.find(".tag-files").is(":checked"),u=r[0].type,f=[];if(r.length<1)c.default.info("Please select some items first.");else{this.modal.disableButton("Import");for(var g=r.length-1;g>=0;g--)void 0!==r[g].li_attr.full_path&&f.push(r[g].li_attr.full_path);if(this.initChainCallControl({length:f.length,action:"adding_datasets"}),"folder"===u){var m=t.source+"_folder";this.chainCallImportingFolders({paths:f,preserve_dirs:o,link_data:n,space_to_tab:l,to_posix_lines:d,source:m,file_type:h,dbkey:_,tag_using_filenames:p})}else if("file"===u){var m=t.source+"_file";this.chainCallImportingUserdirFiles({paths:f,file_type:h,dbkey:_,link_data:n,space_to_tab:l,to_posix_lines:d,source:m,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=new _.default.HistoryContents({id:e}),i=this;t.fetch({success:function(t){var s=i.templateHistoryContents();i.histories.get(e).set({contents:t}),i.modal.$el.find("#selected_history_content").html(s({history_contents:t.models.reverse()})),i.modal.$el.find(".history-import-select-all").bind("click",function(){a("#selected_history_content [type=checkbox]").prop("checked",!0)}),i.modal.$el.find(".history-import-unselect-all").bind("click",function(){a("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],i=[],s=[];if(e.length<1)c.default.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=a(this).closest("li").data("id");if(e){var s=a(this).closest("li").data("name");t.push(e),i.push(s)}});for(var r=t.length-1;r>=0;r--){var o=t[r],n=new _.default.Item;n.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===i[r]?n.set({from_hdca_id:o}):n.set({from_hda_id:o}),s.push(n)}this.initChainCallControl({length:s.length,action:"adding_datasets"}),this.chainCallAddingHdas(s)}},chainCallImportingIntoHistory:function(e,t){var i=this,s=e.pop();if(void 0===s)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location=Galaxy.root}}),Galaxy.modal.hide(),!0;a.when(s.save({content:s.content,source:s.source})).done(function(){i.updateProgress(),i.chainCallImportingIntoHistory(e,t)}).fail(function(){i.options.chain_call_control.failed_number+=1,i.updateProgress(),i.chainCallImportingIntoHistory(e,t)})},chainCallImportingUserdirFiles:function(e){var t=this,i=e.paths.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?(c.default.success("Selected files imported into the current folder"),Galaxy.modal.hide()):c.default.error("An error occured."),!0;a.when(a.post(Galaxy.root+"api/libraries/datasets?encoded_folder_id="+t.id+"&source="+e.source+"&path="+i+"&file_type="+e.file_type+"&link_data="+e.link_data+"&space_to_tab="+e.space_to_tab+"&to_posix_lines="+e.to_posix_lines+"&dbkey="+e.dbkey+"&tag_using_filenames="+e.tag_using_filenames)).done(function(i){t.updateProgress(),t.chainCallImportingUserdirFiles(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallImportingUserdirFiles(e)})},chainCallImportingFolders:function(e){var t=this,i=e.paths.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?(c.default.success("Selected folders and their contents imported into the current folder."),Galaxy.modal.hide()):c.default.error("An error occured."),!0;a.when(a.post(Galaxy.root+"api/libraries/datasets?encoded_folder_id="+t.id+"&source="+e.source+"&path="+i+"&preserve_dirs="+e.preserve_dirs+"&link_data="+e.link_data+"&to_posix_lines="+e.to_posix_lines+"&space_to_tab="+e.space_to_tab+"&file_type="+e.file_type+"&dbkey="+e.dbkey+"&tag_using_filenames="+e.tag_using_filenames)).done(function(i){t.updateProgress(),t.chainCallImportingFolders(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallImportingFolders(e)})},chainCallAddingHdas:function(e){var t=this;this.added_hdas=new _.default.Folder;var i=e.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected datasets from history added to the folder"):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no datasets were added to the folder."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the datasets could not be added to the folder"),Galaxy.modal.hide(),this.added_hdas;a.when(i.save({from_hda_id:i.get("from_hda_id")})).done(function(i){Galaxy.libraries.folderListView.collection.add(i),t.updateProgress(),t.chainCallAddingHdas(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallAddingHdas(e)})},chainCallDeletingItems:function(e){var t=this;this.deleted_items=new _.default.Folder;var i=e.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected items were deleted."):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no items were deleted. Please make sure you have sufficient permissions."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the items could not be deleted. Please make sure you have sufficient permissions."),Galaxy.modal.hide(),this.deleted_items;i.destroy().done(function(s){if(Galaxy.libraries.folderListView.collection.remove(i.id),t.updateProgress(),Galaxy.libraries.folderListView.options.include_deleted){var a=null;"folder"===s.type||"LibraryFolder"===s.model_class?a=new _.default.FolderAsModel(s):"file"===s.type||"LibraryDataset"===s.model_class?a=new _.default.Item(s):(Galaxy.emit.error("Unknown library item type found.","datalibs"),Galaxy.emit.error(s.type||s.model_class,"datalibs")),Galaxy.libraries.folderListView.collection.add(a)}t.chainCallDeletingItems(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallDeletingItems(e)})},checkIncludeDeleted:function(e){e.target.checked?Galaxy.libraries.folderListView.fetchFolder({include_deleted:!0}):Galaxy.libraries.folderListView.fetchFolder({include_deleted:!1})},deleteSelectedItems:function(){var e=[],t=[],i=this.findCheckedRows();if(0===i.length)c.default.info("You must select at least one item for deletion.");else{var s=this.templateDeletingItemsProgressBar();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Deleting selected items",body:s({}),buttons:{Close:function(){Galaxy.modal.hide()}}}),this.options.chain_call_control.total_number=0,this.options.chain_call_control.failed_number=0,i.each(function(){var i=a(this).closest("tr").data("id");void 0!==i&&("F"==i.substring(0,1)?t.push(i):e.push(i))});var r=e.length+t.length;this.progressStep=100/r,this.progress=0;for(var o=[],n=e.length-1;n>=0;n--){var l=new _.default.Item({id:e[n]});o.push(l)}for(var n=t.length-1;n>=0;n--){var d=new _.default.FolderAsModel({id:t[n]});o.push(d)}this.options.chain_call_control.total_number=r,this.chainCallDeletingItems(o)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new _.default.Library({id:this.options.parent_library_id}),e.fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}}))},showLocInfoModal:function(e){var t=this,i=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Location Details",body:i({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.default.error("Invalid import source.")}},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(t)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return a("#folder_list_body").find(":checked")},templateToolBar:function(){return s.template(['<div class="library_style_container">','<div id="library_toolbar">','<form class="form-inline" role="form">',"<span><strong>DATA LIBRARIES</strong></span>",'<span class="library-paginator folder-paginator"></span>','<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">',"<label>",'<input id="include_deleted_datasets_chk" type="checkbox">include deleted</input>',"</label>","</div>",'<button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items toolbar-item" type="button">','<span class="fa fa-plus"></span><span class="fa fa-folder"></span>',"</button>","<% if(mutiple_add_dataset_options) { %>",'<div class="btn-group add-library-items" style="display:none;">','<button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">','<span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#folders/<%= id %>/import/history"> from History</a></li>',"<% if(Galaxy.config.user_library_import_dir !== null) { %>",'<li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>',"<% } %>","<% if(Galaxy.config.allow_library_path_paste) { %>",'<li class="divider"></li>','<li class="dropdown-header">Admins only</li>',"<% if(Galaxy.config.library_import_dir !== null) { %>",'<li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>',"<% } %>","<% if(Galaxy.config.allow_library_path_paste) { %>",'<li><a href="#folders/<%= id %>/import/path">from Path</a></li>',"<% } %>","<% } %>","</ul>","</div>","<% } else { %>",'<a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button">','<span class="fa fa-plus"></span><span class="fa fa-file"></span>',"</a>","<% } %>",'<button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<div class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">','<button title="Download selected items as archive" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">','<span class="fa fa-download"></span> Download <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>','<li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>','<li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>',"</ul>","</div>",'<button data-toggle="tooltip" data-placement="top" title="Mark selected items deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button">','<span class="fa fa-times"></span> Delete</button>','<button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show location details" class="primary-button toolbtn-show-locinfo" style="margin-left: 0.5em;" type="button">','<span class="fa fa-info-circle"></span>',"&nbsp;Details","</button>",'<span class="help-button" data-toggle="tooltip" data-placement="top" title="See this screen annotated">','<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">','<button class="primary-button" type="button">','<span class="fa fa-question-circle"></span>',"&nbsp;Help","</button>","</a>","</span>","</div>","</form>",'<div id="folder_items_element">',"</div>",'<div class="folder-paginator paginator-bottom"></div>',"</div>"].join(""))},templateLocInfoInModal:function(){return s.template(["<div>",'<table class="grid table table-condensed">',"<thead>",'<th style="width: 25%;">library</th>',"<th></th>","</thead>","<tbody>","<tr>","<td>name</td>",'<td><%- library.get("name") %></td>',"</tr>",'<% if(library.get("description") !== "") { %>',"<tr>","<td>description</td>",'<td><%- library.get("description") %></td>',"</tr>","<% } %>",'<% if(library.get("synopsis") !== "") { %>',"<tr>","<td>synopsis</td>",'<td><%- library.get("synopsis") %></td>',"</tr>","<% } %>",'<% if(library.get("create_time_pretty") !== "") { %>',"<tr>","<td>created</td>",'<td><span title="<%- library.get("create_time") %>"><%- library.get("create_time_pretty") %></span></td>',"</tr>","<% } %>","<tr>","<td>id</td>",'<td><%- library.get("id") %></td>',"</tr>","</tbody>","</table>",'<table class="grid table table-condensed">',"<thead>",'<th style="width: 25%;">folder</th>',"<th></th>","</thead>","<tbody>","<tr>","<td>name</td>","<td><%- options.folder_name %></td>","</tr>",'<% if(options.folder_description !== "") { %>',"<tr>","<td>description</td>","<td><%- options.folder_description %></td>","</tr>","<% } %>","<tr>","<td>id</td>","<td><%- options.id %></td>","</tr>","</tbody>","</table>","</div>"].join(""))},templateNewFolderInModal:function(){return s.template(['<div id="new_folder_modal">',"<form>",'<input type="text" name="Name" value="" placeholder="Name" autofocus>','<input type="text" name="Description" value="" placeholder="Description">',"</form>","</div>"].join(""))},templateBulkImportInModal:function(){return s.template(["<div>",'<div class="library-modal-item">',"Select history: ",'<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; " autofocus>',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>",'<div class="library-modal-item">',"or create new: ",'<input type="text" name="history_name" value="" placeholder="name 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s.template(['<div class="import_text">',"</div>",'<div class="progress">','<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">','<span class="completion_span">0% Complete</span>',"</div>","</div>"].join(""))},templateBrowserModal:function(){return s.template(['<div id="file_browser_modal">','<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder ignoring their folder structure.</div>','<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>','<div style="margin-bottom:1em;">','<label title="Switch to selecting files" class="radio-inline import-type-switch">','<input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Choose Files',"</label>",'<label title="Switch to selecting folders" class="radio-inline import-type-switch">','<input type="radio" name="jstree-radio" value="jstree-disable-files"> Choose Folders',"</label>","</div>",'<div style="margin-bottom:1em;">','<label class="checkbox-inline jstree-preserve-structure" style="display:none;">','<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',"Preserve directory structure","</label>",'<label class="checkbox-inline">','<input class="link-checkbox" type="checkbox" value="link_files">',"Link files instead of copying","</label>",'<label class="checkbox-inline">','<input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">',"Convert line endings to POSIX","</label>",'<label class="checkbox-inline">','<input class="spacetab-checkbox" type="checkbox" value="space_to_tab">',"Convert spaces to tabs","</label>","</div>",'<button title="Select all files" type="button" class="button primary-button libimport-select-all">',"Select all","</button>",'<button 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o=i(42),n=r(o),l=i(156),d=r(l),c=i(139),h=r(c),_=e.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=s.extend(this.options,e),this.options.id&&this.fetchLibrary()},fetchLibrary:function(e){this.options=s.extend(this.options,e),this.model=new d.default.Library({id:this.options.id});var t=this;this.model.fetch({success:function(){t.options.show_permissions&&t.showPermissions()},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):n.default.error("An error occurred. 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0!==t.responseJSON?n.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):n.default.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=s.extend(this.options,e);var t=this.templateFolder();a(".tooltip").hide();var i,r=this.folderContainer.attributes.metadata.full_path;if(i=1===r.length?0:r[r.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:i,order:this.current_sort_order})),this.options.dataset_id){var o=s.findWhere(self.rowViews,{id:this.options.dataset_id});o?o.showDatasetDetails():n.default.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();a("#center [data-toggle]").tooltip(),a("#center").css("overflow","auto")},paginate:function(e){this.options=s.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),i=null;i=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=i.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(i=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(i)},rePaint:function(e){this.options=s.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){s.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{current_sort_order:!1})}),a("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;s.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new h.default.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return a(this).data("id")&&a(this).data("id")===e.id}).remove()},removeAllRows:function(){a(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),this.current_sort_order="asc"===this.current_sort_order?"desc":"asc",this.current_sort_key=e.currentTarget.className.replace("sort-folder-",""),this.collection.sortFolder(this.current_sort_key,this.current_sort_order),this.renderSortIcon()},selectAll:function(e){var t=e.target.checked,i=this;a(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=a(this).closest("tr");t?i.makeDarkRow(e):i.makeWhiteRow(e)})},selectClickedRow:function(e){var t,i,s="";t=a(e.target).closest("tr"),"input"===e.target.localName?(s=e.target,i="input"):"td"===e.target.localName&&(s=t.find(":checkbox")[0],i="td"),s.checked?"td"===i?(s.checked="",this.makeWhiteRow(t)):"input"===i&&this.makeDarkRow(t):"td"===i?(s.checked="selected",this.makeDarkRow(t)):"input"===i&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.current_sort_order?(a('[class*="sort-icon"]').removeClass("fa-sort-alpha-desc").removeClass("fa-sort-alpha-asc"),a(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-asc")):a(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-desc")},templateFolder:function(){return s.template(['<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>',"<% _.each(path, function(path_item) { %>","<% if (path_item[0] != id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<table data-library-id="<%- parent_library_id  %>" class="grid table table-condensed">',"<thead>",'<th class="button_heading"></th>','<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>','<th><a class="sort-folder-name" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon-name fa fa-sort-alpha-<%- order %>"></span></th>','<th style="width:20%;"><a class="sort-folder-description" title="Click to reverse order" href="#">description</a> <span title="Sorted alphabetically" class="sort-icon-description fa"></span></th>','<th style="width:5%;"><a class="sort-folder-file_ext" title="Click to reverse order" href="#">data type</a> <span title="Sorted alphabetically" class="sort-icon-file_ext fa"></span></th>','<th style="width:10%;">size</th>','<th style="width:160px;">time updated (UTC)</th>','<th style="width:5%;"><a class="sort-folder-state" title="Click to reverse order" href="#">state</a> <span title="Sorted alphabetically" class="sort-icon-state fa"></span></th>','<th style="width:150px;"></th> ',"</thead>",'<tbody id="folder_list_body">','<tr id="first_folder_item">',"<td>",'<a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a>',"</td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","<td></td>","</tr>","</tbody>","</table>",'<div class="empty-folder-message" style="display:none;">',"This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up",' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>"].join(""))}});t.default={FolderListView:_}}).call(t,i(1),i(2),i(0))},302:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=i(225),h=r(c),_=e.View.extend({events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder","click .edit_folder_btn":"startModifications","click .cancel_folder_btn":"cancelModifications","click .save_folder_btn":"saveModifications"},defaults:{type:null,visibility_config:{edit_folder_btn:!1,save_folder_btn:!1,cancel_folder_btn:!1,permission_folder_btn:!1},edit_mode:!1},initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.render(this.options)},render:function(e){this.options=s.extend(this.options,e);var t=this.options.model,i=null;return"folder"===t.get("type")||"LibraryFolder"===t.get("model_class")?(this.options.type="folder",this.prepareButtons(t),i=t.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===t.get("type")||"LibraryDatasetDatasetAssociation"===t.get("model_class")||"LibraryDataset"===t.get("model_class")?(this.options.type="file",i=t.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(Galaxy.emit.error("Unknown library item type found."),Galaxy.emit.error(t.get("type")||t.get("model_class"))),this.setElement(i({content_item:t,edit_mode:this.options.edit_mode,button_config:this.options.visibility_config})),this.$el.show(),this},prepareButtons:function(e){var t=this.options.visibility_config;!1===this.options.edit_mode?(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("deleted")?(t.edit_folder_btn=!1,t.permission_folder_btn=!1):!1===e.get("deleted")&&(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("can_modify")&&(t.edit_folder_btn=!0),!0===e.get("can_manage")&&(t.permission_folder_btn=!0))):!0===this.options.edit_mode&&(t.edit_folder_btn=!1,t.permission_folder_btn=!1,t.save_folder_btn=!0,t.cancel_folder_btn=!0),this.options.visibility_config=t},showDatasetDetails:function(){Galaxy.libraries.datasetView=new h.default.LibraryDatasetView({id:this.id})},undeleteDataset:function(e){a(".tooltip").hide();var t=this,i=a(e.target).closest("tr").data("id"),s=Galaxy.libraries.folderListView.collection.get(i);s.url=s.urlRoot+s.id+"?undelete=true",s.destroy({success:function(e,s){Galaxy.libraries.folderListView.collection.remove(i);var a=new d.default.Item(s);Galaxy.libraries.folderListView.collection.add(a),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var e=t.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+e+"/datasets/"+t.id}})},error:function(e,t){void 0!==t.responseJSON?n.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){a(".tooltip").hide();var t=a(e.target).closest("tr").data("id"),i=Galaxy.libraries.folderListView.collection.get(t);i.url=i.urlRoot+i.id+"?undelete=true",i.destroy({success:function(e,i){Galaxy.libraries.folderListView.collection.remove(t);var s=new d.default.FolderAsModel(i);Galaxy.libraries.folderListView.collection.add(s),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?n.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_folder_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void n.default.warning("Folder name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_folder_description").val();if(void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.options.edit_mode=!1,a.repaint(e),n.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),n.default.info("Nothing has changed.")},repaint:function(){a(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return s.template(['<tr class="folder_row light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Folder" class="fa fa-folder-o"/>',"</td>",'<td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>',"<% if(!edit_mode) { %>","<td>",'<a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>',"</td>","<td>",'<%- content_item.get("description") %>',"</td>","<% } else if(edit_mode){ %>",'<td><textarea rows="4" class="form-control input_folder_name" placeholder="name" ><%- content_item.get("name") %></textarea></td>','<td><textarea rows="4" class="form-control input_folder_description" placeholder="description" ><%- content_item.get("description") %></textarea></td>',"<% } %>","<td>folder</td>","<td></td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td></td>","<td>","<% if(edit_mode) { %>",'<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-floppy-o"/> Save',"</button>",'<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-times"/> Cancel',"</button>","<% } else if (!edit_mode){%>",'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- content_item.get("name") %>\'" class="primary-button btn-xs edit_folder_btn" type="button" style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-pencil"/> Edit',"</button>",'<a href="#/folders/<%- content_item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permission_folder_btn" title="Permissions of \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">','<span class="fa fa-group"/> Manage',"</button>","</a>","<% } %>","</td>","</tr>"].join(""))},templateRowFile:function(){return s.template(['<tr class="dataset_row light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Dataset" class="fa fa-file-o"/>',"</td>",'<td style="text-align: center; ">','<input style="margin: 0;" type="checkbox">',"</td>","<td>",'<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"<a>","</td>",'<td><%- content_item.get("message") %></td>','<td><%= _.escape(content_item.get("file_ext")) %></td>','<td><%= _.escape(content_item.get("file_size")) %></td>','<td><%= _.escape(content_item.get("update_time")) %></td>',"<td>",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","</td>","<td>",'<% if (content_item.get("is_unrestricted")) { %>','<span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"/>',"<% } %>",'<% if (content_item.get("is_private")) { %>','<span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"/>',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','<span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"/>',"<% } %>",'<% if (content_item.get("can_manage")) { %>','<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Permissions of \'<%- content_item.get("name") %>\'">','<span class="fa fa-group"/> Manage',"</button>","</a>","<% } %>","</td>","</tr>"].join(""))},templateRowDeletedFile:function(){return s.template(['<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Dataset" class="fa fa-file-o"/>',"</td>","<td></td>",'<td style="color:grey;">','<%- content_item.get("name") %>',"</td>","<td>",'<%- content_item.get("message") %>',"</td>","<td>",'<%= _.escape(content_item.get("file_ext")) %>',"</td>","<td>",'<%= _.escape(content_item.get("file_size")) %>',"</td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td>",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","</td>","<td>",'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;">','<span class="fa fa-unlock"/> Undelete',"</button>","</td>","</tr>"].join(""))},templateRowDeletedFolder:function(){return s.template(['<tr class="active deleted_folder light library-row" data-id="<%- content_item.id %>">',"<td>",'<span title="Folder" class="fa fa-folder-o"/>',"</td>","<td></td>",'<td style="color:grey;">','<%- content_item.get("name") %>',"</td>","<td>",'<%- content_item.get("description") %>',"</td>","<td>","folder","</td>","<td></td>","<td>",'<%= _.escape(content_item.get("update_time")) %>',"</td>","<td></td>","<td>",'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;">','<span class="fa fa-unlock"/> Undelete',"</button>","</td>","</tr>"].join(""))}});t.default={FolderRowView:_}}).call(t,i(1),i(2),i(0))},303:function(e,t,i){"use strict";(function(e,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=a(r),n=i(156),l=a(n),d=i(304),c=a(d),h=i(2),_=a(h),p=e.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(e){this.options=_.default.defaults(this.options||{},e,this.defaults);var t=this;this.modal=null,this.collection=new l.default.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){t.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})},render:function(e){this.options=_.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),i=null,a=null,r=function(e){return!0===e.get("public")};if(s(".tooltip").hide(),void 0!==e&&(a=void 0!==e.models?e.models:null),null!==this.collection&&null===a)this.sortLibraries(),i=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r));else if(null!==a){if(Galaxy.libraries.preferences.get("with_deleted"))i=a;else{var o=function(e){return!1===e.get("deleted")};i=_.default.filter(a,o)}Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r))}else i=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=i.length;var n=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&n<this.options.total_libraries_count?(i=i.slice(n,n+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=i.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(i=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(i)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),s("#center [data-toggle]").tooltip(),s("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t<e.length;t++){var i=e[t];this.renderOne({library:i})}},renderOne:function(e){var t=e.library,i=new c.default.LibraryRowView(t);this.$el.find("#library_list_body").append(i.el)},sort_clicked:function(){"asc"===Galaxy.libraries.preferences.get("sort_order")?Galaxy.libraries.preferences.set({sort_order:"desc"}):Galaxy.libraries.preferences.set({sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortLibraries("name","asc"):"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortLibraries("name","desc"))},searchLibraries:function(e){if(""!==s.trim(e)){var t=null;t=this.collection.search(e),this.options.searching=!0,this.render({models:t,show_page:1})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return _.default.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});t.default={LibraryListView:p}}).call(t,i(1),i(0))},304:function(e,t,i){"use strict";(function(e,s,a){Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=function(e){return e&&e.__esModule?e:{default:e}}(r),n=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){s(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_library_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_library_description").val();void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0);var a=this.$el.find(".input_library_synopsis").val();if(void 0!==a&&a!==e.get("synopsis")&&(e.set("synopsis",a),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.edit_mode=!1,r.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(s(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return a.template(['<tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<td style="color:grey;"><%- library.get("name") %></td>',"<% } else { %>",'<td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>',"<% } else { %>",'<td><%= _.escape(library.get("description"))%></td>',"<% } %>","<% } else { %>","<td></td>","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>',"<% } else { %>",'<td><%= _.escape(library.get("synopsis"))%></td>',"<% } %>","<% } else { %>","<td></td>","<% } %>","<% } else if(edit_mode){ %>",'<td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>','<td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>','<td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>',"<% } %>",'<td class="right-center">','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>','<span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg"> </span>',"<% }%>",'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- library.get("name") %>\'" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span> Edit</button>','<a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Permissions of \'<%- library.get("name") %>\'" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span> Manage</button></a>','<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"></span> Save</button>','<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"></span> Cancel</button>','<button data-toggle="tooltip" data-placement="top" title="Delete \'<%- library.get("name") %>\'" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"></span> Delete</button>','<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey; <% if(button_config.undelete_library_btn === false) { print("display:none;") } %>" class="fa fa-ban fa-lg"></span>','<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- library.get("name") %>\' " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"></span> Undelete</button>',"</td>","</tr>"].join(""))}});t.default={LibraryRowView:n}}).call(t,i(1),i(0),i(2))},305:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=e.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click .page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=s.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),t=!1,i=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:i})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){t.createNewLibrary()},Close:function(){t.modal.hide()}}})},createNewLibrary:function(){var e=this.serializeNewLibrary();if(this.validateNewLibrary(e)){var t=new d.default.Library,i=this;t.save(e,{success:function(e){Galaxy.libraries.libraryListView.collection.add(e),i.modal.hide(),i.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),n.default.success("Library created.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured.")}})}else n.default.error("Library's name is missing.");return!1},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(t)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){a("input[name='Name']").val(""),a("input[name='Description']").val(""),a("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val(),synopsis:a("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var t=a(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return s.template(['<div class="library_style_container">','<div id="toolbar_form">','<div id="library_toolbar">','<form class="form-inline" role="form">','<span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>','<span id="library_paginator" class="library-paginator">',"</span>",'<div class="form-group toolbar-item">','<input type="text" class="form-control library-search-input" placeholder="Search" size="30">',"</div>","<% if(admin_user === true) { %>",'<div class="checkbox toolbar-item" style="height: 20px;">',"<label>",'<input id="include_deleted_chk" type="checkbox">',"include deleted ","</input>","</label>","<label>",'<input id="exclude_restricted_chk" type="checkbox">',"exclude restricted","</input>","</label>","</div>",'<span class="toolbar-item" data-toggle="tooltip" data-placement="top" title="Create New Library">','<button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button>',"</span>","<% } %>",'<span class="help-button" data-toggle="tooltip" data-placement="top" title="See this screen annotated">','<a href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">','<button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button>',"</a>","</span>","</form>","</div>","</div>",'<div id="libraries_element">',"</div>","</div>"].join(""))},templatePaginator:function(){return s.template(['<ul class="pagination pagination-sm">',"<% if ( ( show_page - 1 ) > 0 ) { %>","<% if ( ( show_page - 1 ) > page_count ) { %>",'<li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',"<% } else { %>",'<li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>',"<% } %>","<% } else { %>",'<li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>','<li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',"<% } %>",'<li class="active">','<a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>',"</li>","<% if ( ( show_page ) < page_count ) { %>",'<li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>','<li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',"<% } else { %>",'<li class="disabled"><a href="#page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>','<li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',"<% } %>","</ul>","<span>",' <%- libraries_shown %> libraries shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- library_page_size %> per page" class="page_size_prompt">(change)</a>',"</span>","<span>"," <%- total_libraries_count %> total","</span>"].join(""))},templateNewLibraryInModal:function(){return s.template(['<div id="new_library_modal">',"<form>",'<input type="text" name="Name" value="" placeholder="Name" autofocus>','<input type="text" name="Description" value="" placeholder="Description">','<input type="text" name="Synopsis" value="" placeholder="Synopsis">',"</form>","</div>"].join(""))}});t.default={LibraryToolbarView:c}}).call(t,i(1),i(2),i(0))},306:function(e,t,i){"use strict";(function(e,s,a,r){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),l=o(n),d=i(42),c=o(d),h=i(156),_=o(h),p=i(139),u=o(p);i(198);var f=e.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=s.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();a("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=s.extend(this.options,e),!0===this.options.can_add_library_item?a(".add-library-items").show():a(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(a(".dataset-manipulation").show(),a(".logged-dataset-manipulation").hide()):(a(".logged-dataset-manipulation").show(),a(".dataset-manipulation").show()):(a(".logged-dataset-manipulation").hide(),a(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var t=this.serialize_new_folder();if(this.validate_new_folder(t)){var i,s=new _.default.FolderAsModel,a=e.history.fragment.split("/");i=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],s.url=s.urlRoot+i,s.save(t,{success:function(e){Galaxy.modal.hide(),c.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})}else c.default.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)c.default.info("You must select some datasets first.");else{var e=this;this.histories=new _.default.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)a.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,i){c.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var i=a("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=i;var s=a("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(i,s),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=a(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});for(var o=[],n=i.length-1;n>=0;n--){var l=i[n],d=new _.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=l,d.source="library",o.push(d)}for(var n=s.length-1;n>=0;n--){var c=s[n],d=new _.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=c,d.source="library_folder",o.push(d)}this.initChainCallControl({length:o.length,action:"to_history",history_name:t}),r.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(o,t)},updateProgress:function(){this.progress+=this.progressStep,a(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";a(".completion_span").text(e)},download:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=a(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});var r=Galaxy.root+"api/libraries/datasets/download/"+t,o={ld_ids:i,folder_ids:s};this.processDownload(r,o,"get")},processDownload:function(e,t,i){if(e&&t){t="string"==typeof t?t:a.param(t);var s="";a.each(t.split("&"),function(){var e=this.split("=");s+='<input type="hidden" name="'+e[0]+'" value="'+e[1]+'" />'}),a('<form action="'+e+'" method="'+(i||"post")+'">'+s+"</form>").appendTo("body").submit().remove(),c.default.info("Your download will begin soon.")}else c.default.error("An error occurred.")},addFilesFromHistoryModal:function(){this.histories=new _.default.GalaxyHistories;var e=this;this.histories.fetch().done(function(){e.modal=Galaxy.modal;var t=e.templateAddFilesFromHistory();e.modal.show({closing_events:!0,title:"Adding datasets from your history",body:t({histories:e.histories.models}),buttons:{Add:function(){e.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),e.fetchAndDisplayHistoryContents(e.histories.models[0].id),a("#dataset_add_bulk").change(function(t){e.fetchAndDisplayHistoryContents(t.target.value)})}).fail(function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")})},importFilesFromPathModal:function(){var e=this;this.modal=Galaxy.modal;var t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.id<t.id?-1:0}),e.list_extensions.unshift(e.auto)},cache:!0}),l.default.get({url:Galaxy.root+"api/genomes",success:function(t){e.list_genomes=[];for(var i in t)e.list_genomes.push({id:t[i][1],text:t[i][0]});e.list_genomes.sort(function(e,t){return e.id>t.id?1:e.id<t.id?-1:0})},cache:!0})},renderSelectBoxes:function(){var e=this;this.select_genome=new u.default.View({css:"library-genome-select",data:e.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"}),this.select_extension=new u.default.View({css:"library-extension-select",data:e.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(e){var t=this,i=this.templateBrowserModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Please select folders or files",body:i({}),buttons:{Import:function(){t.importFromJstreePath(t,e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+t.id,{trigger:!0})}}),a(".libimport-select-all").bind("click",function(){a("#jstree_browser").jstree("check_all")}),a(".libimport-select-none").bind("click",function(){a("#jstree_browser").jstree("uncheck_all")}),this.renderSelectBoxes(),e.disabled_jstree_element="folders",this.renderJstree(e),a("input[type=radio]").change(function(i){"jstree-disable-folders"===i.target.value?(e.disabled_jstree_element="folders",t.renderJstree(e),a(".jstree-folders-message").hide(),a(".jstree-preserve-structure").hide(),a(".jstree-files-message").show()):"jstree-disable-files"===i.target.value&&(a(".jstree-files-message").hide(),a(".jstree-folders-message").show(),a(".jstree-preserve-structure").show(),e.disabled_jstree_element="files",t.renderJstree(e))})},renderJstree:function(e){this.options=s.extend(this.options,e);var t=e.source||"userdir",i=this.options.disabled_jstree_element;this.jstree=new _.default.Jstree,this.jstree.url=this.jstree.urlRoot+"?target="+t+"&format=jstree&disable="+i,this.jstree.fetch({success:function(e,t){a("#jstree_browser").jstree("destroy"),a("#jstree_browser").jstree({core:{data:e},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:!1}})},error:function(e,t){void 0!==t.responseJSON?404001===t.responseJSON.err_code?c.default.warning(t.responseJSON.err_msg):c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})},importFromPathsClicked:function(){var e=this.modal.$el.find(".preserve-checkbox").is(":checked"),t=this.modal.$el.find(".link-checkbox").is(":checked"),i=this.modal.$el.find(".spacetab-checkbox").is(":checked"),s=this.modal.$el.find(".posix-checkbox").is(":checked"),r=this.modal.$el.find(".tag-files").is(":checked"),o=this.select_extension.value(),n=this.select_genome.value(),l=a("textarea#import_paths").val(),d=[];if(l){this.modal.disableButton("Import"),l=l.split("\n");for(var h=l.length-1;h>=0;h--){var _=l[h].trim();0!==_.length&&d.push(_)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:i,to_posix_lines:s,source:"admin_path",file_type:o,tag_using_filenames:r,dbkey:n})}else c.default.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var i=a("#jstree_browser").jstree().get_selected(!0),r=s.filter(i,function(e){return 0==e.state.disabled}),o=this.modal.$el.find(".preserve-checkbox").is(":checked"),n=this.modal.$el.find(".link-checkbox").is(":checked"),l=this.modal.$el.find(".spacetab-checkbox").is(":checked"),d=this.modal.$el.find(".posix-checkbox").is(":checked"),h=this.select_extension.value(),_=this.select_genome.value(),p=this.modal.$el.find(".tag-files").is(":checked"),u=r[0].type,f=[];if(r.length<1)c.default.info("Please select some items first.");else{this.modal.disableButton("Import");for(var g=r.length-1;g>=0;g--)void 0!==r[g].li_attr.full_path&&f.push(r[g].li_attr.full_path);if(this.initChainCallControl({length:f.length,action:"adding_datasets"}),"folder"===u){var m=t.source+"_folder";this.chainCallImportingFolders({paths:f,preserve_dirs:o,link_data:n,space_to_tab:l,to_posix_lines:d,source:m,file_type:h,dbkey:_,tag_using_filenames:p})}else if("file"===u){var m=t.source+"_file";this.chainCallImportingUserdirFiles({paths:f,file_type:h,dbkey:_,link_data:n,space_to_tab:l,to_posix_lines:d,source:m,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=new _.default.HistoryContents({id:e}),i=this;t.fetch({success:function(t){var s=i.templateHistoryContents();i.histories.get(e).set({contents:t}),i.modal.$el.find("#selected_history_content").html(s({history_contents:t.models.reverse()})),i.modal.$el.find(".history-import-select-all").bind("click",function(){a("#selected_history_content [type=checkbox]").prop("checked",!0)}),i.modal.$el.find(".history-import-unselect-all").bind("click",function(){a("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],i=[],s=[];if(e.length<1)c.default.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=a(this).closest("li").data("id");if(e){var s=a(this).closest("li").data("name");t.push(e),i.push(s)}});for(var r=t.length-1;r>=0;r--){var o=t[r],n=new _.default.Item;n.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===i[r]?n.set({from_hdca_id:o}):n.set({from_hda_id:o}),s.push(n)}this.initChainCallControl({length:s.length,action:"adding_datasets"}),this.chainCallAddingHdas(s)}},chainCallImportingIntoHistory:function(e,t){var i=this,s=e.pop();if(void 0===s)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location=Galaxy.root}}),Galaxy.modal.hide(),!0;a.when(s.save({content:s.content,source:s.source})).done(function(){i.updateProgress(),i.chainCallImportingIntoHistory(e,t)}).fail(function(){i.options.chain_call_control.failed_number+=1,i.updateProgress(),i.chainCallImportingIntoHistory(e,t)})},chainCallImportingUserdirFiles:function(e){var t=this,i=e.paths.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?(c.default.success("Selected files imported into the current folder"),Galaxy.modal.hide()):c.default.error("An error occured."),!0;a.when(a.post(Galaxy.root+"api/libraries/datasets?encoded_folder_id="+t.id+"&source="+e.source+"&path="+i+"&file_type="+e.file_type+"&link_data="+e.link_data+"&space_to_tab="+e.space_to_tab+"&to_posix_lines="+e.to_posix_lines+"&dbkey="+e.dbkey+"&tag_using_filenames="+e.tag_using_filenames)).done(function(i){t.updateProgress(),t.chainCallImportingUserdirFiles(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallImportingUserdirFiles(e)})},chainCallImportingFolders:function(e){var t=this,i=e.paths.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?(c.default.success("Selected folders and their contents imported into the current folder."),Galaxy.modal.hide()):c.default.error("An error occured."),!0;a.when(a.post(Galaxy.root+"api/libraries/datasets?encoded_folder_id="+t.id+"&source="+e.source+"&path="+i+"&preserve_dirs="+e.preserve_dirs+"&link_data="+e.link_data+"&to_posix_lines="+e.to_posix_lines+"&space_to_tab="+e.space_to_tab+"&file_type="+e.file_type+"&dbkey="+e.dbkey+"&tag_using_filenames="+e.tag_using_filenames)).done(function(i){t.updateProgress(),t.chainCallImportingFolders(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallImportingFolders(e)})},chainCallAddingHdas:function(e){var t=this;this.added_hdas=new _.default.Folder;var i=e.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected datasets from history added to the folder"):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no datasets were added to the folder."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the datasets could not be added to the folder"),Galaxy.modal.hide(),this.added_hdas;a.when(i.save({from_hda_id:i.get("from_hda_id")})).done(function(i){Galaxy.libraries.folderListView.collection.add(i),t.updateProgress(),t.chainCallAddingHdas(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallAddingHdas(e)})},chainCallDeletingItems:function(e){var t=this;this.deleted_items=new _.default.Folder;var i=e.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected items were deleted."):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.default.error("There was an error and no items were deleted. Please make sure you have sufficient permissions."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.default.warning("Some of the items could not be deleted. Please make sure you have sufficient permissions."),Galaxy.modal.hide(),this.deleted_items;i.destroy().done(function(s){if(Galaxy.libraries.folderListView.collection.remove(i.id),t.updateProgress(),Galaxy.libraries.folderListView.options.include_deleted){var a=null;"folder"===s.type||"LibraryFolder"===s.model_class?a=new _.default.FolderAsModel(s):"file"===s.type||"LibraryDataset"===s.model_class?a=new _.default.Item(s):(Galaxy.emit.error("Unknown library item type found.","datalibs"),Galaxy.emit.error(s.type||s.model_class,"datalibs")),Galaxy.libraries.folderListView.collection.add(a)}t.chainCallDeletingItems(e)}).fail(function(){t.options.chain_call_control.failed_number+=1,t.updateProgress(),t.chainCallDeletingItems(e)})},checkIncludeDeleted:function(e){e.target.checked?Galaxy.libraries.folderListView.fetchFolder({include_deleted:!0}):Galaxy.libraries.folderListView.fetchFolder({include_deleted:!1})},deleteSelectedItems:function(){var e=[],t=[],i=this.findCheckedRows();if(0===i.length)c.default.info("You must select at least one item for deletion.");else{var s=this.templateDeletingItemsProgressBar();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Deleting selected items",body:s({}),buttons:{Close:function(){Galaxy.modal.hide()}}}),this.options.chain_call_control.total_number=0,this.options.chain_call_control.failed_number=0,i.each(function(){var i=a(this).closest("tr").data("id");void 0!==i&&("F"==i.substring(0,1)?t.push(i):e.push(i))});var r=e.length+t.length;this.progressStep=100/r,this.progress=0;for(var o=[],n=e.length-1;n>=0;n--){var l=new _.default.Item({id:e[n]});o.push(l)}for(var n=t.length-1;n>=0;n--){var d=new _.default.FolderAsModel({id:t[n]});o.push(d)}this.options.chain_call_control.total_number=r,this.chainCallDeletingItems(o)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new _.default.Library({id:this.options.parent_library_id}),e.fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}}))},showLocInfoModal:function(e){var t=this,i=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Location Details",body:i({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.default.error("Invalid import source.")}},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(t)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return a("#folder_list_body").find(":checked")},templateToolBar:function(){return s.template(['<div class="library_style_container">','<div id="library_toolbar">','<form class="form-inline" role="form">',"<span><strong>DATA LIBRARIES</strong></span>",'<span class="library-paginator folder-paginator"></span>','<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">',"<label>",'<input id="include_deleted_datasets_chk" type="checkbox">include deleted</input>',"</label>","</div>",'<button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items toolbar-item" type="button">','<span class="fa fa-plus"></span><span class="fa fa-folder"></span>',"</button>","<% if(mutiple_add_dataset_options) { %>",'<div class="btn-group add-library-items" style="display:none;">','<button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">','<span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#folders/<%= id %>/import/history"> from History</a></li>',"<% if(Galaxy.config.user_library_import_dir !== null) { %>",'<li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>',"<% } %>","<% if(Galaxy.config.allow_library_path_paste) { %>",'<li class="divider"></li>','<li class="dropdown-header">Admins only</li>',"<% if(Galaxy.config.library_import_dir !== null) { %>",'<li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>',"<% } %>","<% if(Galaxy.config.allow_library_path_paste) { %>",'<li><a href="#folders/<%= id %>/import/path">from Path</a></li>',"<% } %>","<% } %>","</ul>","</div>","<% } else { %>",'<a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button">','<span class="fa fa-plus"></span><span class="fa fa-file"></span>',"</a>","<% } %>",'<button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<div class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">','<button title="Download selected items as archive" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">','<span class="fa fa-download"></span> Download <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>','<li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>','<li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>',"</ul>","</div>",'<button data-toggle="tooltip" data-placement="top" title="Mark selected items deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button">','<span class="fa fa-times"></span> Delete</button>','<button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show location details" class="primary-button toolbtn-show-locinfo" style="margin-left: 0.5em;" type="button">','<span class="fa fa-info-circle"></span>',"&nbsp;Details","</button>",'<span class="help-button" data-toggle="tooltip" data-placement="top" title="See this screen annotated">','<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">','<button class="primary-button" type="button">','<span class="fa fa-question-circle"></span>',"&nbsp;Help","</button>","</a>","</span>","</div>","</form>",'<div id="folder_items_element">',"</div>",'<div class="folder-paginator paginator-bottom"></div>',"</div>"].join(""))},templateLocInfoInModal:function(){return s.template(["<div>",'<table class="grid table table-condensed">',"<thead>",'<th style="width: 25%;">library</th>',"<th></th>","</thead>","<tbody>","<tr>","<td>name</td>",'<td><%- library.get("name") %></td>',"</tr>",'<% if(library.get("description") !== "") { %>',"<tr>","<td>description</td>",'<td><%- library.get("description") %></td>',"</tr>","<% } %>",'<% if(library.get("synopsis") !== "") { %>',"<tr>","<td>synopsis</td>",'<td><%- library.get("synopsis") %></td>',"</tr>","<% } %>",'<% if(library.get("create_time_pretty") !== "") { %>',"<tr>","<td>created</td>",'<td><span title="<%- library.get("create_time") %>"><%- library.get("create_time_pretty") %></span></td>',"</tr>","<% } %>","<tr>","<td>id</td>",'<td><%- library.get("id") %></td>',"</tr>","</tbody>","</table>",'<table class="grid table table-condensed">',"<thead>",'<th style="width: 25%;">folder</th>',"<th></th>","</thead>","<tbody>","<tr>","<td>name</td>","<td><%- options.folder_name %></td>","</tr>",'<% if(options.folder_description !== "") { %>',"<tr>","<td>description</td>","<td><%- options.folder_description %></td>","</tr>","<% } %>","<tr>","<td>id</td>","<td><%- options.id %></td>","</tr>","</tbody>","</table>","</div>"].join(""))},templateNewFolderInModal:function(){return s.template(['<div id="new_folder_modal">',"<form>",'<input type="text" name="Name" value="" placeholder="Name" autofocus>','<input type="text" name="Description" value="" placeholder="Description">',"</form>","</div>"].join(""))},templateBulkImportInModal:function(){return s.template(["<div>",'<div class="library-modal-item">',"Select history: ",'<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; " autofocus>',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>",'<div class="library-modal-item">',"or create new: ",'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',"</input>","</div>","</div>"].join(""))},templateImportIntoHistoryProgressBar:function(){return s.template(['<div class="import_text">',"Importing selected items to history <b><%= _.escape(history_name) %></b>","</div>",'<div class="progress">','<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">','<span class="completion_span">0% Complete</span>',"</div>","</div>"].join(""))},templateAddingDatasetsProgressBar:function(){return s.template(['<div class="import_text">',"Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>","</div>",'<div class="progress">','<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">','<span class="completion_span">0% Complete</span>',"</div>","</div>"].join(""))},templateDeletingItemsProgressBar:function(){return s.template(['<div class="import_text">',"</div>",'<div class="progress">','<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">','<span class="completion_span">0% Complete</span>',"</div>","</div>"].join(""))},templateBrowserModal:function(){return s.template(['<div id="file_browser_modal">','<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder ignoring their folder structure.</div>','<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>','<div style="margin-bottom:1em;">','<label title="Switch to selecting files" class="radio-inline import-type-switch">','<input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Choose Files',"</label>",'<label title="Switch to selecting folders" class="radio-inline import-type-switch">','<input type="radio" name="jstree-radio" value="jstree-disable-files"> Choose Folders',"</label>","</div>",'<div style="margin-bottom:1em;">','<label class="checkbox-inline jstree-preserve-structure" style="display:none;">','<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',"Preserve directory structure","</label>",'<label class="checkbox-inline">','<input class="link-checkbox" type="checkbox" value="link_files">',"Link files instead of copying","</label>",'<label class="checkbox-inline">','<input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">',"Convert line endings to POSIX","</label>",'<label class="checkbox-inline">','<input class="spacetab-checkbox" type="checkbox" value="space_to_tab">',"Convert spaces to tabs","</label>","</div>",'<button title="Select all files" type="button" class="button primary-button libimport-select-all">',"Select all","</button>",'<button 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class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',"Preserve directory structure","</label>",'<label class="checkbox-inline">','<input class="link-checkbox" type="checkbox" value="link_files">',"Link files instead of copying","</label>","<br>",'<label class="checkbox-inline">','<input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">',"Convert line endings to POSIX","</label>",'<label class="checkbox-inline">','<input class="spacetab-checkbox" type="checkbox" value="space_to_tab">',"Convert spaces to tabs","</label>","</div>",'<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline" autofocus></textarea>',"<hr />","<p>You can set extension type and genome for all imported datasets at once:</p>","<div>",'Type: <span id="library_extension_select" class="library-extension-select" />','Genome: <span id="library_genome_select" class="library-genome-select" />',"</div>","<div>",'<label class="checkbox-inline tag-files">',"Tag datasets based on file names.",'<input class="tag-files" type="checkbox" value="tag_using_filenames" checked="checked">',"</label>","</div>","</div>"].join(""))},templateAddFilesFromHistory:function(){return s.template(['<div id="add_files_modal">',"<div>","1.&nbsp;Select history:&nbsp;",'<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>","<br/>",'<div id="selected_history_content">',"</div>","</div>"].join(""))},templateHistoryContents:function(){return s.template(["<p>2.&nbsp;Choose the datasets to import:</p>","<div>",'<button title="Select all datasets" type="button" class="button primary-button history-import-select-all">',"Select all","</button>",'<button title="Select all 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o=i(42),n=r(o),l=i(156),d=r(l),c=i(139),h=r(c),_=e.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=s.extend(this.options,e),this.options.id&&this.fetchLibrary()},fetchLibrary:function(e){this.options=s.extend(this.options,e),this.model=new d.default.Library({id:this.options.id});var t=this;this.model.fetch({success:function(){t.options.show_permissions&&t.showPermissions()},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):n.default.error("An error occurred. 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Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},showPermissions:function(e){this.options=s.extend(this.options,e),a(".tooltip").remove();var t=!1;Galaxy.user&&(t=Galaxy.user.isAdmin());var i=this.templateFolderPermissions();this.$el.html(i({folder:this.model,is_admin:t}));var r=this;a.get(Galaxy.root+"api/folders/"+r.id+"/permissions?scope=current").done(function(e){r.prepareSelectBoxes({fetched_permissions:e})}).fail(function(){n.default.error("An error occurred while attempting to fetch folder permissions.")}),a("#center [data-toggle]").tooltip(),a("#center").css("overflow","auto")},_serializeRoles:function(e){for(var t=[],i=0;i<e.length;i++)t.push(e[i][1]+":"+e[i][0]);return t},prepareSelectBoxes:function(e){this.options=s.extend(this.options,e);var t=this.options.fetched_permissions,i=this,a=this._serializeRoles(t.add_library_item_role_list),r=this._serializeRoles(t.manage_folder_role_list),o=this._serializeRoles(t.modify_folder_role_list);i.addSelectObject=new h.default.View(this._createSelectOptions(this,"add_perm",a,!1)),i.manageSelectObject=new h.default.View(this._createSelectOptions(this,"manage_perm",r,!1)),i.modifySelectObject=new h.default.View(this._createSelectOptions(this,"modify_perm",o,!1))},_createSelectOptions:function(e,t,i){return{minimumInputLength:0,css:t,multiple:!0,placeholder:"Click to select a role",container:e.$el.find("#"+t),ajax:{url:Galaxy.root+"api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(e,t){return{q:e,page_limit:10,page:t}},results:function(e,t){var i=10*t<e.total;return{results:e.roles,more:i}}},formatResult:function(e){return e.name+" type: "+e.type},formatSelection:function(e){return e.name},initSelection:function(e,t){var i=[];a(e.val().split(",")).each(function(){var e=this.split(":");i.push({id:e[0],name:e[1]})}),t(i)},initialData:i.join(","),dropdownCssClass:"bigdrop"}},_extractIds:function(e){for(var t=[],i=e.length-1;i>=0;i--)t.push(e[i].id);return t},savePermissions:function(e){var t=this,i=this._extractIds(this.addSelectObject.$el.select2("data")),s=this._extractIds(this.manageSelectObject.$el.select2("data")),r=this._extractIds(this.modifySelectObject.$el.select2("data"));a.post(Galaxy.root+"api/folders/"+t.id+"/permissions?action=set_permissions",{"add_ids[]":i,"manage_ids[]":s,"modify_ids[]":r}).done(function(e){t.showPermissions({fetched_permissions:e}),n.default.success("Permissions saved.")}).fail(function(){n.default.error("An error occurred while attempting to set folder permissions.")})},templateFolderPermissions:function(){return s.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#/folders/<%= folder.get("parent_id") %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button">','<span class="fa fa-caret-left fa-lg"/>',"&nbsp;Parent folder","</button>","</a>","</div>","<h1>",'Folder: <%= _.escape(folder.get("name")) %>',"</h1>",'<div class="alert alert-warning">',"<% if (is_admin) { %>","You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. 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_=[];for(h=0,d=i.length;h<d;h+=1)p=i[h],g=!0===p.disabled,f=!g&&a(p)!==e,v=p.children&&p.children.length>0,m=t("<li></li>"),m.addClass("select2-results-dept-"+c),m.addClass("select2-result"),m.addClass(f?"select2-result-selectable":"select2-result-unselectable"),g&&m.addClass("select2-disabled"),v&&m.addClass("select2-result-with-children"),m.addClass(u.opts.formatResultCssClass(p)),m.attr("role","presentation"),y=t(document.createElement("div")),y.addClass("select2-result-label"),y.attr("id","select2-result-label-"+N()),y.attr("role","option"),w=n.formatResult(p,y,o,u.opts.escapeMarkup),w!==e&&(y.html(w),m.append(y)),v&&(b=t("<ul></ul>"),b.addClass("select2-result-sub"),s(p.children,b,c+1),m.append(b)),m.data("select2-data",p),_.push(m[0]);r.append(_),l.text(n.formatMatches(i.length))})(r,i,0)}},t.fn.select2.defaults,n),"function"!=typeof n.id&&(o=n.id,n.id=function(t){return t[o]}),t.isArray(n.element.data("select2Tags"))){if("tags"in n)throw"tags specified as both an attribute 'data-select2-tags' and in options of Select2 "+n.element.attr("id");n.tags=n.element.data("select2Tags")}if(r?(n.query=this.bind(function(t){var n,r,o,s={results:[],more:!1},a=t.term;o=function(e,n){var i;e.is("option")?t.matcher(a,e.text(),e)&&n.push(u.optionToData(e)):e.is("optgroup")&&(i=u.optionToData(e),e.children().each2(function(t,e){o(e,i.children)}),i.children.length>0&&n.push(i))},n=i.children(),this.getPlaceholder()!==e&&n.length>0&&(r=this.getPlaceholderOption())&&(n=n.not(r)),n.each2(function(t,e){o(e,s.results)}),t.callback(s)}),n.id=function(t){return t.id}):"query"in n||("ajax"in n?(l=n.element.data("ajax-url"),l&&l.length>0&&(n.ajax.url=l),n.query=_.call(n.element,n.ajax)):"data"in n?n.query=x(n.data):"tags"in n&&(n.query=C(n.tags),n.createSearchChoice===e&&(n.createSearchChoice=function(e){return{id:t.trim(e),text:t.trim(e)}}),n.initSelection===e&&(n.initSelection=function(e,i){var r=[];t(a(e.val(),n.separator)).each(function(){var e={id:this,text:this},i=n.tags;t.isFunction(i)&&(i=i()),t(i).each(function(){if(s(this.id,e.id))return e=this,!1}),r.push(e)}),i(r)}))),"function"!=typeof n.query)throw"query function not defined for Select2 "+n.element.attr("id");if("top"===n.createSearchChoicePosition)n.createSearchChoicePosition=function(t,e){t.unshift(e)};else if("bottom"===n.createSearchChoicePosition)n.createSearchChoicePosition=function(t,e){t.push(e)};else if("function"!=typeof n.createSearchChoicePosition)throw"invalid createSearchChoicePosition option must be 'top', 'bottom' or a custom function";return n},monitorSource:function(){var n,i=this.opts.element,r=this;i.on("change.select2",this.bind(function(t){!0!==this.opts.element.data("select2-change-triggered")&&this.initSelection()})),this._sync=this.bind(function(){var t=i.prop("disabled");t===e&&(t=!1),this.enable(!t);var n=i.prop("readonly");n===e&&(n=!1),this.readonly(n),y(this.container,this.opts.element,this.opts.adaptContainerCssClass),this.container.addClass(S(this.opts.containerCssClass,this.opts.element)),y(this.dropdown,this.opts.element,this.opts.adaptDropdownCssClass),this.dropdown.addClass(S(this.opts.dropdownCssClass,this.opts.element))}),i.length&&i[0].attachEvent&&i.each(function(){this.attachEvent("onpropertychange",r._sync)}),(n=window.MutationObserver||window.WebKitMutationObserver||window.MozMutationObserver)!==e&&(this.propertyObserver&&(delete this.propertyObserver,this.propertyObserver=null),this.propertyObserver=new n(function(e){t.each(e,r._sync)}),this.propertyObserver.observe(i.get(0),{attributes:!0,subtree:!1}))},triggerSelect:function(e){var n=t.Event("select2-selecting",{val:this.id(e),object:e,choice:e});return this.opts.element.trigger(n),!n.isDefaultPrevented()},triggerChange:function(e){e=e||{},e=t.extend({},e,{type:"change",val:this.val()}),this.opts.element.data("select2-change-triggered",!0),this.opts.element.trigger(e),this.opts.element.data("select2-change-triggered",!1),this.opts.element.click(),this.opts.blurOnChange&&this.opts.element.blur()},isInterfaceEnabled:function(){return!0===this.enabledInterface},enableInterface:function(){var t=this._enabled&&!this._readonly,e=!t;return t!==this.enabledInterface&&(this.container.toggleClass("select2-container-disabled",e),this.close(),this.enabledInterface=t,!0)},enable:function(t){t===e&&(t=!0),this._enabled!==t&&(this._enabled=t,this.opts.element.prop("disabled",!t),this.enableInterface())},disable:function(){this.enable(!1)},readonly:function(t){t===e&&(t=!1),this._readonly!==t&&(this._readonly=t,this.opts.element.prop("readonly",t),this.enableInterface())},opened:function(){return!!this.container&&this.container.hasClass("select2-dropdown-open")},positionDropdown:function(){var e,n,i,r,o,s=this.dropdown,a=this.container.offset(),l=this.container.outerHeight(!1),u=this.container.outerWidth(!1),c=s.outerHeight(!1),h=t(window),d=h.width(),p=h.height(),f=h.scrollLeft()+d,g=h.scrollTop()+p,v=a.top+l,m=a.left,y=v+c<=g,b=a.top-c>=h.scrollTop(),w=s.outerWidth(!1),_=m+w<=f,x=s.hasClass("select2-drop-above");x?(n=!0,!b&&y&&(i=!0,n=!1)):(n=!1,!y&&b&&(i=!0,n=!0)),i&&(s.hide(),a=this.container.offset(),l=this.container.outerHeight(!1),u=this.container.outerWidth(!1),c=s.outerHeight(!1),f=h.scrollLeft()+d,g=h.scrollTop()+p,v=a.top+l,m=a.left,w=s.outerWidth(!1),_=m+w<=f,s.show(),this.focusSearch()),this.opts.dropdownAutoWidth?(o=t(".select2-results",s)[0],s.addClass("select2-drop-auto-width"),s.css("width",""),w=s.outerWidth(!1)+(o.scrollHeight===o.clientHeight?0:$.width),w>u?u=w:w=u,c=s.outerHeight(!1),_=m+w<=f):this.container.removeClass("select2-drop-auto-width"),"static"!==this.body.css("position")&&(e=this.body.offset(),v-=e.top,m-=e.left),_||(m=a.left+this.container.outerWidth(!1)-w),r={left:m,width:u},n?(r.top=a.top-c,r.bottom="auto",this.container.addClass("select2-drop-above"),s.addClass("select2-drop-above")):(r.top=v,r.bottom="auto",this.container.removeClass("select2-drop-above"),s.removeClass("select2-drop-above")),r=t.extend(r,S(this.opts.dropdownCss,this.opts.element)),s.css(r)},shouldOpen:function(){var e;return!this.opened()&&(!1!==this._enabled&&!0!==this._readonly&&(e=t.Event("select2-opening"),this.opts.element.trigger(e),!e.isDefaultPrevented()))},clearDropdownAlignmentPreference:function(){this.container.removeClass("select2-drop-above"),this.dropdown.removeClass("select2-drop-above")},open:function(){return!!this.shouldOpen()&&(this.opening(),I.on("mousemove.select2Event",function(t){L.x=t.pageX,L.y=t.pageY}),!0)},opening:function(){var e,i=this.containerEventName,r="scroll."+i,o="resize."+i,s="orientationchange."+i;this.container.addClass("select2-dropdown-open").addClass("select2-container-active"),this.clearDropdownAlignmentPreference(),this.dropdown[0]!==this.body.children().last()[0]&&this.dropdown.detach().appendTo(this.body),e=t("#select2-drop-mask"),0==e.length&&(e=t(document.createElement("div")),e.attr("id","select2-drop-mask").attr("class","select2-drop-mask"),e.hide(),e.appendTo(this.body),e.on("mousedown touchstart click",function(i){n(e);var r,o=t("#select2-drop");o.length>0&&(r=o.data("select2"),r.opts.selectOnBlur&&r.selectHighlighted({noFocus:!0}),r.close(),i.preventDefault(),i.stopPropagation())})),this.dropdown.prev()[0]!==e[0]&&this.dropdown.before(e),t("#select2-drop").removeAttr("id"),this.dropdown.attr("id","select2-drop"),e.show(),this.positionDropdown(),this.dropdown.show(),this.positionDropdown(),this.dropdown.addClass("select2-drop-active");var a=this;this.container.parents().add(window).each(function(){t(this).on(o+" "+r+" "+s,function(t){a.opened()&&a.positionDropdown()})})},close:function(){if(this.opened()){var e=this.containerEventName,n="scroll."+e,i="resize."+e,r="orientationchange."+e;this.container.parents().add(window).each(function(){t(this).off(n).off(i).off(r)}),this.clearDropdownAlignmentPreference(),t("#select2-drop-mask").hide(),this.dropdown.removeAttr("id"),this.dropdown.hide(),this.container.removeClass("select2-dropdown-open").removeClass("select2-container-active"),this.results.empty(),I.off("mousemove.select2Event"),this.clearSearch(),this.search.removeClass("select2-active"),this.opts.element.trigger(t.Event("select2-close"))}},externalSearch:function(t){this.open(),this.search.val(t),this.updateResults(!1)},clearSearch:function(){},getMaximumSelectionSize:function(){return S(this.opts.maximumSelectionSize,this.opts.element)},ensureHighlightVisible:function(){var e,n,i,r,o,s,a,l,u=this.results;if(!((n=this.highlight())<0)){if(0==n)return void u.scrollTop(0);e=this.findHighlightableChoices().find(".select2-result-label"),i=t(e[n]),l=(i.offset()||{}).top||0,r=l+i.outerHeight(!0),n===e.length-1&&(a=u.find("li.select2-more-results"),a.length>0&&(r=a.offset().top+a.outerHeight(!0))),o=u.offset().top+u.outerHeight(!0),r>o&&u.scrollTop(u.scrollTop()+(r-o)),s=l-u.offset().top,s<0&&"none"!=i.css("display")&&u.scrollTop(u.scrollTop()+s)}},findHighlightableChoices:function(){return this.results.find(".select2-result-selectable:not(.select2-disabled):not(.select2-selected)")},moveHighlight:function(e){for(var n=this.findHighlightableChoices(),i=this.highlight();i>-1&&i<n.length;){i+=e;var r=t(n[i]);if(r.hasClass("select2-result-selectable")&&!r.hasClass("select2-disabled")&&!r.hasClass("select2-selected")){this.highlight(i);break}}},highlight:function(e){var n,i,o=this.findHighlightableChoices();if(0===arguments.length)return r(o.filter(".select2-highlighted")[0],o.get());e>=o.length&&(e=o.length-1),e<0&&(e=0),this.removeHighlight(),n=t(o[e]),n.addClass("select2-highlighted"),this.search.attr("aria-activedescendant",n.find(".select2-result-label").attr("id")),this.ensureHighlightVisible(),this.liveRegion.text(n.text()),(i=n.data("select2-data"))&&this.opts.element.trigger({type:"select2-highlight",val:this.id(i),choice:i})},removeHighlight:function(){this.results.find(".select2-highlighted").removeClass("select2-highlighted")},touchMoved:function(){this._touchMoved=!0},clearTouchMoved:function(){this._touchMoved=!1},countSelectableResults:function(){return this.findHighlightableChoices().length},highlightUnderEvent:function(e){var n=t(e.target).closest(".select2-result-selectable");if(n.length>0&&!n.is(".select2-highlighted")){var i=this.findHighlightableChoices();this.highlight(i.index(n))}else 0==n.length&&this.removeHighlight()},loadMoreIfNeeded:function(){var t=this.results,e=t.find("li.select2-more-results"),n=this.resultsPage+1,i=this,r=this.search.val(),o=this.context;0!==e.length&&e.offset().top-t.offset().top-t.height()<=this.opts.loadMorePadding&&(e.addClass("select2-active"),this.opts.query({element:this.opts.element,term:r,page:n,context:o,matcher:this.opts.matcher,callback:this.bind(function(s){i.opened()&&(i.opts.populateResults.call(this,t,s.results,{term:r,page:n,context:o}),i.postprocessResults(s,!1,!1),!0===s.more?(e.detach().appendTo(t).text(S(i.opts.formatLoadMore,i.opts.element,n+1)),window.setTimeout(function(){i.loadMoreIfNeeded()},10)):e.remove(),i.positionDropdown(),i.resultsPage=n,i.context=s.context,this.opts.element.trigger({type:"select2-loaded",items:s}))})}))},tokenize:function(){},updateResults:function(n){function i(){u.removeClass("select2-active"),d.positionDropdown(),c.find(".select2-no-results,.select2-selection-limit,.select2-searching").length?d.liveRegion.text(c.text()):d.liveRegion.text(d.opts.formatMatches(c.find(".select2-result-selectable").length))}function r(t){c.html(t),i()}var o,a,l,u=this.search,c=this.results,h=this.opts,d=this,p=u.val(),f=t.data(this.container,"select2-last-term");if((!0===n||!f||!s(p,f))&&(t.data(this.container,"select2-last-term",p),!0===n||!1!==this.showSearchInput&&this.opened())){l=++this.queryCount;var g=this.getMaximumSelectionSize();if(g>=1&&(o=this.data(),t.isArray(o)&&o.length>=g&&k(h.formatSelectionTooBig,"formatSelectionTooBig")))return void r("<li class='select2-selection-limit'>"+S(h.formatSelectionTooBig,h.element,g)+"</li>");if(u.val().length<h.minimumInputLength)return r(k(h.formatInputTooShort,"formatInputTooShort")?"<li class='select2-no-results'>"+S(h.formatInputTooShort,h.element,u.val(),h.minimumInputLength)+"</li>":""),void(n&&this.showSearch&&this.showSearch(!0));if(h.maximumInputLength&&u.val().length>h.maximumInputLength)return void r(k(h.formatInputTooLong,"formatInputTooLong")?"<li class='select2-no-results'>"+S(h.formatInputTooLong,h.element,u.val(),h.maximumInputLength)+"</li>":"");h.formatSearching&&0===this.findHighlightableChoices().length&&r("<li class='select2-searching'>"+S(h.formatSearching,h.element)+"</li>"),u.addClass("select2-active"),this.removeHighlight(),a=this.tokenize(),a!=e&&null!=a&&u.val(a),this.resultsPage=1,h.query({element:h.element,term:u.val(),page:this.resultsPage,context:null,matcher:h.matcher,callback:this.bind(function(o){var a;if(l==this.queryCount){if(!this.opened())return void this.search.removeClass("select2-active");if(o.hasError!==e&&k(h.formatAjaxError,"formatAjaxError"))return void r("<li class='select2-ajax-error'>"+S(h.formatAjaxError,h.element,o.jqXHR,o.textStatus,o.errorThrown)+"</li>");if(this.context=o.context===e?null:o.context,this.opts.createSearchChoice&&""!==u.val()&&(a=this.opts.createSearchChoice.call(d,u.val(),o.results))!==e&&null!==a&&d.id(a)!==e&&null!==d.id(a)&&0===t(o.results).filter(function(){return s(d.id(this),d.id(a))}).length&&this.opts.createSearchChoicePosition(o.results,a),0===o.results.length&&k(h.formatNoMatches,"formatNoMatches"))return void r("<li class='select2-no-results'>"+S(h.formatNoMatches,h.element,u.val())+"</li>");c.empty(),d.opts.populateResults.call(this,c,o.results,{term:u.val(),page:this.resultsPage,context:null}),!0===o.more&&k(h.formatLoadMore,"formatLoadMore")&&(c.append("<li class='select2-more-results'>"+h.escapeMarkup(S(h.formatLoadMore,h.element,this.resultsPage))+"</li>"),window.setTimeout(function(){d.loadMoreIfNeeded()},10)),this.postprocessResults(o,n),i(),this.opts.element.trigger({type:"select2-loaded",items:o})}})})}},cancel:function(){this.close()},blur:function(){this.opts.selectOnBlur&&this.selectHighlighted({noFocus:!0}),this.close(),this.container.removeClass("select2-container-active"),this.search[0]===document.activeElement&&this.search.blur(),this.clearSearch(),this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")},focusSearch:function(){p(this.search)},selectHighlighted:function(t){if(this._touchMoved)return void this.clearTouchMoved();var e=this.highlight(),n=this.results.find(".select2-highlighted"),i=n.closest(".select2-result").data("select2-data");i?(this.highlight(e),this.onSelect(i,t)):t&&t.noFocus&&this.close()},getPlaceholder:function(){var t;return this.opts.element.attr("placeholder")||this.opts.element.attr("data-placeholder")||this.opts.element.data("placeholder")||this.opts.placeholder||((t=this.getPlaceholderOption())!==e?t.text():e)},getPlaceholderOption:function(){if(this.select){var n=this.select.children("option").first();if(this.opts.placeholderOption!==e)return"first"===this.opts.placeholderOption&&n||"function"==typeof this.opts.placeholderOption&&this.opts.placeholderOption(this.select);if(""===t.trim(n.text())&&""===n.val())return n}},initContainerWidth:function(){function n(){var n,i,r,o,s,a;if("off"===this.opts.width)return null;if("element"===this.opts.width)return 0===this.opts.element.outerWidth(!1)?"auto":this.opts.element.outerWidth(!1)+"px";if("copy"===this.opts.width||"resolve"===this.opts.width){if((n=this.opts.element.attr("style"))!==e)for(i=n.split(";"),o=0,s=i.length;o<s;o+=1)if(a=i[o].replace(/\s/g,""),null!==(r=a.match(/^width:(([-+]?([0-9]*\.)?[0-9]+)(px|em|ex|%|in|cm|mm|pt|pc))/i))&&r.length>=1)return r[1];return"resolve"===this.opts.width?(n=this.opts.element.css("width"),n.indexOf("%")>0?n:0===this.opts.element.outerWidth(!1)?"auto":this.opts.element.outerWidth(!1)+"px"):null}return t.isFunction(this.opts.width)?this.opts.width():this.opts.width}var i=n.call(this);null!==i&&this.container.css("width",i)}}),M=O(D,{createContainer:function(){return t(document.createElement("div")).attr({class:"select2-container"}).html(["<a href='javascript:void(0)' class='select2-choice' tabindex='-1'>","   <span class='select2-chosen'>&#160;</span><abbr class='select2-search-choice-close'></abbr>","   <span class='select2-arrow' role='presentation'><b role='presentation'></b></span>","</a>","<label for='' class='select2-offscreen'></label>","<input class='select2-focusser select2-offscreen' type='text' aria-haspopup='true' role='button' />","<div class='select2-drop select2-display-none'>","   <div class='select2-search'>","       <label for='' class='select2-offscreen'></label>","       <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input' role='combobox' aria-expanded='true'","       aria-autocomplete='list' />","   </div>","   <ul class='select2-results' role='listbox'>","   </ul>","</div>"].join(""))},enableInterface:function(){this.parent.enableInterface.apply(this,arguments)&&this.focusser.prop("disabled",!this.isInterfaceEnabled())},opening:function(){var n,i,r;this.opts.minimumResultsForSearch>=0&&this.showSearch(!0),this.parent.opening.apply(this,arguments),!1!==this.showSearchInput&&this.search.val(this.focusser.val()),this.opts.shouldFocusInput(this)&&(this.search.focus(),n=this.search.get(0),n.createTextRange?(i=n.createTextRange(),i.collapse(!1),i.select()):n.setSelectionRange&&(r=this.search.val().length,n.setSelectionRange(r,r))),""===this.search.val()&&this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.search.select()),this.focusser.prop("disabled",!0).val(""),this.updateResults(!0),this.opts.element.trigger(t.Event("select2-open"))},close:function(){this.opened()&&(this.parent.close.apply(this,arguments),this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus())},focus:function(){this.opened()?this.close():(this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus())},isFocused:function(){return this.container.hasClass("select2-container-active")},cancel:function(){this.parent.cancel.apply(this,arguments),this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus()},destroy:function(){t("label[for='"+this.focusser.attr("id")+"']").attr("for",this.opts.element.attr("id")),this.parent.destroy.apply(this,arguments),E.call(this,"selection","focusser")},initContainer:function(){var e,i,r=this.container,o=this.dropdown,s=N();this.opts.minimumResultsForSearch<0?this.showSearch(!1):this.showSearch(!0),this.selection=e=r.find(".select2-choice"),this.focusser=r.find(".select2-focusser"),e.find(".select2-chosen").attr("id","select2-chosen-"+s),this.focusser.attr("aria-labelledby","select2-chosen-"+s),this.results.attr("id","select2-results-"+s),this.search.attr("aria-owns","select2-results-"+s),this.focusser.attr("id","s2id_autogen"+s),i=t("label[for='"+this.opts.element.attr("id")+"']"),this.focusser.prev().text(i.text()).attr("for",this.focusser.attr("id"));var a=this.opts.element.attr("title");this.opts.element.attr("title",a||i.text()),this.focusser.attr("tabindex",this.elementTabIndex),this.search.attr("id",this.focusser.attr("id")+"_search"),this.search.prev().text(t("label[for='"+this.focusser.attr("id")+"']").text()).attr("for",this.search.attr("id")),this.search.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()&&229!=t.keyCode){if(t.which===j.PAGE_UP||t.which===j.PAGE_DOWN)return void g(t);switch(t.which){case j.UP:case j.DOWN:return this.moveHighlight(t.which===j.UP?-1:1),void g(t);case j.ENTER:return this.selectHighlighted(),void g(t);case j.TAB:return void this.selectHighlighted({noFocus:!0});case j.ESC:return this.cancel(t),void g(t)}}})),this.search.on("blur",this.bind(function(t){document.activeElement===this.body.get(0)&&window.setTimeout(this.bind(function(){this.opened()&&this.search.focus()}),0)})),this.focusser.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()&&t.which!==j.TAB&&!j.isControl(t)&&!j.isFunctionKey(t)&&t.which!==j.ESC){if(!1===this.opts.openOnEnter&&t.which===j.ENTER)return void g(t);if(t.which==j.DOWN||t.which==j.UP||t.which==j.ENTER&&this.opts.openOnEnter){if(t.altKey||t.ctrlKey||t.shiftKey||t.metaKey)return;return this.open(),void g(t)}return t.which==j.DELETE||t.which==j.BACKSPACE?(this.opts.allowClear&&this.clear(),void g(t)):void 0}})),u(this.focusser),this.focusser.on("keyup-change input",this.bind(function(t){if(this.opts.minimumResultsForSearch>=0){if(t.stopPropagation(),this.opened())return;this.open()}})),e.on("mousedown touchstart","abbr",this.bind(function(t){this.isInterfaceEnabled()&&(this.clear(),v(t),this.close(),this.selection.focus())})),e.on("mousedown touchstart",this.bind(function(i){n(e),this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.opened()?this.close():this.isInterfaceEnabled()&&this.open(),g(i)})),o.on("mousedown touchstart",this.bind(function(){this.opts.shouldFocusInput(this)&&this.search.focus()})),e.on("focus",this.bind(function(t){g(t)})),this.focusser.on("focus",this.bind(function(){this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active")})).on("blur",this.bind(function(){this.opened()||(this.container.removeClass("select2-container-active"),this.opts.element.trigger(t.Event("select2-blur")))})),this.search.on("focus",this.bind(function(){this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active")})),this.initContainerWidth(),this.opts.element.addClass("select2-offscreen"),this.setPlaceholder()},clear:function(e){var n=this.selection.data("select2-data");if(n){var i=t.Event("select2-clearing");if(this.opts.element.trigger(i),i.isDefaultPrevented())return;var r=this.getPlaceholderOption();this.opts.element.val(r?r.val():""),this.selection.find(".select2-chosen").empty(),this.selection.removeData("select2-data"),this.setPlaceholder(),!1!==e&&(this.opts.element.trigger({type:"select2-removed",val:this.id(n),choice:n}),this.triggerChange({removed:n}))}},initSelection:function(){if(this.isPlaceholderOptionSelected())this.updateSelection(null),this.close(),this.setPlaceholder();else{var t=this;this.opts.initSelection.call(null,this.opts.element,function(n){n!==e&&null!==n&&(t.updateSelection(n),t.close(),t.setPlaceholder(),t.nextSearchTerm=t.opts.nextSearchTerm(n,t.search.val()))})}},isPlaceholderOptionSelected:function(){var t;return this.getPlaceholder()!==e&&((t=this.getPlaceholderOption())!==e&&t.prop("selected")||""===this.opts.element.val()||this.opts.element.val()===e||null===this.opts.element.val())},prepareOpts:function(){var e=this.parent.prepareOpts.apply(this,arguments),n=this;return"select"===e.element.get(0).tagName.toLowerCase()?e.initSelection=function(t,e){var i=t.find("option").filter(function(){return this.selected&&!this.disabled});e(n.optionToData(i))}:"data"in e&&(e.initSelection=e.initSelection||function(n,i){var r=n.val(),o=null;e.query({matcher:function(t,n,i){var a=s(r,e.id(i));return a&&(o=i),a},callback:t.isFunction(i)?function(){i(o)}:t.noop})}),e},getPlaceholder:function(){return this.select&&this.getPlaceholderOption()===e?e:this.parent.getPlaceholder.apply(this,arguments)},setPlaceholder:function(){var t=this.getPlaceholder();if(this.isPlaceholderOptionSelected()&&t!==e){if(this.select&&this.getPlaceholderOption()===e)return;this.selection.find(".select2-chosen").html(this.opts.escapeMarkup(t)),this.selection.addClass("select2-default"),this.container.removeClass("select2-allowclear")}},postprocessResults:function(t,e,n){var i=0,r=this;if(this.findHighlightableChoices().each2(function(t,e){if(s(r.id(e.data("select2-data")),r.opts.element.val()))return i=t,!1}),!1!==n&&(!0===e&&i>=0?this.highlight(i):this.highlight(0)),!0===e){var o=this.opts.minimumResultsForSearch;o>=0&&this.showSearch(T(t.results)>=o)}},showSearch:function(e){this.showSearchInput!==e&&(this.showSearchInput=e,this.dropdown.find(".select2-search").toggleClass("select2-search-hidden",!e),this.dropdown.find(".select2-search").toggleClass("select2-offscreen",!e),t(this.dropdown,this.container).toggleClass("select2-with-searchbox",e))},onSelect:function(t,e){if(this.triggerSelect(t)){var n=this.opts.element.val(),i=this.data();this.opts.element.val(this.id(t)),this.updateSelection(t),this.opts.element.trigger({type:"select2-selected",val:this.id(t),choice:t}),this.nextSearchTerm=this.opts.nextSearchTerm(t,this.search.val()),this.close(),e&&e.noFocus||!this.opts.shouldFocusInput(this)||this.focusser.focus(),s(n,this.id(t))||this.triggerChange({added:t,removed:i})}},updateSelection:function(t){var n,i,r=this.selection.find(".select2-chosen");this.selection.data("select2-data",t),r.empty(),null!==t&&(n=this.opts.formatSelection(t,r,this.opts.escapeMarkup)),n!==e&&r.append(n),i=this.opts.formatSelectionCssClass(t,r),i!==e&&r.addClass(i),this.selection.removeClass("select2-default"),this.opts.allowClear&&this.getPlaceholder()!==e&&this.container.addClass("select2-allowclear")},val:function(){var t,n=!1,i=null,r=this,o=this.data();if(0===arguments.length)return this.opts.element.val();if(t=arguments[0],arguments.length>1&&(n=arguments[1]),this.select)this.select.val(t).find("option").filter(function(){return this.selected}).each2(function(t,e){return i=r.optionToData(e),!1}),this.updateSelection(i),this.setPlaceholder(),n&&this.triggerChange({added:i,removed:o});else{if(!t&&0!==t)return void this.clear(n);if(this.opts.initSelection===e)throw new Error("cannot call val() if initSelection() is not defined");this.opts.element.val(t),this.opts.initSelection(this.opts.element,function(t){r.opts.element.val(t?r.id(t):""),r.updateSelection(t),r.setPlaceholder(),n&&r.triggerChange({added:t,removed:o})})}},clearSearch:function(){this.search.val(""),this.focusser.val("")},data:function(t){var n,i=!1;if(0===arguments.length)return n=this.selection.data("select2-data"),n==e&&(n=null),n;arguments.length>1&&(i=arguments[1]),t?(n=this.data(),this.opts.element.val(t?this.id(t):""),this.updateSelection(t),i&&this.triggerChange({added:t,removed:n})):this.clear(i)}}),P=O(D,{createContainer:function(){return t(document.createElement("div")).attr({class:"select2-container select2-container-multi"}).html(["<ul class='select2-choices'>","  <li class='select2-search-field'>","    <label for='' class='select2-offscreen'></label>","    <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'>","  </li>","</ul>","<div class='select2-drop select2-drop-multi select2-display-none'>","   <ul class='select2-results'>","   </ul>","</div>"].join(""))},prepareOpts:function(){var e=this.parent.prepareOpts.apply(this,arguments),n=this;return"select"===e.element.get(0).tagName.toLowerCase()?e.initSelection=function(t,e){var i=[];t.find("option").filter(function(){return this.selected&&!this.disabled}).each2(function(t,e){i.push(n.optionToData(e))}),e(i)}:"data"in e&&(e.initSelection=e.initSelection||function(n,i){var r=a(n.val(),e.separator),o=[];e.query({matcher:function(n,i,a){var l=t.grep(r,function(t){return s(t,e.id(a))}).length;return l&&o.push(a),l},callback:t.isFunction(i)?function(){for(var t=[],n=0;n<r.length;n++)for(var a=r[n],l=0;l<o.length;l++){var u=o[l];if(s(a,e.id(u))){t.push(u),o.splice(l,1);break}}i(t)}:t.noop})}),e},selectChoice:function(t){var e=this.container.find(".select2-search-choice-focus");e.length&&t&&t[0]==e[0]||(e.length&&this.opts.element.trigger("choice-deselected",e),e.removeClass("select2-search-choice-focus"),t&&t.length&&(this.close(),t.addClass("select2-search-choice-focus"),this.opts.element.trigger("choice-selected",t)))},destroy:function(){t("label[for='"+this.search.attr("id")+"']").attr("for",this.opts.element.attr("id")),this.parent.destroy.apply(this,arguments),E.call(this,"searchContainer","selection")},initContainer:function(){var e,n=".select2-choices";this.searchContainer=this.container.find(".select2-search-field"),this.selection=e=this.container.find(n);var i=this;this.selection.on("click",".select2-search-choice:not(.select2-locked)",function(e){i.search[0].focus(),i.selectChoice(t(this))}),this.search.attr("id","s2id_autogen"+N()),this.search.prev().text(t("label[for='"+this.opts.element.attr("id")+"']").text()).attr("for",this.search.attr("id")),this.search.on("input paste",this.bind(function(){this.search.attr("placeholder")&&0==this.search.val().length||this.isInterfaceEnabled()&&(this.opened()||this.open())})),this.search.attr("tabindex",this.elementTabIndex),this.keydowns=0,this.search.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()){++this.keydowns;var n=e.find(".select2-search-choice-focus"),i=n.prev(".select2-search-choice:not(.select2-locked)"),r=n.next(".select2-search-choice:not(.select2-locked)"),o=f(this.search);if(n.length&&(t.which==j.LEFT||t.which==j.RIGHT||t.which==j.BACKSPACE||t.which==j.DELETE||t.which==j.ENTER)){var s=n;return t.which==j.LEFT&&i.length?s=i:t.which==j.RIGHT?s=r.length?r:null:t.which===j.BACKSPACE?this.unselect(n.first())&&(this.search.width(10),s=i.length?i:r):t.which==j.DELETE?this.unselect(n.first())&&(this.search.width(10),s=r.length?r:null):t.which==j.ENTER&&(s=null),this.selectChoice(s),g(t),void(s&&s.length||this.open())}if((t.which===j.BACKSPACE&&1==this.keydowns||t.which==j.LEFT)&&0==o.offset&&!o.length)return this.selectChoice(e.find(".select2-search-choice:not(.select2-locked)").last()),void g(t);if(this.selectChoice(null),this.opened())switch(t.which){case j.UP:case j.DOWN:return this.moveHighlight(t.which===j.UP?-1:1),void g(t);case j.ENTER:return this.selectHighlighted(),void g(t);case j.TAB:return this.selectHighlighted({noFocus:!0}),void this.close();case j.ESC:return this.cancel(t),void g(t)}if(t.which!==j.TAB&&!j.isControl(t)&&!j.isFunctionKey(t)&&t.which!==j.BACKSPACE&&t.which!==j.ESC){if(t.which===j.ENTER){if(!1===this.opts.openOnEnter)return;if(t.altKey||t.ctrlKey||t.shiftKey||t.metaKey)return}this.open(),t.which!==j.PAGE_UP&&t.which!==j.PAGE_DOWN||g(t),t.which===j.ENTER&&g(t)}}})),this.search.on("keyup",this.bind(function(t){this.keydowns=0,this.resizeSearch()})),this.search.on("blur",this.bind(function(e){this.container.removeClass("select2-container-active"),this.search.removeClass("select2-focused"),this.selectChoice(null),this.opened()||this.clearSearch(),e.stopImmediatePropagation(),this.opts.element.trigger(t.Event("select2-blur"))})),this.container.on("click",n,this.bind(function(e){this.isInterfaceEnabled()&&(t(e.target).closest(".select2-search-choice").length>0||(this.selectChoice(null),this.clearPlaceholder(),this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.open(),this.focusSearch(),e.preventDefault()))})),this.container.on("focus",n,this.bind(function(){this.isInterfaceEnabled()&&(this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active"),this.dropdown.addClass("select2-drop-active"),this.clearPlaceholder())})),this.initContainerWidth(),this.opts.element.addClass("select2-offscreen"),this.clearSearch()},enableInterface:function(){this.parent.enableInterface.apply(this,arguments)&&this.search.prop("disabled",!this.isInterfaceEnabled())},initSelection:function(){if(""===this.opts.element.val()&&""===this.opts.element.text()&&(this.updateSelection([]),this.close(),this.clearSearch()),this.select||""!==this.opts.element.val()){var t=this;this.opts.initSelection.call(null,this.opts.element,function(n){n!==e&&null!==n&&(t.updateSelection(n),t.close(),t.clearSearch())})}},clearSearch:function(){var t=this.getPlaceholder(),n=this.getMaxSearchWidth();t!==e&&0===this.getVal().length&&!1===this.search.hasClass("select2-focused")?(this.search.val(t).addClass("select2-default"),this.search.width(n>0?n:this.container.css("width"))):this.search.val("").width(10)},clearPlaceholder:function(){this.search.hasClass("select2-default")&&this.search.val("").removeClass("select2-default")},opening:function(){this.clearPlaceholder(),this.resizeSearch(),this.parent.opening.apply(this,arguments),this.focusSearch(),""===this.search.val()&&this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.search.select()),this.updateResults(!0),this.opts.shouldFocusInput(this)&&this.search.focus(),this.opts.element.trigger(t.Event("select2-open"))},close:function(){this.opened()&&this.parent.close.apply(this,arguments)},focus:function(){this.close(),this.search.focus()},isFocused:function(){return this.search.hasClass("select2-focused")},updateSelection:function(e){var n=[],i=[],o=this;t(e).each(function(){r(o.id(this),n)<0&&(n.push(o.id(this)),i.push(this))}),e=i,this.selection.find(".select2-search-choice").remove(),t(e).each(function(){o.addSelectedChoice(this)}),o.postprocessResults()},tokenize:function(){var t=this.search.val();null!=(t=this.opts.tokenizer.call(this,t,this.data(),this.bind(this.onSelect),this.opts))&&t!=e&&(this.search.val(t),t.length>0&&this.open())},onSelect:function(t,n){this.triggerSelect(t)&&""!==t.text&&(this.addSelectedChoice(t),this.opts.element.trigger({type:"selected",val:this.id(t),choice:t}),this.nextSearchTerm=this.opts.nextSearchTerm(t,this.search.val()),this.moveHighlight(1),!this.select&&this.opts.closeOnSelect||this.postprocessResults(t,!1,!0===this.opts.closeOnSelect),this.opts.closeOnSelect?(this.clearSearch(),this.updateResults(),this.close(),this.search.width(10)):this.countSelectableResults()>0?(this.search.width(10),this.resizeSearch(),this.getMaximumSelectionSize()>0&&this.val().length>=this.getMaximumSelectionSize()?this.updateResults(!0):this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.updateResults(),this.search.select()),this.positionDropdown()):(this.close(),this.search.width(10)),this.triggerChange({added:t}),n&&n.noFocus||this.focusSearch())},cancel:function(){this.close(),this.focusSearch()},addSelectedChoice:function(n){var i,r,o=!n.locked,s=t("<li class='select2-search-choice'>    <div></div>    <a href='#' class='select2-search-choice-close' tabindex='-1'></a></li>"),a=t("<li class='select2-search-choice select2-locked'><div></div></li>"),l=o?s:a,u=this.id(n),c=this.getVal();i=this.opts.formatSelection(n,l.find("div"),this.opts.escapeMarkup),i!=e&&l.find("div").replaceWith("<div>"+i+"</div>"),r=this.opts.formatSelectionCssClass(n,l.find("div")),r!=e&&l.addClass(r),o&&l.find(".select2-search-choice-close").on("mousedown",g).on("click dblclick",this.bind(function(e){this.isInterfaceEnabled()&&(this.unselect(t(e.target)),this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus"),g(e),this.close(),this.focusSearch())})).on("focus",this.bind(function(){this.isInterfaceEnabled()&&(this.container.addClass("select2-container-active"),this.dropdown.addClass("select2-drop-active"))})),l.data("select2-data",n),l.insertBefore(this.searchContainer),c.push(u),this.setVal(c)},unselect:function(e){var n,i,o=this.getVal();if(e=e.closest(".select2-search-choice"),0===e.length)throw"Invalid argument: "+e+". Must be .select2-search-choice";if(n=e.data("select2-data")){var s=t.Event("select2-removing");if(s.val=this.id(n),s.choice=n,this.opts.element.trigger(s),s.isDefaultPrevented())return!1;for(;(i=r(this.id(n),o))>=0;)o.splice(i,1),this.setVal(o),this.select&&this.postprocessResults();return e.remove(),this.opts.element.trigger({type:"select2-removed",val:this.id(n),choice:n}),this.triggerChange({removed:n}),!0}},postprocessResults:function(t,e,n){var i=this.getVal(),o=this.results.find(".select2-result"),s=this.results.find(".select2-result-with-children"),a=this;o.each2(function(t,e){r(a.id(e.data("select2-data")),i)>=0&&(e.addClass("select2-selected"),e.find(".select2-result-selectable").addClass("select2-selected"))}),s.each2(function(t,e){e.is(".select2-result-selectable")||0!==e.find(".select2-result-selectable:not(.select2-selected)").length||e.addClass("select2-selected")}),-1==this.highlight()&&!1!==n&&a.highlight(0),!this.opts.createSearchChoice&&!o.filter(".select2-result:not(.select2-selected)").length>0&&(!t||t&&!t.more&&0===this.results.find(".select2-no-results").length)&&k(a.opts.formatNoMatches,"formatNoMatches")&&this.results.append("<li class='select2-no-results'>"+S(a.opts.formatNoMatches,a.opts.element,a.search.val())+"</li>")},getMaxSearchWidth:function(){return this.selection.width()-l(this.search)},resizeSearch:function(){var t,e,n,i,r,o=l(this.search);t=m(this.search)+10,e=this.search.offset().left,n=this.selection.width(),i=this.selection.offset().left,r=n-(e-i)-o,r<t&&(r=n-o),r<40&&(r=n-o),r<=0&&(r=t),this.search.width(Math.floor(r))},getVal:function(){var t;return this.select?(t=this.select.val(),null===t?[]:t):(t=this.opts.element.val(),a(t,this.opts.separator))},setVal:function(e){var n;this.select?this.select.val(e):(n=[],t(e).each(function(){r(this,n)<0&&n.push(this)}),this.opts.element.val(0===n.length?"":n.join(this.opts.separator)))},buildChangeDetails:function(t,e){for(var e=e.slice(0),t=t.slice(0),n=0;n<e.length;n++)for(var i=0;i<t.length;i++)s(this.opts.id(e[n]),this.opts.id(t[i]))&&(e.splice(n,1),n>0&&n--,t.splice(i,1),i--);return{added:e,removed:t}},val:function(n,i){var r,o=this;if(0===arguments.length)return this.getVal();if(r=this.data(),r.length||(r=[]),!n&&0!==n)return this.opts.element.val(""),this.updateSelection([]),this.clearSearch(),void(i&&this.triggerChange({added:this.data(),removed:r}));if(this.setVal(n),this.select)this.opts.initSelection(this.select,this.bind(this.updateSelection)),i&&this.triggerChange(this.buildChangeDetails(r,this.data()));else{if(this.opts.initSelection===e)throw new Error("val() cannot be called if initSelection() is not defined");this.opts.initSelection(this.opts.element,function(e){var n=t.map(e,o.id);o.setVal(n),o.updateSelection(e),o.clearSearch(),i&&o.triggerChange(o.buildChangeDetails(r,o.data()))})}this.clearSearch()},onSortStart:function(){if(this.select)throw new Error("Sorting of elements is not supported when attached to <select>. Attach to <input type='hidden'/> instead.");this.search.width(0),this.searchContainer.hide()},onSortEnd:function(){var e=[],n=this;this.searchContainer.show(),this.searchContainer.appendTo(this.searchContainer.parent()),this.resizeSearch(),this.selection.find(".select2-search-choice").each(function(){e.push(n.opts.id(t(this).data("select2-data")))}),this.setVal(e),this.triggerChange()},data:function(e,n){var i,r,o=this;if(0===arguments.length)return this.selection.children(".select2-search-choice").map(function(){return t(this).data("select2-data")}).get();r=this.data(),e||(e=[]),i=t.map(e,function(t){return o.opts.id(t)}),this.setVal(i),this.updateSelection(e),this.clearSearch(),n&&this.triggerChange(this.buildChangeDetails(r,this.data()))}}),t.fn.select2=function(){var n,i,o,s,a,l=Array.prototype.slice.call(arguments,0),u=["val","destroy","opened","open","close","focus","isFocused","container","dropdown","onSortStart","onSortEnd","enable","disable","readonly","positionDropdown","data","search"],c=["opened","isFocused","container","dropdown"],h=["val","data"],d={search:"externalSearch"};return this.each(function(){if(0===l.length||"object"==typeof l[0])n=0===l.length?{}:t.extend({},l[0]),n.element=t(this),"select"===n.element.get(0).tagName.toLowerCase()?a=n.element.prop("multiple"):(a=n.multiple||!1,"tags"in n&&(n.multiple=a=!0)),i=a?new window.Select2.class.multi:new window.Select2.class.single,i.init(n);else{if("string"!=typeof l[0])throw"Invalid arguments to select2 plugin: "+l;if(r(l[0],u)<0)throw"Unknown method: "+l[0];if(s=e,(i=t(this).data("select2"))===e)return;if(o=l[0],"container"===o?s=i.container:"dropdown"===o?s=i.dropdown:(d[o]&&(o=d[o]),s=i[o].apply(i,l.slice(1))),r(l[0],c)>=0||r(l[0],h)>=0&&1==l.length)return!1}}),s===e?this:s},t.fn.select2.defaults={width:"copy",loadMorePadding:0,closeOnSelect:!0,openOnEnter:!0,containerCss:{},dropdownCss:{},containerCssClass:"",dropdownCssClass:"",formatResult:function(t,e,n,i){var r=[];return b(t.text,n.term,r,i),r.join("")},formatSelection:function(t,n,i){return t?i(t.text):e},sortResults:function(t,e,n){return t},formatResultCssClass:function(t){return t.css},formatSelectionCssClass:function(t,n){return e},minimumResultsForSearch:0,minimumInputLength:0,maximumInputLength:null,maximumSelectionSize:0,id:function(t){return t==e?null:t.id},matcher:function(t,e){return i(""+e).toUpperCase().indexOf(i(""+t).toUpperCase())>=0},separator:",",tokenSeparators:[],tokenizer:A,escapeMarkup:w,blurOnChange:!1,selectOnBlur:!1,adaptContainerCssClass:function(t){return t},adaptDropdownCssClass:function(t){return null},nextSearchTerm:function(t,n){return e},searchInputPlaceholder:"",createSearchChoicePosition:"top",shouldFocusInput:function(t){return!(("ontouchstart"in window||navigator.msMaxTouchPoints>0)&&t.opts.minimumResultsForSearch<0)}},t.fn.select2.locales=[],t.fn.select2.locales.en={formatMatches:function(t){return 1===t?"One result is available, press enter to select it.":t+" results are available, use up and down arrow keys to navigate."},formatNoMatches:function(){return"No matches found"},formatAjaxError:function(t,e,n){return"Loading failed"},formatInputTooShort:function(t,e){var n=e-t.length;return"Please enter "+n+" or more character"+(1==n?"":"s")},formatInputTooLong:function(t,e){var n=t.length-e;return"Please delete "+n+" character"+(1==n?"":"s")},formatSelectionTooBig:function(t){return"You can only select "+t+" item"+(1==t?"":"s")},formatLoadMore:function(t){return"Loading more results…"},formatSearching:function(){return"Searching…"}},t.extend(t.fn.select2.defaults,t.fn.select2.locales.en),t.fn.select2.ajaxDefaults={transport:t.ajax,params:{type:"GET",cache:!1,dataType:"json"}},window.Select2={query:{ajax:_,local:x,tags:C},util:{debounce:h,markMatch:b,escapeMarkup:w,stripDiacritics:i},class:{abstract:D,single:M,multi:P}}}}(t)}).call(e,n(0))},176:function(t,e,n){"use strict";function i(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}Object.defineProperty(e,"__esModule",{value:!0});var r=n(0),o=function(t){return t&&t.__esModule?t:{default:t}}(r),s=n(2),a=i(s),l=n(1),u=i(l),c=160,h=800,d=u.View.extend({initialize:function(t){this.view=t.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var t=this,e=this.view,n=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),a.each(n.buttons,function(e){t.$(".panel-header-buttons").append(e.$el)}),this.$el.addClass(n.cls),this.$(".panel-header-text").html(a.escape(n.title)),this.$(".unified-panel-body").append(e.$el),e.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(t){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(t){return'<div class="unified-panel-body"/>'},_templateFooter:function(t){return['<div class="unified-panel-footer">','<div class="panel-collapse ',a.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(t){function e(t){var e=t.pageX-r;r=t.pageX;var o=n.$el.width(),s=i?o+e:o-e;s=Math.min(h,Math.max(c,s)),n.resize(s)}var n=this,i="left"===this.id,r=t.pageX;(0,o.default)("#dd-helper").show().on("mousemove",e).one("mouseup",function(t){(0,o.default)(this).hide().off("mousemove",e)})},resize:function(t){return this.$el.css("width",t),this.$center().css(this.id,t),this},show:function(){if(this.hidden){var t=this,e={},n=this.id;return e[n]=0,t.$el.css(n,-this.saved_size).show().animate(e,"fast",function(){t.resize(t.saved_size)}),t.hidden=!1,t.$toggleButton().removeClass("hidden"),this}},hide:function(){if(!this.hidden){var t={},e=this.id;return this.saved_size=this.$el.width(),t[e]=-this.saved_size,this.$el.animate(t,"fast"),this.$center().css(e,0),this.hidden=!0,this.$toggleButton().addClass("hidden"),this}},toggle:function(t){return this.hidden?this.show():this.hide(),this.hiddenByTool=!1,this},handle_minwidth_hint:function(t){return this.$center().width()-(this.hidden?this.saved_size:0)<t?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(t){return"show"==t?this.show():"hide"==t?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),p=d.extend({id:"left"}),f=d.extend({id:"right"}),g=u.View.extend({initialize:function(t){this.setElement((0,o.default)(this.template())),this.$frame=this.$(".center-frame"),this.$panel=this.$(".center-panel"),this.$frame.on("load",a.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(t){var e=t.currentTarget,n=e.contentWindow&&e.contentWindow.location;n&&n.host&&((0,o.default)(e).show(),this.$panel.empty().hide(),Galaxy.trigger("center-frame:load",{fullpath:n.pathname+n.search+n.hash,pathname:n.pathname,search:n.search,hash:n.hash}))},display:function(t){var e=this.$frame[0].contentWindow||{},n=e.onbeforeunload&&e.onbeforeunload();n&&!confirm(n)||(e.onbeforeunload=void 0,this.$frame.attr("src","about:blank").hide(),this.$panel.empty().scrollTop(0).append(t.$el||t).show(),Galaxy.trigger("center-panel:load",t))},template:function(){return'<div class="center-container"><iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" /><div class="center-panel" /></div>'},toString:function(){return"CenterPanel"}});e.default={SidePanel:d,LeftPanel:p,RightPanel:f,CenterPanel:g}},199:function(t,e,n){(function(t){!function(t,e){var n,i;i=e.document,n=function(){function n(n){var i;try{i=e.localStorage}catch(t){i=!1}this._options=t.extend({name:"tour",steps:[],container:"body",autoscroll:!0,keyboard:!0,storage:i,debug:!1,backdrop:!1,backdropContainer:"body",backdropPadding:0,redirect:!0,orphan:!1,duration:!1,delay:!1,basePath:"",template:'<div class="popover" role="tooltip"> <div class="arrow"></div> <h3 class="popover-title"></h3> <div class="popover-content"></div> <div class="popover-navigation"> <div class="btn-group"> <button class="btn btn-sm btn-default" data-role="prev">&laquo; Prev</button> <button class="btn btn-sm btn-default" data-role="next">Next &raquo;</button> <button class="btn btn-sm btn-default" data-role="pause-resume" data-pause-text="Pause" data-resume-text="Resume">Pause</button> </div> <button class="btn btn-sm btn-default" data-role="end">End tour</button> </div> </div>',afterSetState:function(t,e){},afterGetState:function(t,e){},afterRemoveState:function(t){},onStart:function(t){},onEnd:function(t){},onShow:function(t){},onShown:function(t){},onHide:function(t){},onHidden:function(t){},onNext:function(t){},onPrev:function(t){},onPause:function(t,e){},onResume:function(t,e){},onRedirectError:function(t){}},n),this._force=!1,this._inited=!1,this._current=null,this.backdrop={overlay:null,$element:null,$background:null,backgroundShown:!1,overlayElementShown:!1}}return n.prototype.addSteps=function(t){var e,n,i;for(n=0,i=t.length;n<i;n++)e=t[n],this.addStep(e);return this},n.prototype.addStep=function(t){return this._options.steps.push(t),this},n.prototype.getStep=function(e){if(null!=this._options.steps[e])return t.extend({id:"step-"+e,path:"",host:"",placement:"right",title:"",content:"<p></p>",next:e===this._options.steps.length-1?-1:e+1,prev:e-1,animation:!0,container:this._options.container,autoscroll:this._options.autoscroll,backdrop:this._options.backdrop,backdropContainer:this._options.backdropContainer,backdropPadding:this._options.backdropPadding,redirect:this._options.redirect,reflexElement:this._options.steps[e].element,orphan:this._options.orphan,duration:this._options.duration,delay:this._options.delay,template:this._options.template,onShow:this._options.onShow,onShown:this._options.onShown,onHide:this._options.onHide,onHidden:this._options.onHidden,onNext:this._options.onNext,onPrev:this._options.onPrev,onPause:this._options.onPause,onResume:this._options.onResume,onRedirectError:this._options.onRedirectError},this._options.steps[e])},n.prototype.init=function(t){return this._force=t,this.ended()?(this._debug("Tour ended, init prevented."),this):(this.setCurrentStep(),this._initMouseNavigation(),this._initKeyboardNavigation(),this._onResize(function(t){return function(){return t.showStep(t._current)}}(this)),null!==this._current&&this.showStep(this._current),this._inited=!0,this)},n.prototype.start=function(t){var e;return null==t&&(t=!1),this._inited||this.init(t),null===this._current&&(e=this._makePromise(null!=this._options.onStart?this._options.onStart(this):void 0),this._callOnPromiseDone(e,this.showStep,0)),this},n.prototype.next=function(){var t;return t=this.hideStep(this._current),this._callOnPromiseDone(t,this._showNextStep)},n.prototype.prev=function(){var t;return t=this.hideStep(this._current),this._callOnPromiseDone(t,this._showPrevStep)},n.prototype.goTo=function(t){var e;return e=this.hideStep(this._current),this._callOnPromiseDone(e,this.showStep,t)},n.prototype.end=function(){var n,r;return n=function(n){return function(r){if(t(i).off("click.tour-"+n._options.name),t(i).off("keyup.tour-"+n._options.name),t(e).off("resize.tour-"+n._options.name),n._setState("end","yes"),n._inited=!1,n._force=!1,n._clearTimer(),null!=n._options.onEnd)return n._options.onEnd(n)}}(this),r=this.hideStep(this._current),this._callOnPromiseDone(r,n)},n.prototype.ended=function(){return!this._force&&!!this._getState("end")},n.prototype.restart=function(){return this._removeState("current_step"),this._removeState("end"),this._removeState("redirect_to"),this.start()},n.prototype.pause=function(){var t;return(t=this.getStep(this._current))&&t.duration?(this._paused=!0,this._duration-=(new Date).getTime()-this._start,e.clearTimeout(this._timer),this._debug("Paused/Stopped step "+(this._current+1)+" timer ("+this._duration+" remaining)."),null!=t.onPause?t.onPause(this,this._duration):void 0):this},n.prototype.resume=function(){var t;return(t=this.getStep(this._current))&&t.duration?(this._paused=!1,this._start=(new Date).getTime(),this._duration=this._duration||t.duration,this._timer=e.setTimeout(function(t){return function(){return t._isLast()?t.next():t.end()}}(this),this._duration),this._debug("Started step "+(this._current+1)+" timer with duration "+this._duration),null!=t.onResume&&this._duration!==t.duration?t.onResume(this,this._duration):void 0):this},n.prototype.hideStep=function(e){var n,i,r;if(r=this.getStep(e))return this._clearTimer(),i=this._makePromise(null!=r.onHide?r.onHide(this,e):void 0),n=function(n){return function(i){var o;if(o=t(r.element),o.data("bs.popover")||o.data("popover")||(o=t("body")),o.popover("destroy").removeClass("tour-"+n._options.name+"-element tour-"+n._options.name+"-"+e+"-element"),o.removeData("bs.popover"),r.reflex&&t(r.reflexElement).removeClass("tour-step-element-reflex").off(n._reflexEvent(r.reflex)+".tour-"+n._options.name),r.backdrop&&n._hideBackdrop(),null!=r.onHidden)return r.onHidden(n)}}(this),this._callOnPromiseDone(i,n),i},n.prototype.showStep=function(t){var n,r,o,s;return this.ended()?(this._debug("Tour ended, showStep prevented."),this):(s=this.getStep(t))?(o=t<this._current,n=this._makePromise(null!=s.onShow?s.onShow(this,t):void 0),r=function(e){return function(n){var r,a;if(e.setCurrentStep(t),r=function(){switch({}.toString.call(s.path)){case"[object Function]":return s.path();case"[object String]":return this._options.basePath+s.path;default:return s.path}}.call(e),!e._isRedirect(s.host,r,i.location)||(e._redirect(s,t,r),e._isJustPathHashDifferent(s.host,r,i.location))){if(e._isOrphan(s)){if(!1===s.orphan)return e._debug("Skip the orphan step "+(e._current+1)+".\nOrphan option is false and the element does not exist or is hidden."),void(o?e._showPrevStep():e._showNextStep());e._debug("Show the orphan step "+(e._current+1)+". Orphans option is true.")}return s.backdrop&&e._showBackdrop(s),a=function(){if(e.getCurrentStep()===t&&!e.ended())return null!=s.element&&s.backdrop&&e._showOverlayElement(s),e._showPopover(s,t),null!=s.onShown&&s.onShown(e),e._debug("Step "+(e._current+1)+" of "+e._options.steps.length)},s.autoscroll?e._scrollIntoView(s.element,a):a(),s.duration?e.resume():void 0}}}(this),s.delay?(this._debug("Wait "+s.delay+" milliseconds to show the step "+(this._current+1)),e.setTimeout(function(t){return function(){return t._callOnPromiseDone(n,r)}}(this),s.delay)):this._callOnPromiseDone(n,r),n):void 0},n.prototype.getCurrentStep=function(){return this._current},n.prototype.setCurrentStep=function(t){return null!=t?(this._current=t,this._setState("current_step",t)):(this._current=this._getState("current_step"),this._current=null===this._current?null:parseInt(this._current,10)),this},n.prototype.redraw=function(){return this._showOverlayElement(this.getStep(this.getCurrentStep()).element,!0)},n.prototype._setState=function(t,e){var n,i;if(this._options.storage){i=this._options.name+"_"+t;try{this._options.storage.setItem(i,e)}catch(t){n=t,n.code===DOMException.QUOTA_EXCEEDED_ERR&&this._debug("LocalStorage quota exceeded. State storage failed.")}return this._options.afterSetState(i,e)}return null==this._state&&(this._state={}),this._state[t]=e},n.prototype._removeState=function(t){var e;return this._options.storage?(e=this._options.name+"_"+t,this._options.storage.removeItem(e),this._options.afterRemoveState(e)):null!=this._state?delete this._state[t]:void 0},n.prototype._getState=function(t){var e,n;return this._options.storage?(e=this._options.name+"_"+t,n=this._options.storage.getItem(e)):null!=this._state&&(n=this._state[t]),void 0!==n&&"null"!==n||(n=null),this._options.afterGetState(t,n),n},n.prototype._showNextStep=function(){var t,e,n;return n=this.getStep(this._current),e=function(t){return function(e){return t.showStep(n.next)}}(this),t=this._makePromise(null!=n.onNext?n.onNext(this):void 0),this._callOnPromiseDone(t,e)},n.prototype._showPrevStep=function(){var t,e,n;return n=this.getStep(this._current),e=function(t){return function(e){return t.showStep(n.prev)}}(this),t=this._makePromise(null!=n.onPrev?n.onPrev(this):void 0),this._callOnPromiseDone(t,e)},n.prototype._debug=function(t){if(this._options.debug)return e.console.log("Bootstrap Tour '"+this._options.name+"' | "+t)},n.prototype._isRedirect=function(t,e,n){var i;return!(""===t||!this._isHostDifferent(t,n.href))||(i=[n.pathname,n.search,n.hash].join(""),null!=e&&""!==e&&("[object RegExp]"==={}.toString.call(e)&&!e.test(i)||"[object String]"==={}.toString.call(e)&&this._isPathDifferent(e,i)))},n.prototype._isHostDifferent=function(t,e){return this._getProtocol(t)!==this._getProtocol(e)||this._getHost(t)!==this._getHost(e)},n.prototype._isPathDifferent=function(t,e){return this._getPath(t)!==this._getPath(e)||!this._equal(this._getQuery(t),this._getQuery(e))||!this._equal(this._getHash(t),this._getHash(e))},n.prototype._isJustPathHashDifferent=function(t,e,n){var i;return(""===t||!this._isHostDifferent(t,n.href))&&(i=[n.pathname,n.search,n.hash].join(""),"[object String]"==={}.toString.call(e)&&(this._getPath(e)===this._getPath(i)&&this._equal(this._getQuery(e),this._getQuery(i))&&!this._equal(this._getHash(e),this._getHash(i))))},n.prototype._redirect=function(e,n,r){if(t.isFunction(e.redirect))return e.redirect.call(this,r);if(!0===e.redirect){if(this._debug("Redirect to "+e.host+r),this._getState("redirect_to")!==""+n)return this._setState("redirect_to",""+n),i.location.href=""+e.host+r;if(this._debug("Error redirection loop to "+r),this._removeState("redirect_to"),null!=e.onRedirectError)return e.onRedirectError(this)}},n.prototype._isOrphan=function(e){return null==e.element||!t(e.element).length||t(e.element).is(":hidden")&&"http://www.w3.org/2000/svg"!==t(e.element)[0].namespaceURI},n.prototype._isLast=function(){return this._current<this._options.steps.length-1},n.prototype._showPopover=function(e,n){var i,r,o,s,a;if(t(".tour-"+this._options.name).remove(),s=t.extend({},this._options),o=this._isOrphan(e),e.template=this._template(e,n),o&&(e.element="body",e.placement="top"),i=t(e.element),i.addClass("tour-"+this._options.name+"-element tour-"+this._options.name+"-"+n+"-element"),e.options&&t.extend(s,e.options),e.reflex&&!o&&t(e.reflexElement).addClass("tour-step-element-reflex").off(this._reflexEvent(e.reflex)+".tour-"+this._options.name).on(this._reflexEvent(e.reflex)+".tour-"+this._options.name,function(t){return function(){return t._isLast()?t.next():t.end()}}(this)),a=!0===e.smartPlacement&&-1===e.placement.search(/auto/i),i.popover({placement:a?"auto "+e.placement:e.placement,trigger:"manual",title:e.title,content:e.content,html:!0,animation:e.animation,container:e.container,template:e.template,selector:e.element}).popover("show"),r=i.data("bs.popover")?i.data("bs.popover").tip():i.data("popover").tip(),r.attr("id",e.id),this._reposition(r,e),o)return this._center(r)},n.prototype._template=function(e,n){var i,r,o,s,a,l;return l=e.template,this._isOrphan(e)&&"[object Boolean]"!=={}.toString.call(e.orphan)&&(l=e.orphan),a=t(t.isFunction(l)?l(n,e):l),i=a.find(".popover-navigation"),o=i.find('[data-role="prev"]'),r=i.find('[data-role="next"]'),s=i.find('[data-role="pause-resume"]'),this._isOrphan(e)&&a.addClass("orphan"),a.addClass("tour-"+this._options.name+" tour-"+this._options.name+"-"+n),e.reflex&&a.addClass("tour-"+this._options.name+"-reflex"),e.prev<0&&(o.addClass("disabled"),o.prop("disabled",!0)),e.next<0&&(r.addClass("disabled"),r.prop("disabled",!0)),e.duration||s.remove(),a.clone().wrap("<div>").parent().html()},n.prototype._reflexEvent=function(t){return"[object Boolean]"==={}.toString.call(t)?"click":t},n.prototype._reposition=function(e,n){var r,o,s,a,l,u,c;if(a=e[0].offsetWidth,o=e[0].offsetHeight,c=e.offset(),l=c.left,u=c.top,r=t(i).outerHeight()-c.top-e.outerHeight(),r<0&&(c.top=c.top+r),s=t("html").outerWidth()-c.left-e.outerWidth(),s<0&&(c.left=c.left+s),c.top<0&&(c.top=0),c.left<0&&(c.left=0),e.offset(c),"bottom"===n.placement||"top"===n.placement){if(l!==c.left)return this._replaceArrow(e,2*(c.left-l),a,"left")}else if(u!==c.top)return this._replaceArrow(e,2*(c.top-u),o,"top")},n.prototype._center=function(n){return n.css("top",t(e).outerHeight()/2-n.outerHeight()/2)},n.prototype._replaceArrow=function(t,e,n,i){return t.find(".arrow").css(i,e?50*(1-e/n)+"%":"")},n.prototype._scrollIntoView=function(n,i){var r,o,s,a,l,u;return r=t(n),r.length?(o=t(e),a=r.offset().top,u=o.height(),l=Math.max(0,a-u/2),this._debug("Scroll into view. ScrollTop: "+l+". Element offset: "+a+". 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n=i.prop("readonly");n===e&&(n=!1),this.readonly(n),y(this.container,this.opts.element,this.opts.adaptContainerCssClass),this.container.addClass(S(this.opts.containerCssClass,this.opts.element)),y(this.dropdown,this.opts.element,this.opts.adaptDropdownCssClass),this.dropdown.addClass(S(this.opts.dropdownCssClass,this.opts.element))}),i.length&&i[0].attachEvent&&i.each(function(){this.attachEvent("onpropertychange",r._sync)}),(n=window.MutationObserver||window.WebKitMutationObserver||window.MozMutationObserver)!==e&&(this.propertyObserver&&(delete this.propertyObserver,this.propertyObserver=null),this.propertyObserver=new n(function(e){t.each(e,r._sync)}),this.propertyObserver.observe(i.get(0),{attributes:!0,subtree:!1}))},triggerSelect:function(e){var n=t.Event("select2-selecting",{val:this.id(e),object:e,choice:e});return this.opts.element.trigger(n),!n.isDefaultPrevented()},triggerChange:function(e){e=e||{},e=t.extend({},e,{type:"change",val:this.val()}),this.opts.element.data("select2-change-triggered",!0),this.opts.element.trigger(e),this.opts.element.data("select2-change-triggered",!1),this.opts.element.click(),this.opts.blurOnChange&&this.opts.element.blur()},isInterfaceEnabled:function(){return!0===this.enabledInterface},enableInterface:function(){var t=this._enabled&&!this._readonly,e=!t;return t!==this.enabledInterface&&(this.container.toggleClass("select2-container-disabled",e),this.close(),this.enabledInterface=t,!0)},enable:function(t){t===e&&(t=!0),this._enabled!==t&&(this._enabled=t,this.opts.element.prop("disabled",!t),this.enableInterface())},disable:function(){this.enable(!1)},readonly:function(t){t===e&&(t=!1),this._readonly!==t&&(this._readonly=t,this.opts.element.prop("readonly",t),this.enableInterface())},opened:function(){return!!this.container&&this.container.hasClass("select2-dropdown-open")},positionDropdown:function(){var e,n,i,r,o,s=this.dropdown,a=this.container.offset(),l=this.container.outerHeight(!1),u=this.container.outerWidth(!1),c=s.outerHeight(!1),h=t(window),d=h.width(),p=h.height(),f=h.scrollLeft()+d,g=h.scrollTop()+p,v=a.top+l,m=a.left,y=v+c<=g,b=a.top-c>=h.scrollTop(),w=s.outerWidth(!1),_=m+w<=f,x=s.hasClass("select2-drop-above");x?(n=!0,!b&&y&&(i=!0,n=!1)):(n=!1,!y&&b&&(i=!0,n=!0)),i&&(s.hide(),a=this.container.offset(),l=this.container.outerHeight(!1),u=this.container.outerWidth(!1),c=s.outerHeight(!1),f=h.scrollLeft()+d,g=h.scrollTop()+p,v=a.top+l,m=a.left,w=s.outerWidth(!1),_=m+w<=f,s.show(),this.focusSearch()),this.opts.dropdownAutoWidth?(o=t(".select2-results",s)[0],s.addClass("select2-drop-auto-width"),s.css("width",""),w=s.outerWidth(!1)+(o.scrollHeight===o.clientHeight?0:$.width),w>u?u=w:w=u,c=s.outerHeight(!1),_=m+w<=f):this.container.removeClass("select2-drop-auto-width"),"static"!==this.body.css("position")&&(e=this.body.offset(),v-=e.top,m-=e.left),_||(m=a.left+this.container.outerWidth(!1)-w),r={left:m,width:u},n?(r.top=a.top-c,r.bottom="auto",this.container.addClass("select2-drop-above"),s.addClass("select2-drop-above")):(r.top=v,r.bottom="auto",this.container.removeClass("select2-drop-above"),s.removeClass("select2-drop-above")),r=t.extend(r,S(this.opts.dropdownCss,this.opts.element)),s.css(r)},shouldOpen:function(){var e;return!this.opened()&&(!1!==this._enabled&&!0!==this._readonly&&(e=t.Event("select2-opening"),this.opts.element.trigger(e),!e.isDefaultPrevented()))},clearDropdownAlignmentPreference:function(){this.container.removeClass("select2-drop-above"),this.dropdown.removeClass("select2-drop-above")},open:function(){return!!this.shouldOpen()&&(this.opening(),I.on("mousemove.select2Event",function(t){L.x=t.pageX,L.y=t.pageY}),!0)},opening:function(){var e,i=this.containerEventName,r="scroll."+i,o="resize."+i,s="orientationchange."+i;this.container.addClass("select2-dropdown-open").addClass("select2-container-active"),this.clearDropdownAlignmentPreference(),this.dropdown[0]!==this.body.children().last()[0]&&this.dropdown.detach().appendTo(this.body),e=t("#select2-drop-mask"),0==e.length&&(e=t(document.createElement("div")),e.attr("id","select2-drop-mask").attr("class","select2-drop-mask"),e.hide(),e.appendTo(this.body),e.on("mousedown touchstart click",function(i){n(e);var r,o=t("#select2-drop");o.length>0&&(r=o.data("select2"),r.opts.selectOnBlur&&r.selectHighlighted({noFocus:!0}),r.close(),i.preventDefault(),i.stopPropagation())})),this.dropdown.prev()[0]!==e[0]&&this.dropdown.before(e),t("#select2-drop").removeAttr("id"),this.dropdown.attr("id","select2-drop"),e.show(),this.positionDropdown(),this.dropdown.show(),this.positionDropdown(),this.dropdown.addClass("select2-drop-active");var a=this;this.container.parents().add(window).each(function(){t(this).on(o+" "+r+" "+s,function(t){a.opened()&&a.positionDropdown()})})},close:function(){if(this.opened()){var e=this.containerEventName,n="scroll."+e,i="resize."+e,r="orientationchange."+e;this.container.parents().add(window).each(function(){t(this).off(n).off(i).off(r)}),this.clearDropdownAlignmentPreference(),t("#select2-drop-mask").hide(),this.dropdown.removeAttr("id"),this.dropdown.hide(),this.container.removeClass("select2-dropdown-open").removeClass("select2-container-active"),this.results.empty(),I.off("mousemove.select2Event"),this.clearSearch(),this.search.removeClass("select2-active"),this.opts.element.trigger(t.Event("select2-close"))}},externalSearch:function(t){this.open(),this.search.val(t),this.updateResults(!1)},clearSearch:function(){},getMaximumSelectionSize:function(){return S(this.opts.maximumSelectionSize,this.opts.element)},ensureHighlightVisible:function(){var e,n,i,r,o,s,a,l,u=this.results;if(!((n=this.highlight())<0)){if(0==n)return void u.scrollTop(0);e=this.findHighlightableChoices().find(".select2-result-label"),i=t(e[n]),l=(i.offset()||{}).top||0,r=l+i.outerHeight(!0),n===e.length-1&&(a=u.find("li.select2-more-results"),a.length>0&&(r=a.offset().top+a.outerHeight(!0))),o=u.offset().top+u.outerHeight(!0),r>o&&u.scrollTop(u.scrollTop()+(r-o)),s=l-u.offset().top,s<0&&"none"!=i.css("display")&&u.scrollTop(u.scrollTop()+s)}},findHighlightableChoices:function(){return this.results.find(".select2-result-selectable:not(.select2-disabled):not(.select2-selected)")},moveHighlight:function(e){for(var n=this.findHighlightableChoices(),i=this.highlight();i>-1&&i<n.length;){i+=e;var r=t(n[i]);if(r.hasClass("select2-result-selectable")&&!r.hasClass("select2-disabled")&&!r.hasClass("select2-selected")){this.highlight(i);break}}},highlight:function(e){var n,i,o=this.findHighlightableChoices();if(0===arguments.length)return r(o.filter(".select2-highlighted")[0],o.get());e>=o.length&&(e=o.length-1),e<0&&(e=0),this.removeHighlight(),n=t(o[e]),n.addClass("select2-highlighted"),this.search.attr("aria-activedescendant",n.find(".select2-result-label").attr("id")),this.ensureHighlightVisible(),this.liveRegion.text(n.text()),(i=n.data("select2-data"))&&this.opts.element.trigger({type:"select2-highlight",val:this.id(i),choice:i})},removeHighlight:function(){this.results.find(".select2-highlighted").removeClass("select2-highlighted")},touchMoved:function(){this._touchMoved=!0},clearTouchMoved:function(){this._touchMoved=!1},countSelectableResults:function(){return this.findHighlightableChoices().length},highlightUnderEvent:function(e){var n=t(e.target).closest(".select2-result-selectable");if(n.length>0&&!n.is(".select2-highlighted")){var i=this.findHighlightableChoices();this.highlight(i.index(n))}else 0==n.length&&this.removeHighlight()},loadMoreIfNeeded:function(){var t=this.results,e=t.find("li.select2-more-results"),n=this.resultsPage+1,i=this,r=this.search.val(),o=this.context;0!==e.length&&e.offset().top-t.offset().top-t.height()<=this.opts.loadMorePadding&&(e.addClass("select2-active"),this.opts.query({element:this.opts.element,term:r,page:n,context:o,matcher:this.opts.matcher,callback:this.bind(function(s){i.opened()&&(i.opts.populateResults.call(this,t,s.results,{term:r,page:n,context:o}),i.postprocessResults(s,!1,!1),!0===s.more?(e.detach().appendTo(t).text(S(i.opts.formatLoadMore,i.opts.element,n+1)),window.setTimeout(function(){i.loadMoreIfNeeded()},10)):e.remove(),i.positionDropdown(),i.resultsPage=n,i.context=s.context,this.opts.element.trigger({type:"select2-loaded",items:s}))})}))},tokenize:function(){},updateResults:function(n){function i(){u.removeClass("select2-active"),d.positionDropdown(),c.find(".select2-no-results,.select2-selection-limit,.select2-searching").length?d.liveRegion.text(c.text()):d.liveRegion.text(d.opts.formatMatches(c.find(".select2-result-selectable").length))}function r(t){c.html(t),i()}var o,a,l,u=this.search,c=this.results,h=this.opts,d=this,p=u.val(),f=t.data(this.container,"select2-last-term");if((!0===n||!f||!s(p,f))&&(t.data(this.container,"select2-last-term",p),!0===n||!1!==this.showSearchInput&&this.opened())){l=++this.queryCount;var g=this.getMaximumSelectionSize();if(g>=1&&(o=this.data(),t.isArray(o)&&o.length>=g&&k(h.formatSelectionTooBig,"formatSelectionTooBig")))return void r("<li class='select2-selection-limit'>"+S(h.formatSelectionTooBig,h.element,g)+"</li>");if(u.val().length<h.minimumInputLength)return r(k(h.formatInputTooShort,"formatInputTooShort")?"<li class='select2-no-results'>"+S(h.formatInputTooShort,h.element,u.val(),h.minimumInputLength)+"</li>":""),void(n&&this.showSearch&&this.showSearch(!0));if(h.maximumInputLength&&u.val().length>h.maximumInputLength)return void r(k(h.formatInputTooLong,"formatInputTooLong")?"<li class='select2-no-results'>"+S(h.formatInputTooLong,h.element,u.val(),h.maximumInputLength)+"</li>":"");h.formatSearching&&0===this.findHighlightableChoices().length&&r("<li class='select2-searching'>"+S(h.formatSearching,h.element)+"</li>"),u.addClass("select2-active"),this.removeHighlight(),a=this.tokenize(),a!=e&&null!=a&&u.val(a),this.resultsPage=1,h.query({element:h.element,term:u.val(),page:this.resultsPage,context:null,matcher:h.matcher,callback:this.bind(function(o){var a;if(l==this.queryCount){if(!this.opened())return void this.search.removeClass("select2-active");if(o.hasError!==e&&k(h.formatAjaxError,"formatAjaxError"))return void r("<li class='select2-ajax-error'>"+S(h.formatAjaxError,h.element,o.jqXHR,o.textStatus,o.errorThrown)+"</li>");if(this.context=o.context===e?null:o.context,this.opts.createSearchChoice&&""!==u.val()&&(a=this.opts.createSearchChoice.call(d,u.val(),o.results))!==e&&null!==a&&d.id(a)!==e&&null!==d.id(a)&&0===t(o.results).filter(function(){return s(d.id(this),d.id(a))}).length&&this.opts.createSearchChoicePosition(o.results,a),0===o.results.length&&k(h.formatNoMatches,"formatNoMatches"))return void r("<li class='select2-no-results'>"+S(h.formatNoMatches,h.element,u.val())+"</li>");c.empty(),d.opts.populateResults.call(this,c,o.results,{term:u.val(),page:this.resultsPage,context:null}),!0===o.more&&k(h.formatLoadMore,"formatLoadMore")&&(c.append("<li class='select2-more-results'>"+h.escapeMarkup(S(h.formatLoadMore,h.element,this.resultsPage))+"</li>"),window.setTimeout(function(){d.loadMoreIfNeeded()},10)),this.postprocessResults(o,n),i(),this.opts.element.trigger({type:"select2-loaded",items:o})}})})}},cancel:function(){this.close()},blur:function(){this.opts.selectOnBlur&&this.selectHighlighted({noFocus:!0}),this.close(),this.container.removeClass("select2-container-active"),this.search[0]===document.activeElement&&this.search.blur(),this.clearSearch(),this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")},focusSearch:function(){p(this.search)},selectHighlighted:function(t){if(this._touchMoved)return void this.clearTouchMoved();var e=this.highlight(),n=this.results.find(".select2-highlighted"),i=n.closest(".select2-result").data("select2-data");i?(this.highlight(e),this.onSelect(i,t)):t&&t.noFocus&&this.close()},getPlaceholder:function(){var t;return this.opts.element.attr("placeholder")||this.opts.element.attr("data-placeholder")||this.opts.element.data("placeholder")||this.opts.placeholder||((t=this.getPlaceholderOption())!==e?t.text():e)},getPlaceholderOption:function(){if(this.select){var n=this.select.children("option").first();if(this.opts.placeholderOption!==e)return"first"===this.opts.placeholderOption&&n||"function"==typeof this.opts.placeholderOption&&this.opts.placeholderOption(this.select);if(""===t.trim(n.text())&&""===n.val())return n}},initContainerWidth:function(){function n(){var n,i,r,o,s,a;if("off"===this.opts.width)return null;if("element"===this.opts.width)return 0===this.opts.element.outerWidth(!1)?"auto":this.opts.element.outerWidth(!1)+"px";if("copy"===this.opts.width||"resolve"===this.opts.width){if((n=this.opts.element.attr("style"))!==e)for(i=n.split(";"),o=0,s=i.length;o<s;o+=1)if(a=i[o].replace(/\s/g,""),null!==(r=a.match(/^width:(([-+]?([0-9]*\.)?[0-9]+)(px|em|ex|%|in|cm|mm|pt|pc))/i))&&r.length>=1)return r[1];return"resolve"===this.opts.width?(n=this.opts.element.css("width"),n.indexOf("%")>0?n:0===this.opts.element.outerWidth(!1)?"auto":this.opts.element.outerWidth(!1)+"px"):null}return t.isFunction(this.opts.width)?this.opts.width():this.opts.width}var i=n.call(this);null!==i&&this.container.css("width",i)}}),M=O(D,{createContainer:function(){return t(document.createElement("div")).attr({class:"select2-container"}).html(["<a href='javascript:void(0)' class='select2-choice' tabindex='-1'>","   <span class='select2-chosen'>&#160;</span><abbr class='select2-search-choice-close'></abbr>","   <span class='select2-arrow' role='presentation'><b role='presentation'></b></span>","</a>","<label for='' class='select2-offscreen'></label>","<input class='select2-focusser select2-offscreen' type='text' aria-haspopup='true' role='button' />","<div class='select2-drop select2-display-none'>","   <div class='select2-search'>","       <label for='' class='select2-offscreen'></label>","       <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input' role='combobox' aria-expanded='true'","       aria-autocomplete='list' />","   </div>","   <ul class='select2-results' role='listbox'>","   </ul>","</div>"].join(""))},enableInterface:function(){this.parent.enableInterface.apply(this,arguments)&&this.focusser.prop("disabled",!this.isInterfaceEnabled())},opening:function(){var n,i,r;this.opts.minimumResultsForSearch>=0&&this.showSearch(!0),this.parent.opening.apply(this,arguments),!1!==this.showSearchInput&&this.search.val(this.focusser.val()),this.opts.shouldFocusInput(this)&&(this.search.focus(),n=this.search.get(0),n.createTextRange?(i=n.createTextRange(),i.collapse(!1),i.select()):n.setSelectionRange&&(r=this.search.val().length,n.setSelectionRange(r,r))),""===this.search.val()&&this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.search.select()),this.focusser.prop("disabled",!0).val(""),this.updateResults(!0),this.opts.element.trigger(t.Event("select2-open"))},close:function(){this.opened()&&(this.parent.close.apply(this,arguments),this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus())},focus:function(){this.opened()?this.close():(this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus())},isFocused:function(){return this.container.hasClass("select2-container-active")},cancel:function(){this.parent.cancel.apply(this,arguments),this.focusser.prop("disabled",!1),this.opts.shouldFocusInput(this)&&this.focusser.focus()},destroy:function(){t("label[for='"+this.focusser.attr("id")+"']").attr("for",this.opts.element.attr("id")),this.parent.destroy.apply(this,arguments),E.call(this,"selection","focusser")},initContainer:function(){var e,i,r=this.container,o=this.dropdown,s=N();this.opts.minimumResultsForSearch<0?this.showSearch(!1):this.showSearch(!0),this.selection=e=r.find(".select2-choice"),this.focusser=r.find(".select2-focusser"),e.find(".select2-chosen").attr("id","select2-chosen-"+s),this.focusser.attr("aria-labelledby","select2-chosen-"+s),this.results.attr("id","select2-results-"+s),this.search.attr("aria-owns","select2-results-"+s),this.focusser.attr("id","s2id_autogen"+s),i=t("label[for='"+this.opts.element.attr("id")+"']"),this.focusser.prev().text(i.text()).attr("for",this.focusser.attr("id"));var a=this.opts.element.attr("title");this.opts.element.attr("title",a||i.text()),this.focusser.attr("tabindex",this.elementTabIndex),this.search.attr("id",this.focusser.attr("id")+"_search"),this.search.prev().text(t("label[for='"+this.focusser.attr("id")+"']").text()).attr("for",this.search.attr("id")),this.search.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()&&229!=t.keyCode){if(t.which===j.PAGE_UP||t.which===j.PAGE_DOWN)return void g(t);switch(t.which){case j.UP:case j.DOWN:return this.moveHighlight(t.which===j.UP?-1:1),void g(t);case j.ENTER:return this.selectHighlighted(),void g(t);case j.TAB:return void this.selectHighlighted({noFocus:!0});case j.ESC:return this.cancel(t),void g(t)}}})),this.search.on("blur",this.bind(function(t){document.activeElement===this.body.get(0)&&window.setTimeout(this.bind(function(){this.opened()&&this.search.focus()}),0)})),this.focusser.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()&&t.which!==j.TAB&&!j.isControl(t)&&!j.isFunctionKey(t)&&t.which!==j.ESC){if(!1===this.opts.openOnEnter&&t.which===j.ENTER)return void g(t);if(t.which==j.DOWN||t.which==j.UP||t.which==j.ENTER&&this.opts.openOnEnter){if(t.altKey||t.ctrlKey||t.shiftKey||t.metaKey)return;return this.open(),void g(t)}return t.which==j.DELETE||t.which==j.BACKSPACE?(this.opts.allowClear&&this.clear(),void g(t)):void 0}})),u(this.focusser),this.focusser.on("keyup-change input",this.bind(function(t){if(this.opts.minimumResultsForSearch>=0){if(t.stopPropagation(),this.opened())return;this.open()}})),e.on("mousedown touchstart","abbr",this.bind(function(t){this.isInterfaceEnabled()&&(this.clear(),v(t),this.close(),this.selection.focus())})),e.on("mousedown touchstart",this.bind(function(i){n(e),this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.opened()?this.close():this.isInterfaceEnabled()&&this.open(),g(i)})),o.on("mousedown touchstart",this.bind(function(){this.opts.shouldFocusInput(this)&&this.search.focus()})),e.on("focus",this.bind(function(t){g(t)})),this.focusser.on("focus",this.bind(function(){this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active")})).on("blur",this.bind(function(){this.opened()||(this.container.removeClass("select2-container-active"),this.opts.element.trigger(t.Event("select2-blur")))})),this.search.on("focus",this.bind(function(){this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active")})),this.initContainerWidth(),this.opts.element.addClass("select2-offscreen"),this.setPlaceholder()},clear:function(e){var n=this.selection.data("select2-data");if(n){var i=t.Event("select2-clearing");if(this.opts.element.trigger(i),i.isDefaultPrevented())return;var r=this.getPlaceholderOption();this.opts.element.val(r?r.val():""),this.selection.find(".select2-chosen").empty(),this.selection.removeData("select2-data"),this.setPlaceholder(),!1!==e&&(this.opts.element.trigger({type:"select2-removed",val:this.id(n),choice:n}),this.triggerChange({removed:n}))}},initSelection:function(){if(this.isPlaceholderOptionSelected())this.updateSelection(null),this.close(),this.setPlaceholder();else{var t=this;this.opts.initSelection.call(null,this.opts.element,function(n){n!==e&&null!==n&&(t.updateSelection(n),t.close(),t.setPlaceholder(),t.nextSearchTerm=t.opts.nextSearchTerm(n,t.search.val()))})}},isPlaceholderOptionSelected:function(){var t;return this.getPlaceholder()!==e&&((t=this.getPlaceholderOption())!==e&&t.prop("selected")||""===this.opts.element.val()||this.opts.element.val()===e||null===this.opts.element.val())},prepareOpts:function(){var e=this.parent.prepareOpts.apply(this,arguments),n=this;return"select"===e.element.get(0).tagName.toLowerCase()?e.initSelection=function(t,e){var i=t.find("option").filter(function(){return this.selected&&!this.disabled});e(n.optionToData(i))}:"data"in e&&(e.initSelection=e.initSelection||function(n,i){var r=n.val(),o=null;e.query({matcher:function(t,n,i){var a=s(r,e.id(i));return a&&(o=i),a},callback:t.isFunction(i)?function(){i(o)}:t.noop})}),e},getPlaceholder:function(){return this.select&&this.getPlaceholderOption()===e?e:this.parent.getPlaceholder.apply(this,arguments)},setPlaceholder:function(){var t=this.getPlaceholder();if(this.isPlaceholderOptionSelected()&&t!==e){if(this.select&&this.getPlaceholderOption()===e)return;this.selection.find(".select2-chosen").html(this.opts.escapeMarkup(t)),this.selection.addClass("select2-default"),this.container.removeClass("select2-allowclear")}},postprocessResults:function(t,e,n){var i=0,r=this;if(this.findHighlightableChoices().each2(function(t,e){if(s(r.id(e.data("select2-data")),r.opts.element.val()))return i=t,!1}),!1!==n&&(!0===e&&i>=0?this.highlight(i):this.highlight(0)),!0===e){var o=this.opts.minimumResultsForSearch;o>=0&&this.showSearch(T(t.results)>=o)}},showSearch:function(e){this.showSearchInput!==e&&(this.showSearchInput=e,this.dropdown.find(".select2-search").toggleClass("select2-search-hidden",!e),this.dropdown.find(".select2-search").toggleClass("select2-offscreen",!e),t(this.dropdown,this.container).toggleClass("select2-with-searchbox",e))},onSelect:function(t,e){if(this.triggerSelect(t)){var n=this.opts.element.val(),i=this.data();this.opts.element.val(this.id(t)),this.updateSelection(t),this.opts.element.trigger({type:"select2-selected",val:this.id(t),choice:t}),this.nextSearchTerm=this.opts.nextSearchTerm(t,this.search.val()),this.close(),e&&e.noFocus||!this.opts.shouldFocusInput(this)||this.focusser.focus(),s(n,this.id(t))||this.triggerChange({added:t,removed:i})}},updateSelection:function(t){var n,i,r=this.selection.find(".select2-chosen");this.selection.data("select2-data",t),r.empty(),null!==t&&(n=this.opts.formatSelection(t,r,this.opts.escapeMarkup)),n!==e&&r.append(n),i=this.opts.formatSelectionCssClass(t,r),i!==e&&r.addClass(i),this.selection.removeClass("select2-default"),this.opts.allowClear&&this.getPlaceholder()!==e&&this.container.addClass("select2-allowclear")},val:function(){var t,n=!1,i=null,r=this,o=this.data();if(0===arguments.length)return this.opts.element.val();if(t=arguments[0],arguments.length>1&&(n=arguments[1]),this.select)this.select.val(t).find("option").filter(function(){return this.selected}).each2(function(t,e){return i=r.optionToData(e),!1}),this.updateSelection(i),this.setPlaceholder(),n&&this.triggerChange({added:i,removed:o});else{if(!t&&0!==t)return void this.clear(n);if(this.opts.initSelection===e)throw new Error("cannot call val() if initSelection() is not defined");this.opts.element.val(t),this.opts.initSelection(this.opts.element,function(t){r.opts.element.val(t?r.id(t):""),r.updateSelection(t),r.setPlaceholder(),n&&r.triggerChange({added:t,removed:o})})}},clearSearch:function(){this.search.val(""),this.focusser.val("")},data:function(t){var n,i=!1;if(0===arguments.length)return n=this.selection.data("select2-data"),n==e&&(n=null),n;arguments.length>1&&(i=arguments[1]),t?(n=this.data(),this.opts.element.val(t?this.id(t):""),this.updateSelection(t),i&&this.triggerChange({added:t,removed:n})):this.clear(i)}}),P=O(D,{createContainer:function(){return t(document.createElement("div")).attr({class:"select2-container select2-container-multi"}).html(["<ul class='select2-choices'>","  <li class='select2-search-field'>","    <label for='' class='select2-offscreen'></label>","    <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'>","  </li>","</ul>","<div class='select2-drop select2-drop-multi select2-display-none'>","   <ul class='select2-results'>","   </ul>","</div>"].join(""))},prepareOpts:function(){var e=this.parent.prepareOpts.apply(this,arguments),n=this;return"select"===e.element.get(0).tagName.toLowerCase()?e.initSelection=function(t,e){var i=[];t.find("option").filter(function(){return this.selected&&!this.disabled}).each2(function(t,e){i.push(n.optionToData(e))}),e(i)}:"data"in e&&(e.initSelection=e.initSelection||function(n,i){var r=a(n.val(),e.separator),o=[];e.query({matcher:function(n,i,a){var l=t.grep(r,function(t){return s(t,e.id(a))}).length;return l&&o.push(a),l},callback:t.isFunction(i)?function(){for(var t=[],n=0;n<r.length;n++)for(var a=r[n],l=0;l<o.length;l++){var u=o[l];if(s(a,e.id(u))){t.push(u),o.splice(l,1);break}}i(t)}:t.noop})}),e},selectChoice:function(t){var e=this.container.find(".select2-search-choice-focus");e.length&&t&&t[0]==e[0]||(e.length&&this.opts.element.trigger("choice-deselected",e),e.removeClass("select2-search-choice-focus"),t&&t.length&&(this.close(),t.addClass("select2-search-choice-focus"),this.opts.element.trigger("choice-selected",t)))},destroy:function(){t("label[for='"+this.search.attr("id")+"']").attr("for",this.opts.element.attr("id")),this.parent.destroy.apply(this,arguments),E.call(this,"searchContainer","selection")},initContainer:function(){var e,n=".select2-choices";this.searchContainer=this.container.find(".select2-search-field"),this.selection=e=this.container.find(n);var i=this;this.selection.on("click",".select2-search-choice:not(.select2-locked)",function(e){i.search[0].focus(),i.selectChoice(t(this))}),this.search.attr("id","s2id_autogen"+N()),this.search.prev().text(t("label[for='"+this.opts.element.attr("id")+"']").text()).attr("for",this.search.attr("id")),this.search.on("input paste",this.bind(function(){this.search.attr("placeholder")&&0==this.search.val().length||this.isInterfaceEnabled()&&(this.opened()||this.open())})),this.search.attr("tabindex",this.elementTabIndex),this.keydowns=0,this.search.on("keydown",this.bind(function(t){if(this.isInterfaceEnabled()){++this.keydowns;var n=e.find(".select2-search-choice-focus"),i=n.prev(".select2-search-choice:not(.select2-locked)"),r=n.next(".select2-search-choice:not(.select2-locked)"),o=f(this.search);if(n.length&&(t.which==j.LEFT||t.which==j.RIGHT||t.which==j.BACKSPACE||t.which==j.DELETE||t.which==j.ENTER)){var s=n;return t.which==j.LEFT&&i.length?s=i:t.which==j.RIGHT?s=r.length?r:null:t.which===j.BACKSPACE?this.unselect(n.first())&&(this.search.width(10),s=i.length?i:r):t.which==j.DELETE?this.unselect(n.first())&&(this.search.width(10),s=r.length?r:null):t.which==j.ENTER&&(s=null),this.selectChoice(s),g(t),void(s&&s.length||this.open())}if((t.which===j.BACKSPACE&&1==this.keydowns||t.which==j.LEFT)&&0==o.offset&&!o.length)return this.selectChoice(e.find(".select2-search-choice:not(.select2-locked)").last()),void g(t);if(this.selectChoice(null),this.opened())switch(t.which){case j.UP:case j.DOWN:return this.moveHighlight(t.which===j.UP?-1:1),void g(t);case j.ENTER:return this.selectHighlighted(),void g(t);case j.TAB:return this.selectHighlighted({noFocus:!0}),void this.close();case j.ESC:return this.cancel(t),void g(t)}if(t.which!==j.TAB&&!j.isControl(t)&&!j.isFunctionKey(t)&&t.which!==j.BACKSPACE&&t.which!==j.ESC){if(t.which===j.ENTER){if(!1===this.opts.openOnEnter)return;if(t.altKey||t.ctrlKey||t.shiftKey||t.metaKey)return}this.open(),t.which!==j.PAGE_UP&&t.which!==j.PAGE_DOWN||g(t),t.which===j.ENTER&&g(t)}}})),this.search.on("keyup",this.bind(function(t){this.keydowns=0,this.resizeSearch()})),this.search.on("blur",this.bind(function(e){this.container.removeClass("select2-container-active"),this.search.removeClass("select2-focused"),this.selectChoice(null),this.opened()||this.clearSearch(),e.stopImmediatePropagation(),this.opts.element.trigger(t.Event("select2-blur"))})),this.container.on("click",n,this.bind(function(e){this.isInterfaceEnabled()&&(t(e.target).closest(".select2-search-choice").length>0||(this.selectChoice(null),this.clearPlaceholder(),this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.open(),this.focusSearch(),e.preventDefault()))})),this.container.on("focus",n,this.bind(function(){this.isInterfaceEnabled()&&(this.container.hasClass("select2-container-active")||this.opts.element.trigger(t.Event("select2-focus")),this.container.addClass("select2-container-active"),this.dropdown.addClass("select2-drop-active"),this.clearPlaceholder())})),this.initContainerWidth(),this.opts.element.addClass("select2-offscreen"),this.clearSearch()},enableInterface:function(){this.parent.enableInterface.apply(this,arguments)&&this.search.prop("disabled",!this.isInterfaceEnabled())},initSelection:function(){if(""===this.opts.element.val()&&""===this.opts.element.text()&&(this.updateSelection([]),this.close(),this.clearSearch()),this.select||""!==this.opts.element.val()){var t=this;this.opts.initSelection.call(null,this.opts.element,function(n){n!==e&&null!==n&&(t.updateSelection(n),t.close(),t.clearSearch())})}},clearSearch:function(){var t=this.getPlaceholder(),n=this.getMaxSearchWidth();t!==e&&0===this.getVal().length&&!1===this.search.hasClass("select2-focused")?(this.search.val(t).addClass("select2-default"),this.search.width(n>0?n:this.container.css("width"))):this.search.val("").width(10)},clearPlaceholder:function(){this.search.hasClass("select2-default")&&this.search.val("").removeClass("select2-default")},opening:function(){this.clearPlaceholder(),this.resizeSearch(),this.parent.opening.apply(this,arguments),this.focusSearch(),""===this.search.val()&&this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.search.select()),this.updateResults(!0),this.opts.shouldFocusInput(this)&&this.search.focus(),this.opts.element.trigger(t.Event("select2-open"))},close:function(){this.opened()&&this.parent.close.apply(this,arguments)},focus:function(){this.close(),this.search.focus()},isFocused:function(){return this.search.hasClass("select2-focused")},updateSelection:function(e){var n=[],i=[],o=this;t(e).each(function(){r(o.id(this),n)<0&&(n.push(o.id(this)),i.push(this))}),e=i,this.selection.find(".select2-search-choice").remove(),t(e).each(function(){o.addSelectedChoice(this)}),o.postprocessResults()},tokenize:function(){var t=this.search.val();null!=(t=this.opts.tokenizer.call(this,t,this.data(),this.bind(this.onSelect),this.opts))&&t!=e&&(this.search.val(t),t.length>0&&this.open())},onSelect:function(t,n){this.triggerSelect(t)&&""!==t.text&&(this.addSelectedChoice(t),this.opts.element.trigger({type:"selected",val:this.id(t),choice:t}),this.nextSearchTerm=this.opts.nextSearchTerm(t,this.search.val()),this.moveHighlight(1),!this.select&&this.opts.closeOnSelect||this.postprocessResults(t,!1,!0===this.opts.closeOnSelect),this.opts.closeOnSelect?(this.clearSearch(),this.updateResults(),this.close(),this.search.width(10)):this.countSelectableResults()>0?(this.search.width(10),this.resizeSearch(),this.getMaximumSelectionSize()>0&&this.val().length>=this.getMaximumSelectionSize()?this.updateResults(!0):this.nextSearchTerm!=e&&(this.search.val(this.nextSearchTerm),this.updateResults(),this.search.select()),this.positionDropdown()):(this.close(),this.search.width(10)),this.triggerChange({added:t}),n&&n.noFocus||this.focusSearch())},cancel:function(){this.close(),this.focusSearch()},addSelectedChoice:function(n){var i,r,o=!n.locked,s=t("<li class='select2-search-choice'>    <div></div>    <a href='#' class='select2-search-choice-close' tabindex='-1'></a></li>"),a=t("<li class='select2-search-choice select2-locked'><div></div></li>"),l=o?s:a,u=this.id(n),c=this.getVal();i=this.opts.formatSelection(n,l.find("div"),this.opts.escapeMarkup),i!=e&&l.find("div").replaceWith("<div>"+i+"</div>"),r=this.opts.formatSelectionCssClass(n,l.find("div")),r!=e&&l.addClass(r),o&&l.find(".select2-search-choice-close").on("mousedown",g).on("click dblclick",this.bind(function(e){this.isInterfaceEnabled()&&(this.unselect(t(e.target)),this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus"),g(e),this.close(),this.focusSearch())})).on("focus",this.bind(function(){this.isInterfaceEnabled()&&(this.container.addClass("select2-container-active"),this.dropdown.addClass("select2-drop-active"))})),l.data("select2-data",n),l.insertBefore(this.searchContainer),c.push(u),this.setVal(c)},unselect:function(e){var n,i,o=this.getVal();if(e=e.closest(".select2-search-choice"),0===e.length)throw"Invalid argument: "+e+". Must be .select2-search-choice";if(n=e.data("select2-data")){var s=t.Event("select2-removing");if(s.val=this.id(n),s.choice=n,this.opts.element.trigger(s),s.isDefaultPrevented())return!1;for(;(i=r(this.id(n),o))>=0;)o.splice(i,1),this.setVal(o),this.select&&this.postprocessResults();return e.remove(),this.opts.element.trigger({type:"select2-removed",val:this.id(n),choice:n}),this.triggerChange({removed:n}),!0}},postprocessResults:function(t,e,n){var i=this.getVal(),o=this.results.find(".select2-result"),s=this.results.find(".select2-result-with-children"),a=this;o.each2(function(t,e){r(a.id(e.data("select2-data")),i)>=0&&(e.addClass("select2-selected"),e.find(".select2-result-selectable").addClass("select2-selected"))}),s.each2(function(t,e){e.is(".select2-result-selectable")||0!==e.find(".select2-result-selectable:not(.select2-selected)").length||e.addClass("select2-selected")}),-1==this.highlight()&&!1!==n&&a.highlight(0),!this.opts.createSearchChoice&&!o.filter(".select2-result:not(.select2-selected)").length>0&&(!t||t&&!t.more&&0===this.results.find(".select2-no-results").length)&&k(a.opts.formatNoMatches,"formatNoMatches")&&this.results.append("<li class='select2-no-results'>"+S(a.opts.formatNoMatches,a.opts.element,a.search.val())+"</li>")},getMaxSearchWidth:function(){return this.selection.width()-l(this.search)},resizeSearch:function(){var t,e,n,i,r,o=l(this.search);t=m(this.search)+10,e=this.search.offset().left,n=this.selection.width(),i=this.selection.offset().left,r=n-(e-i)-o,r<t&&(r=n-o),r<40&&(r=n-o),r<=0&&(r=t),this.search.width(Math.floor(r))},getVal:function(){var t;return this.select?(t=this.select.val(),null===t?[]:t):(t=this.opts.element.val(),a(t,this.opts.separator))},setVal:function(e){var n;this.select?this.select.val(e):(n=[],t(e).each(function(){r(this,n)<0&&n.push(this)}),this.opts.element.val(0===n.length?"":n.join(this.opts.separator)))},buildChangeDetails:function(t,e){for(var e=e.slice(0),t=t.slice(0),n=0;n<e.length;n++)for(var i=0;i<t.length;i++)s(this.opts.id(e[n]),this.opts.id(t[i]))&&(e.splice(n,1),n>0&&n--,t.splice(i,1),i--);return{added:e,removed:t}},val:function(n,i){var r,o=this;if(0===arguments.length)return this.getVal();if(r=this.data(),r.length||(r=[]),!n&&0!==n)return this.opts.element.val(""),this.updateSelection([]),this.clearSearch(),void(i&&this.triggerChange({added:this.data(),removed:r}));if(this.setVal(n),this.select)this.opts.initSelection(this.select,this.bind(this.updateSelection)),i&&this.triggerChange(this.buildChangeDetails(r,this.data()));else{if(this.opts.initSelection===e)throw new Error("val() cannot be called if initSelection() is not defined");this.opts.initSelection(this.opts.element,function(e){var n=t.map(e,o.id);o.setVal(n),o.updateSelection(e),o.clearSearch(),i&&o.triggerChange(o.buildChangeDetails(r,o.data()))})}this.clearSearch()},onSortStart:function(){if(this.select)throw new Error("Sorting of elements is not supported when attached to <select>. Attach to <input type='hidden'/> instead.");this.search.width(0),this.searchContainer.hide()},onSortEnd:function(){var e=[],n=this;this.searchContainer.show(),this.searchContainer.appendTo(this.searchContainer.parent()),this.resizeSearch(),this.selection.find(".select2-search-choice").each(function(){e.push(n.opts.id(t(this).data("select2-data")))}),this.setVal(e),this.triggerChange()},data:function(e,n){var i,r,o=this;if(0===arguments.length)return this.selection.children(".select2-search-choice").map(function(){return t(this).data("select2-data")}).get();r=this.data(),e||(e=[]),i=t.map(e,function(t){return o.opts.id(t)}),this.setVal(i),this.updateSelection(e),this.clearSearch(),n&&this.triggerChange(this.buildChangeDetails(r,this.data()))}}),t.fn.select2=function(){var n,i,o,s,a,l=Array.prototype.slice.call(arguments,0),u=["val","destroy","opened","open","close","focus","isFocused","container","dropdown","onSortStart","onSortEnd","enable","disable","readonly","positionDropdown","data","search"],c=["opened","isFocused","container","dropdown"],h=["val","data"],d={search:"externalSearch"};return this.each(function(){if(0===l.length||"object"==typeof l[0])n=0===l.length?{}:t.extend({},l[0]),n.element=t(this),"select"===n.element.get(0).tagName.toLowerCase()?a=n.element.prop("multiple"):(a=n.multiple||!1,"tags"in n&&(n.multiple=a=!0)),i=a?new window.Select2.class.multi:new window.Select2.class.single,i.init(n);else{if("string"!=typeof l[0])throw"Invalid arguments to select2 plugin: "+l;if(r(l[0],u)<0)throw"Unknown method: "+l[0];if(s=e,(i=t(this).data("select2"))===e)return;if(o=l[0],"container"===o?s=i.container:"dropdown"===o?s=i.dropdown:(d[o]&&(o=d[o]),s=i[o].apply(i,l.slice(1))),r(l[0],c)>=0||r(l[0],h)>=0&&1==l.length)return!1}}),s===e?this:s},t.fn.select2.defaults={width:"copy",loadMorePadding:0,closeOnSelect:!0,openOnEnter:!0,containerCss:{},dropdownCss:{},containerCssClass:"",dropdownCssClass:"",formatResult:function(t,e,n,i){var r=[];return b(t.text,n.term,r,i),r.join("")},formatSelection:function(t,n,i){return t?i(t.text):e},sortResults:function(t,e,n){return t},formatResultCssClass:function(t){return t.css},formatSelectionCssClass:function(t,n){return e},minimumResultsForSearch:0,minimumInputLength:0,maximumInputLength:null,maximumSelectionSize:0,id:function(t){return t==e?null:t.id},matcher:function(t,e){return i(""+e).toUpperCase().indexOf(i(""+t).toUpperCase())>=0},separator:",",tokenSeparators:[],tokenizer:A,escapeMarkup:w,blurOnChange:!1,selectOnBlur:!1,adaptContainerCssClass:function(t){return t},adaptDropdownCssClass:function(t){return null},nextSearchTerm:function(t,n){return e},searchInputPlaceholder:"",createSearchChoicePosition:"top",shouldFocusInput:function(t){return!(("ontouchstart"in window||navigator.msMaxTouchPoints>0)&&t.opts.minimumResultsForSearch<0)}},t.fn.select2.locales=[],t.fn.select2.locales.en={formatMatches:function(t){return 1===t?"One result is available, press enter to select it.":t+" results are available, use up and down arrow keys to navigate."},formatNoMatches:function(){return"No matches found"},formatAjaxError:function(t,e,n){return"Loading failed"},formatInputTooShort:function(t,e){var n=e-t.length;return"Please enter "+n+" or more character"+(1==n?"":"s")},formatInputTooLong:function(t,e){var n=t.length-e;return"Please delete "+n+" character"+(1==n?"":"s")},formatSelectionTooBig:function(t){return"You can only select "+t+" item"+(1==t?"":"s")},formatLoadMore:function(t){return"Loading more results…"},formatSearching:function(){return"Searching…"}},t.extend(t.fn.select2.defaults,t.fn.select2.locales.en),t.fn.select2.ajaxDefaults={transport:t.ajax,params:{type:"GET",cache:!1,dataType:"json"}},window.Select2={query:{ajax:_,local:x,tags:C},util:{debounce:h,markMatch:b,escapeMarkup:w,stripDiacritics:i},class:{abstract:D,single:M,multi:P}}}}(t)}).call(e,n(0))},176:function(t,e,n){"use strict";function i(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}Object.defineProperty(e,"__esModule",{value:!0});var r=n(0),o=function(t){return t&&t.__esModule?t:{default:t}}(r),s=n(2),a=i(s),l=n(1),u=i(l),c=160,h=800,d=u.View.extend({initialize:function(t){this.view=t.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var t=this,e=this.view,n=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),a.each(n.buttons,function(e){t.$(".panel-header-buttons").append(e.$el)}),this.$el.addClass(n.cls),this.$(".panel-header-text").html(a.escape(n.title)),this.$(".unified-panel-body").append(e.$el),e.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(t){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(t){return'<div class="unified-panel-body"/>'},_templateFooter:function(t){return['<div class="unified-panel-footer">','<div class="panel-collapse ',a.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(t){function e(t){var e=t.pageX-r;r=t.pageX;var o=n.$el.width(),s=i?o+e:o-e;s=Math.min(h,Math.max(c,s)),n.resize(s)}var n=this,i="left"===this.id,r=t.pageX;(0,o.default)("#dd-helper").show().on("mousemove",e).one("mouseup",function(t){(0,o.default)(this).hide().off("mousemove",e)})},resize:function(t){return this.$el.css("width",t),this.$center().css(this.id,t),this},show:function(){if(this.hidden){var t=this,e={},n=this.id;return 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this.$center().width()-(this.hidden?this.saved_size:0)<t?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(t){return"show"==t?this.show():"hide"==t?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),p=d.extend({id:"left"}),f=d.extend({id:"right"}),g=u.View.extend({initialize:function(t){this.setElement((0,o.default)(this.template())),this.$frame=this.$(".center-frame"),this.$panel=this.$(".center-panel"),this.$frame.on("load",a.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(t){var e=t.currentTarget,n=e.contentWindow&&e.contentWindow.location;n&&n.host&&((0,o.default)(e).show(),this.$panel.empty().hide(),Galaxy.trigger("center-frame:load",{fullpath:n.pathname+n.search+n.hash,pathname:n.pathname,search:n.search,hash:n.hash}))},display:function(t){var e=this.$frame[0].contentWindow||{},n=e.onbeforeunload&&e.onbeforeunload();n&&!confirm(n)||(e.onbeforeunload=void 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btn-sm btn-default" data-role="prev">&laquo; Prev</button> <button class="btn btn-sm btn-default" data-role="next">Next &raquo;</button> <button class="btn btn-sm btn-default" data-role="pause-resume" data-pause-text="Pause" data-resume-text="Resume">Pause</button> </div> <button class="btn btn-sm btn-default" data-role="end">End tour</button> </div> </div>',afterSetState:function(t,e){},afterGetState:function(t,e){},afterRemoveState:function(t){},onStart:function(t){},onEnd:function(t){},onShow:function(t){},onShown:function(t){},onHide:function(t){},onHidden:function(t){},onNext:function(t){},onPrev:function(t){},onPause:function(t,e){},onResume:function(t,e){},onRedirectError:function(t){}},n),this._force=!1,this._inited=!1,this._current=null,this.backdrop={overlay:null,$element:null,$background:null,backgroundShown:!1,overlayElementShown:!1}}return n.prototype.addSteps=function(t){var e,n,i;for(n=0,i=t.length;n<i;n++)e=t[n],this.addStep(e);return this},n.prototype.addStep=function(t){return this._options.steps.push(t),this},n.prototype.getStep=function(e){if(null!=this._options.steps[e])return t.extend({id:"step-"+e,path:"",host:"",placement:"right",title:"",content:"<p></p>",next:e===this._options.steps.length-1?-1:e+1,prev:e-1,animation:!0,container:this._options.container,autoscroll:this._options.autoscroll,backdrop:this._options.backdrop,backdropContainer:this._options.backdropContainer,backdropPadding:this._options.backdropPadding,redirect:this._options.redirect,reflexElement:this._options.steps[e].element,orphan:this._options.orphan,duration:this._options.duration,delay:this._options.delay,template:this._options.template,onShow:this._options.onShow,onShown:this._options.onShown,onHide:this._options.onHide,onHidden:this._options.onHidden,onNext:this._options.onNext,onPrev:this._options.onPrev,onPause:this._options.onPause,onResume:this._options.onResume,onRedirectError:this._options.onRedirectError},this._options.steps[e])},n.prototype.init=function(t){return this._force=t,this.ended()?(this._debug("Tour ended, init 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function(r){if(t(i).off("click.tour-"+n._options.name),t(i).off("keyup.tour-"+n._options.name),t(e).off("resize.tour-"+n._options.name),n._setState("end","yes"),n._inited=!1,n._force=!1,n._clearTimer(),null!=n._options.onEnd)return n._options.onEnd(n)}}(this),r=this.hideStep(this._current),this._callOnPromiseDone(r,n)},n.prototype.ended=function(){return!this._force&&!!this._getState("end")},n.prototype.restart=function(){return this._removeState("current_step"),this._removeState("end"),this._removeState("redirect_to"),this.start()},n.prototype.pause=function(){var t;return(t=this.getStep(this._current))&&t.duration?(this._paused=!0,this._duration-=(new Date).getTime()-this._start,e.clearTimeout(this._timer),this._debug("Paused/Stopped step "+(this._current+1)+" timer ("+this._duration+" remaining)."),null!=t.onPause?t.onPause(this,this._duration):void 0):this},n.prototype.resume=function(){var t;return(t=this.getStep(this._current))&&t.duration?(this._paused=!1,this._start=(new Date).getTime(),this._duration=this._duration||t.duration,this._timer=e.setTimeout(function(t){return function(){return t._isLast()?t.next():t.end()}}(this),this._duration),this._debug("Started step "+(this._current+1)+" timer with duration "+this._duration),null!=t.onResume&&this._duration!==t.duration?t.onResume(this,this._duration):void 0):this},n.prototype.hideStep=function(e){var n,i,r;if(r=this.getStep(e))return this._clearTimer(),i=this._makePromise(null!=r.onHide?r.onHide(this,e):void 0),n=function(n){return function(i){var o;if(o=t(r.element),o.data("bs.popover")||o.data("popover")||(o=t("body")),o.popover("destroy").removeClass("tour-"+n._options.name+"-element tour-"+n._options.name+"-"+e+"-element"),o.removeData("bs.popover"),r.reflex&&t(r.reflexElement).removeClass("tour-step-element-reflex").off(n._reflexEvent(r.reflex)+".tour-"+n._options.name),r.backdrop&&n._hideBackdrop(),null!=r.onHidden)return r.onHidden(n)}}(this),this._callOnPromiseDone(i,n),i},n.prototype.showStep=function(t){var n,r,o,s;return this.ended()?(this._debug("Tour ended, showStep prevented."),this):(s=this.getStep(t))?(o=t<this._current,n=this._makePromise(null!=s.onShow?s.onShow(this,t):void 0),r=function(e){return function(n){var r,a;if(e.setCurrentStep(t),r=function(){switch({}.toString.call(s.path)){case"[object Function]":return s.path();case"[object String]":return this._options.basePath+s.path;default:return s.path}}.call(e),!e._isRedirect(s.host,r,i.location)||(e._redirect(s,t,r),e._isJustPathHashDifferent(s.host,r,i.location))){if(e._isOrphan(s)){if(!1===s.orphan)return e._debug("Skip the orphan step "+(e._current+1)+".\nOrphan option is false and the element does not exist or is hidden."),void(o?e._showPrevStep():e._showNextStep());e._debug("Show the orphan step "+(e._current+1)+". Orphans option is true.")}return s.backdrop&&e._showBackdrop(s),a=function(){if(e.getCurrentStep()===t&&!e.ended())return null!=s.element&&s.backdrop&&e._showOverlayElement(s),e._showPopover(s,t),null!=s.onShown&&s.onShown(e),e._debug("Step "+(e._current+1)+" of "+e._options.steps.length)},s.autoscroll?e._scrollIntoView(s.element,a):a(),s.duration?e.resume():void 0}}}(this),s.delay?(this._debug("Wait "+s.delay+" milliseconds to show the step "+(this._current+1)),e.setTimeout(function(t){return function(){return t._callOnPromiseDone(n,r)}}(this),s.delay)):this._callOnPromiseDone(n,r),n):void 0},n.prototype.getCurrentStep=function(){return this._current},n.prototype.setCurrentStep=function(t){return null!=t?(this._current=t,this._setState("current_step",t)):(this._current=this._getState("current_step"),this._current=null===this._current?null:parseInt(this._current,10)),this},n.prototype.redraw=function(){return this._showOverlayElement(this.getStep(this.getCurrentStep()).element,!0)},n.prototype._setState=function(t,e){var n,i;if(this._options.storage){i=this._options.name+"_"+t;try{this._options.storage.setItem(i,e)}catch(t){n=t,n.code===DOMException.QUOTA_EXCEEDED_ERR&&this._debug("LocalStorage quota exceeded. State storage failed.")}return this._options.afterSetState(i,e)}return null==this._state&&(this._state={}),this._state[t]=e},n.prototype._removeState=function(t){var e;return this._options.storage?(e=this._options.name+"_"+t,this._options.storage.removeItem(e),this._options.afterRemoveState(e)):null!=this._state?delete this._state[t]:void 0},n.prototype._getState=function(t){var e,n;return this._options.storage?(e=this._options.name+"_"+t,n=this._options.storage.getItem(e)):null!=this._state&&(n=this._state[t]),void 0!==n&&"null"!==n||(n=null),this._options.afterGetState(t,n),n},n.prototype._showNextStep=function(){var t,e,n;return n=this.getStep(this._current),e=function(t){return function(e){return t.showStep(n.next)}}(this),t=this._makePromise(null!=n.onNext?n.onNext(this):void 0),this._callOnPromiseDone(t,e)},n.prototype._showPrevStep=function(){var t,e,n;return n=this.getStep(this._current),e=function(t){return function(e){return t.showStep(n.prev)}}(this),t=this._makePromise(null!=n.onPrev?n.onPrev(this):void 0),this._callOnPromiseDone(t,e)},n.prototype._debug=function(t){if(this._options.debug)return e.console.log("Bootstrap Tour '"+this._options.name+"' | "+t)},n.prototype._isRedirect=function(t,e,n){var i;return!(""===t||!this._isHostDifferent(t,n.href))||(i=[n.pathname,n.search,n.hash].join(""),null!=e&&""!==e&&("[object RegExp]"==={}.toString.call(e)&&!e.test(i)||"[object String]"==={}.toString.call(e)&&this._isPathDifferent(e,i)))},n.prototype._isHostDifferent=function(t,e){return this._getProtocol(t)!==this._getProtocol(e)||this._getHost(t)!==this._getHost(e)},n.prototype._isPathDifferent=function(t,e){return this._getPath(t)!==this._getPath(e)||!this._equal(this._getQuery(t),this._getQuery(e))||!this._equal(this._getHash(t),this._getHash(e))},n.prototype._isJustPathHashDifferent=function(t,e,n){var i;return(""===t||!this._isHostDifferent(t,n.href))&&(i=[n.pathname,n.search,n.hash].join(""),"[object String]"==={}.toString.call(e)&&(this._getPath(e)===this._getPath(i)&&this._equal(this._getQuery(e),this._getQuery(i))&&!this._equal(this._getHash(e),this._getHash(i))))},n.prototype._redirect=function(e,n,r){if(t.isFunction(e.redirect))return e.redirect.call(this,r);if(!0===e.redirect){if(this._debug("Redirect to "+e.host+r),this._getState("redirect_to")!==""+n)return this._setState("redirect_to",""+n),i.location.href=""+e.host+r;if(this._debug("Error redirection loop to "+r),this._removeState("redirect_to"),null!=e.onRedirectError)return e.onRedirectError(this)}},n.prototype._isOrphan=function(e){return null==e.element||!t(e.element).length||t(e.element).is(":hidden")&&"http://www.w3.org/2000/svg"!==t(e.element)[0].namespaceURI},n.prototype._isLast=function(){return this._current<this._options.steps.length-1},n.prototype._showPopover=function(e,n){var i,r,o,s,a;if(t(".tour-"+this._options.name).remove(),s=t.extend({},this._options),o=this._isOrphan(e),e.template=this._template(e,n),o&&(e.element="body",e.placement="top"),i=t(e.element),i.addClass("tour-"+this._options.name+"-element tour-"+this._options.name+"-"+n+"-element"),e.options&&t.extend(s,e.options),e.reflex&&!o&&t(e.reflexElement).addClass("tour-step-element-reflex").off(this._reflexEvent(e.reflex)+".tour-"+this._options.name).on(this._reflexEvent(e.reflex)+".tour-"+this._options.name,function(t){return function(){return t._isLast()?t.next():t.end()}}(this)),a=!0===e.smartPlacement&&-1===e.placement.search(/auto/i),i.popover({placement:a?"auto "+e.placement:e.placement,trigger:"manual",title:e.title,content:e.content,html:!0,animation:e.animation,container:e.container,template:e.template,selector:e.element}).popover("show"),r=i.data("bs.popover")?i.data("bs.popover").tip():i.data("popover").tip(),r.attr("id",e.id),this._reposition(r,e),o)return this._center(r)},n.prototype._template=function(e,n){var i,r,o,s,a,l;return l=e.template,this._isOrphan(e)&&"[object Boolean]"!=={}.toString.call(e.orphan)&&(l=e.orphan),a=t(t.isFunction(l)?l(n,e):l),i=a.find(".popover-navigation"),o=i.find('[data-role="prev"]'),r=i.find('[data-role="next"]'),s=i.find('[data-role="pause-resume"]'),this._isOrphan(e)&&a.addClass("orphan"),a.addClass("tour-"+this._options.name+" tour-"+this._options.name+"-"+n),e.reflex&&a.addClass("tour-"+this._options.name+"-reflex"),e.prev<0&&(o.addClass("disabled"),o.prop("disabled",!0)),e.next<0&&(r.addClass("disabled"),r.prop("disabled",!0)),e.duration||s.remove(),a.clone().wrap("<div>").parent().html()},n.prototype._reflexEvent=function(t){return"[object Boolean]"==={}.toString.call(t)?"click":t},n.prototype._reposition=function(e,n){var r,o,s,a,l,u,c;if(a=e[0].offsetWidth,o=e[0].offsetHeight,c=e.offset(),l=c.left,u=c.top,r=t(i).outerHeight()-c.top-e.outerHeight(),r<0&&(c.top=c.top+r),s=t("html").outerWidth()-c.left-e.outerWidth(),s<0&&(c.left=c.left+s),c.top<0&&(c.top=0),c.left<0&&(c.left=0),e.offset(c),"bottom"===n.placement||"top"===n.placement){if(l!==c.left)return this._replaceArrow(e,2*(c.left-l),a,"left")}else if(u!==c.top)return this._replaceArrow(e,2*(c.top-u),o,"top")},n.prototype._center=function(n){return n.css("top",t(e).outerHeight()/2-n.outerHeight()/2)},n.prototype._replaceArrow=function(t,e,n,i){return t.find(".arrow").css(i,e?50*(1-e/n)+"%":"")},n.prototype._scrollIntoView=function(n,i){var r,o,s,a,l,u;return r=t(n),r.length?(o=t(e),a=r.offset().top,u=o.height(),l=Math.max(0,a-u/2),this._debug("Scroll into view. ScrollTop: "+l+". Element offset: "+a+". Window height: "+u+"."),s=0,t("body, html").stop(!0,!0).animate({scrollTop:Math.ceil(l)},function(t){return function(){if(2==++s)return i(),t._debug("Scroll into view.\nAnimation end element offset: "+r.offset().top+".\nWindow height: "+o.height()+".")}}(this))):i()},n.prototype._onResize=function(n,i){return t(e).on("resize.tour-"+this._options.name,function(){return clearTimeout(i),i=setTimeout(n,100)})},n.prototype._initMouseNavigation=function(){var e;return e=this,t(i).off("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='prev']").off("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='next']").off("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='end']").off("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='pause-resume']").on("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='next']",function(t){return function(e){return e.preventDefault(),t.next()}}(this)).on("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='prev']",function(t){return function(e){return e.preventDefault(),t.prev()}}(this)).on("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='end']",function(t){return function(e){return e.preventDefault(),t.end()}}(this)).on("click.tour-"+this._options.name,".popover.tour-"+this._options.name+" *[data-role='pause-resume']",function(n){var i;return n.preventDefault(),i=t(this),i.text(e._paused?i.data("pause-text"):i.data("resume-text")),e._paused?e.resume():e.pause()})},n.prototype._initKeyboardNavigation=function(){if(this._options.keyboard)return t(i).on("keyup.tour-"+this._options.name,function(t){return function(e){if(e.which)switch(e.which){case 39:return e.preventDefault(),t._isLast()?t.next():t.end();case 37:if(e.preventDefault(),t._current>0)return t.prev();break;case 27:return e.preventDefault(),t.end()}}}(this))},n.prototype._makePromise=function(e){return e&&t.isFunction(e.then)?e:null},n.prototype._callOnPromiseDone=function(t,e,n){return t?t.then(function(t){return function(i){return e.call(t,n)}}(this)):e.call(this,n)},n.prototype._showBackdrop=function(e){if(!this.backdrop.backgroundShown)return this.backdrop=t("<div>",{class:"tour-backdrop"}),this.backdrop.backgroundShown=!0,t(e.backdropContainer).append(this.backdrop)},n.prototype._hideBackdrop=function(){return this._hideOverlayElement(),this._hideBackground()},n.prototype._hideBackground=function(){if(this.backdrop)return this.backdrop.remove(),this.backdrop.overlay=null,this.backdrop.backgroundShown=!1},n.prototype._showOverlayElement=function(e,n){var i,r;if((i=t(e.element))&&0!==i.length&&(!this.backdrop.overlayElementShown||n))return 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  * @fileOverview jquery-autocomplete, the jQuery Autocompleter
  * @author <a href="mailto:dylan@dyve.net">Dylan Verheul</a>
  * @version 2.4.4
@@ -53,4 +53,4 @@ return o&&(a.length<4&&i("jQuery.fn.attr( props, pass ) is deprecated"),e&&!h.te
  * @license MIT | GPL | Apache 2.0, see LICENSE.txt
  * @see https://github.com/dyve/jquery-autocomplete
  */
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i=parseInt(t,10);return n=n||{},(isNaN(i)||n.min&&i<n.min)&&(i=e),i},i=function(t,e){return[t,encodeURIComponent(e)].join("=")},r=function(e,n){var r=[];return t.each(n,function(t,e){r.push(i(t,e))}),r.length&&(e+=-1===e.indexOf("?")?"?":"&",e+=r.join("&")),e},o=function(t,e,n){return t=String(t.value),e=String(e.value),n||(t=t.toLowerCase(),e=e.toLowerCase()),t>e?1:t<e?-1:0},s=function(t,e,n){var i,r,o,s,a,l,u=[];for(l=String(t).replace("\r\n","\n").split(e),i=0;i<l.length;i++){for(s=l[i].split(n),o=[],r=0;r<s.length;r++)o.push(decodeURIComponent(s[r]));a=o.shift(),u.push({value:a,data:o})}return u};t.Autocompleter=function(e,i){if(!e||!(e instanceof t)||1!==e.length||"INPUT"!==e.get(0).tagName.toUpperCase()&&"TEXTAREA"!==e.get(0).tagName.toUpperCase())throw new Error("Invalid parameter for jquery.Autocompleter, jQuery object with one element with INPUT or TEXTAREA tag expected.");var r=this;this.options=i,this.cacheData_={},this.cacheLength_=0,this.selectClass_="jquery-autocomplete-selected-item",this.keyTimeout_=null,this.finishTimeout_=null,this.lastKeyPressed_=null,this.lastProcessedValue_=null,this.lastSelectedValue_=null,this.active_=!1,this.finishOnBlur_=!0,this.options.minChars=n(this.options.minChars,t.fn.autocomplete_verheul.defaults.minChars,{min:0}),this.options.maxItemsToShow=n(this.options.maxItemsToShow,t.fn.autocomplete_verheul.defaults.maxItemsToShow,{min:0}),this.options.maxCacheLength=n(this.options.maxCacheLength,t.fn.autocomplete_verheul.defaults.maxCacheLength,{min:1}),this.options.delay=n(this.options.delay,t.fn.autocomplete_verheul.defaults.delay,{min:0}),2!=this.options.preventDefaultReturn&&(this.options.preventDefaultReturn=this.options.preventDefaultReturn?1:0),2!=this.options.preventDefaultTab&&(this.options.preventDefaultTab=this.options.preventDefaultTab?1:0),this.dom={},this.dom.$elem=e,this.dom.$elem.attr("autocomplete","off").addClass(this.options.inputClass),this.dom.$results=t("<div></div>").hide().addClass(this.options.resultsClass).css({position:"absolute"}),t("body").append(this.dom.$results),e.keydown(function(t){switch(r.lastKeyPressed_=t.keyCode,r.lastKeyPressed_){case r.options.delimiterKeyCode:r.options.useDelimiter&&r.active_&&r.selectCurrent();break;case 35:case 36:case 16:case 17:case 18:case 37:case 39:break;case 38:return t.preventDefault(),r.active_?r.focusPrev():r.activate(),!1;case 40:return t.preventDefault(),r.active_?r.focusNext():r.activate(),!1;case 9:if(r.active_&&(r.selectCurrent(),r.options.preventDefaultTab))return t.preventDefault(),!1;if(2===r.options.preventDefaultTab)return t.preventDefault(),!1;break;case 13:if(r.active_&&(r.selectCurrent(),r.options.preventDefaultReturn))return t.preventDefault(),!1;if(2===r.options.preventDefaultReturn)return t.preventDefault(),!1;break;case 27:if(r.active_)return t.preventDefault(),r.deactivate(!0),!1;break;default:r.activate()}}),e.on("paste",function(){r.activate()});var o=function(){r.deactivate(!0)};e.blur(function(){r.finishOnBlur_&&(r.finishTimeout_=setTimeout(o,200))}),e.parents("form").on("submit",o)},t.Autocompleter.prototype.position=function(){var e=this.dom.$elem.offset(),n=this.dom.$results.outerHeight(),i=t(window).outerHeight(),r=e.top+this.dom.$elem.outerHeight(),o=r+n,s={top:r,left:e.left};if(o>i){var a=e.top-n;a>=0&&(s.top=a)}this.dom.$results.css(s)},t.Autocompleter.prototype.cacheRead=function(t){var e,n,i,r,o;if(this.options.useCache)for(t=String(t),e=t.length,n=this.options.matchSubset?1:e;n<=e;){for(r=this.options.matchInside?e-n:0,o=0;o<=r;){if(i=t.substr(0,n),void 0!==this.cacheData_[i])return this.cacheData_[i];o++}n++}return!1},t.Autocompleter.prototype.cacheWrite=function(t,e){return!!this.options.useCache&&(this.cacheLength_>=this.options.maxCacheLength&&this.cacheFlush(),t=String(t),void 0!==this.cacheData_[t]&&this.cacheLength_++,this.cacheData_[t]=e,this.cacheData_[t])},t.Autocompleter.prototype.cacheFlush=function(){this.cacheData_={},this.cacheLength_=0},t.Autocompleter.prototype.callHook=function(e,n){var i=this.options[e];return!(!i||!t.isFunction(i))&&i(n,this)},t.Autocompleter.prototype.activate=function(){if(this.options.enabled){var t=this;this.keyTimeout_&&clearTimeout(this.keyTimeout_),this.keyTimeout_=setTimeout(function(){t.activateNow()},this.options.delay)}},t.Autocompleter.prototype.activateNow=function(){var t=this.beforeUseConverter(this.dom.$elem.val());t!==this.lastProcessedValue_&&t!==this.lastSelectedValue_&&this.fetchData(t)},t.Autocompleter.prototype.fetchData=function(t){var e=this,n=function(t,n){e.options.processData&&(t=e.options.processData(t)),e.showResults(e.filterResults(t,n),n)};this.lastProcessedValue_=t,t.length<this.options.minChars?n([],t):this.options.data?n(this.options.data,t):this.fetchRemoteData(t,function(e){n(e,t)})},t.Autocompleter.prototype.fetchRemoteData=function(e,n){var i=this.cacheRead(e);if(i)n(i);else{var r=this,o="json"===r.options.remoteDataType?"json":"text",s=function(t){var i=!1;!1!==t&&(i=r.parseRemoteData(t),r.cacheWrite(e,i)),r.dom.$elem.removeClass(r.options.loadingClass),n(i)};this.dom.$elem.addClass(this.options.loadingClass),t.ajax({url:this.makeUrl(e),success:s,error:function(e,n,i){t.isFunction(r.options.onError)?r.options.onError(e,n,i):s(!1)},dataType:o})}},t.Autocompleter.prototype.setExtraParam=function(e,n){var i=t.trim(String(e));return i&&(this.options.extraParams||(this.options.extraParams={}),this.options.extraParams[i]!==n&&(this.options.extraParams[i]=n,this.cacheFlush())),this},t.Autocompleter.prototype.makeUrl=function(e){var n=this.options.url,i=t.extend({},this.options.extraParams);return!1===this.options.queryParamName?n+=encodeURIComponent(e):i[this.options.queryParamName]=e,r(n,i)},t.Autocompleter.prototype.parseRemoteData=function(e){var n,i=e;if("json"===this.options.remoteDataType){switch(n=typeof e){case"object":i=e;break;case"string":i=t.parseJSON(e);break;default:throw new Error("Unexpected remote data type: "+n)}return i}return s(i,this.options.lineSeparator,this.options.cellSeparator)},t.Autocompleter.prototype.defaultFilter=function(t,e){if(!t.value)return!1;if(this.options.filterResults){var n=this.matchStringConverter(e),i=this.matchStringConverter(t.value);this.options.matchCase||(n=n.toLowerCase(),i=i.toLowerCase());var r=i.indexOf(n);return this.options.matchInside?r>-1:0===r}return!0},t.Autocompleter.prototype.filterResult=function(e,n){return!1===this.options.filter||(t.isFunction(this.options.filter)?this.options.filter(e,n):this.defaultFilter(e,n))},t.Autocompleter.prototype.filterResults=function(t,n){var i,r,o=[];for(i=0;i<t.length;i++)r=e(t[i]),this.filterResult(r,n)&&o.push(r);return this.options.sortResults&&(o=this.sortResults(o,n)),this.options.maxItemsToShow>0&&this.options.maxItemsToShow<o.length&&(o.length=this.options.maxItemsToShow),o},t.Autocompleter.prototype.sortResults=function(e,n){var i=this,r=this.options.sortFunction;return t.isFunction(r)||(r=function(t,e,n){return 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i,r,o,s,a=e.length,l=this,u=t("<ul></ul>"),c=!1,h=!1;if(a){for(i=0;i<a;i++)r=e[i],o=this.createItemFromResult(r),u.append(o),!1===c&&(c=String(r.value),h=o,o.addClass(this.options.firstItemClass)),i===a-1&&o.addClass(this.options.lastItemClass);this.dom.$results.html(u).show(),this.position(),this.options.autoWidth&&(s=this.dom.$elem.outerWidth()-this.dom.$results.outerWidth()+this.dom.$results.width(),this.dom.$results.css(this.options.autoWidth,s)),this.getItems().hover(function(){l.focusItem(this)},function(){}),(this.autoFill(c,n)||this.options.selectFirst||this.options.selectOnly&&1===a)&&this.focusItem(h),this.active_=!0}else this.hideResults(),this.active_=!1},t.Autocompleter.prototype.showResult=function(e,n){return t.isFunction(this.options.showResult)?this.options.showResult(e,n):t("<p></p>").text(e).html()},t.Autocompleter.prototype.autoFill=function(t,e){var n,i,r,o;if(this.options.autoFill&&8!==this.lastKeyPressed_&&(n=String(t).toLowerCase(),i=String(e).toLowerCase(),r=t.length,o=e.length,n.substr(0,o)===i)){var s=this.getDelimiterOffsets(),a=s.start?" 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e=t.data("value"),n=t.data("data"),i=this.displayValue(e,n),r=this.beforeUseConverter(i);this.lastProcessedValue_=r,this.lastSelectedValue_=r;var o=this.getDelimiterOffsets(),s=this.options.delimiterChar,a=this.dom.$elem,l=0;this.options.useDelimiter&&(a.val().substring(o.start-1,o.start)==s&&" "!=s&&(i=" "+i),a.val().substring(o.end,o.end+1)!=s&&this.lastKeyPressed_!=this.options.delimiterKeyCode?i+=s:l=1),this.setValue(i),this.setCaret(o.start+i.length+l),this.callHook("onItemSelect",{value:e,data:n}),this.deactivate(!0),a.focus()},t.Autocompleter.prototype.displayValue=function(e,n){return t.isFunction(this.options.displayValue)?this.options.displayValue(e,n):e},t.Autocompleter.prototype.hideResults=function(){this.dom.$results.hide()},t.Autocompleter.prototype.deactivate=function(t){this.finishTimeout_&&clearTimeout(this.finishTimeout_),this.keyTimeout_&&clearTimeout(this.keyTimeout_),t&&(this.lastProcessedValue_!==this.lastSelectedValue_&&(this.options.mustMatch&&this.setValue(""),this.callHook("onNoMatch")),this.active_&&this.callHook("onFinish"),this.lastKeyPressed_=null,this.lastProcessedValue_=null,this.lastSelectedValue_=null,this.active_=!1),this.hideResults()},t.Autocompleter.prototype.selectRange=function(t,e){var n=this.dom.$elem.get(0);if(n.setSelectionRange)n.focus(),n.setSelectionRange(t,e);else if(n.createTextRange){var i=n.createTextRange();i.collapse(!0),i.moveEnd("character",e),i.moveStart("character",t),i.select()}},t.Autocompleter.prototype.setCaret=function(t){this.selectRange(t,t)},t.Autocompleter.prototype.getCaret=function(){var t,e,n,i,r,o,s=this.dom.$elem,a=s[0];return a.createTextRange?(e=document.selection,"textarea"!=a.tagName.toLowerCase()?(t=s.val(),n=e.createRange().duplicate(),n.moveEnd("character",t.length),i=""===n.text?t.length:t.lastIndexOf(n.text),n=e.createRange().duplicate(),n.moveStart("character",-t.length),r=n.text.length):(n=e.createRange(),o=n.duplicate(),o.moveToElementText(a),o.setEndPoint("EndToEnd",n),i=o.text.length-n.text.length,r=i+n.text.length)):(i=s[0].selectionStart,r=s[0].selectionEnd),{start:i,end:r}},t.Autocompleter.prototype.setValue=function(t){if(this.options.useDelimiter){var e=this.dom.$elem.val(),n=this.getDelimiterOffsets();t=e.substring(0,n.start)+t+e.substring(n.end)}this.dom.$elem.val(t)},t.Autocompleter.prototype.getValue=function(t){if(this.options.useDelimiter){var e=this.getDelimiterOffsets();return t.substring(e.start,e.end).trim()}return t},t.Autocompleter.prototype.getDelimiterOffsets=function(){var t=this.dom.$elem.val();if(this.options.useDelimiter){var 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D(t,e,n,i)};else{if(!s.namespaces||s.namespaces.v)return t.fn.sparkline.canvas=!1,!1;s.namespaces.add("v","urn:schemas-microsoft-com:vml","#default#VML"),t.fn.sparkline.canvas=function(t,e,n,i){return new M(t,e,n)}}}return void 0===e&&(e=t(this).innerWidth()),void 0===n&&(n=t(this).innerHeight()),o=t.fn.sparkline.canvas(e,n,this,r),a=t(this).data("_jqs_mhandler"),a&&a.registerCanvas(o),o},t.fn.cleardraw=function(){var t=this.data("_jqs_vcanvas");t&&t.reset()},t.RangeMapClass=v=n({init:function(t){var e,n,i=[];for(e in t)t.hasOwnProperty(e)&&"string"==typeof e&&e.indexOf(":")>-1&&(n=e.split(":"),n[0]=0===n[0].length?-1/0:parseFloat(n[0]),n[1]=0===n[1].length?1/0:parseFloat(n[1]),n[2]=t[e],i.push(n));this.map=t,this.rangelist=i||!1},get:function(t){var e,n,i,r=this.rangelist;if(void 0!==(i=this.map[t]))return i;if(r)for(e=r.length;e--;)if(n=r[e],n[0]<=t&&n[1]>=t)return n[2]}}),t.range_map=function(t){return new v(t)},m=n({init:function(e,n){var i=t(e);this.$el=i,this.options=n,this.currentPageX=0,this.currentPageY=0,this.el=e,this.splist=[],this.tooltip=null,this.over=!1,this.displayTooltips=!n.get("disableTooltips"),this.highlightEnabled=!n.get("disableHighlight")},registerSparkline:function(t){this.splist.push(t),this.over&&this.updateDisplay()},registerCanvas:function(e){var n=t(e.canvas);this.canvas=e,this.$canvas=n,n.mouseenter(t.proxy(this.mouseenter,this)),n.mouseleave(t.proxy(this.mouseleave,this)),n.click(t.proxy(this.mouseclick,this))},reset:function(t){this.splist=[],this.tooltip&&t&&(this.tooltip.remove(),this.tooltip=void 0)},mouseclick:function(e){var n=t.Event("sparklineClick");n.originalEvent=e,n.sparklines=this.splist,this.$el.trigger(n)},mouseenter:function(e){t(s.body).unbind("mousemove.jqs"),t(s.body).bind("mousemove.jqs",t.proxy(this.mousemove,this)),this.over=!0,this.currentPageX=e.pageX,this.currentPageY=e.pageY,this.currentEl=e.target,!this.tooltip&&this.displayTooltips&&(this.tooltip=new y(this.options),this.tooltip.updatePosition(e.pageX,e.pageY)),this.updateDisplay()},mouseleave:function(){t(s.body).unbind("mousemove.jqs");var e,n,i=this.splist,r=i.length,o=!1;for(this.over=!1,this.currentEl=null,this.tooltip&&(this.tooltip.remove(),this.tooltip=null),n=0;n<r;n++)e=i[n],e.clearRegionHighlight()&&(o=!0);o&&this.canvas.render()},mousemove:function(t){this.currentPageX=t.pageX,this.currentPageY=t.pageY,this.currentEl=t.target,this.tooltip&&this.tooltip.updatePosition(t.pageX,t.pageY),this.updateDisplay()},updateDisplay:function(){var e,n,i,r,o,s=this.splist,a=s.length,l=!1,u=this.$canvas.offset(),c=this.currentPageX-u.left,h=this.currentPageY-u.top;if(this.over){for(i=0;i<a;i++)n=s[i],(r=n.setRegionHighlight(this.currentEl,c,h))&&(l=!0);if(l){if(o=t.Event("sparklineRegionChange"),o.sparklines=this.splist,this.$el.trigger(o),this.tooltip){for(e="",i=0;i<a;i++)n=s[i],e+=n.getCurrentRegionTooltip();this.tooltip.setContent(e)}this.disableHighlight||this.canvas.render()}null===r&&this.mouseleave()}}}),y=n({sizeStyle:"position: static !important;display: block !important;visibility: hidden !important;float: left !important;",init:function(e){var n,i=e.get("tooltipClassname","jqstooltip"),r=this.sizeStyle;this.container=e.get("tooltipContainer")||s.body,this.tooltipOffsetX=e.get("tooltipOffsetX",10),this.tooltipOffsetY=e.get("tooltipOffsetY",12),t("#jqssizetip").remove(),t("#jqstooltip").remove(),this.sizetip=t("<div/>",{id:"jqssizetip",style:r,class:i}),this.tooltip=t("<div/>",{id:"jqstooltip",class:i}).appendTo(this.container),n=this.tooltip.offset(),this.offsetLeft=n.left,this.offsetTop=n.top,this.hidden=!0,t(window).unbind("resize.jqs scroll.jqs"),t(window).bind("resize.jqs scroll.jqs",t.proxy(this.updateWindowDims,this)),this.updateWindowDims()},updateWindowDims:function(){this.scrollTop=t(window).scrollTop(),this.scrollLeft=t(window).scrollLeft(),this.scrollRight=this.scrollLeft+t(window).width(),this.updatePosition()},getSize:function(t){this.sizetip.html(t).appendTo(this.container),this.width=this.sizetip.width()+1,this.height=this.sizetip.height(),this.sizetip.remove()},setContent:function(t){if(!t)return this.tooltip.css("visibility","hidden"),void(this.hidden=!0);this.getSize(t),this.tooltip.html(t).css({width:this.width,height:this.height,visibility:"visible"}),this.hidden&&(this.hidden=!1,this.updatePosition())},updatePosition:function(t,e){if(void 0===t){if(void 0===this.mousex)return;t=this.mousex-this.offsetLeft,e=this.mousey-this.offsetTop}else this.mousex=t-=this.offsetLeft,this.mousey=e-=this.offsetTop;this.height&&this.width&&!this.hidden&&(e-=this.height+this.tooltipOffsetY,t+=this.tooltipOffsetX,e<this.scrollTop&&(e=this.scrollTop),t<this.scrollLeft?t=this.scrollLeft:t+this.width>this.scrollRight&&(t=this.scrollRight-this.width),this.tooltip.css({left:t,top:e}))},remove:function(){this.tooltip.remove(),this.sizetip.remove(),this.sizetip=this.tooltip=void 0,t(window).unbind("resize.jqs scroll.jqs")}}),E=function(){p(A)},t(E),P=[],t.fn.sparkline=function(e,n){return this.each(function(){var i,r,o=new t.fn.sparkline.options(this,n),a=t(this);if(i=function(){var n,i,r,l,u,c,h;if("html"===e||void 0===e?(h=this.getAttribute(o.get("tagValuesAttribute")),void 0!==h&&null!==h||(h=a.html()),n=h.replace(/(^\s*<!--)|(-->\s*$)|\s+/g,"").split(",")):n=e,i="auto"===o.get("width")?n.length*o.get("defaultPixelsPerValue"):o.get("width"),"auto"===o.get("height")?o.get("composite")&&t.data(this,"_jqs_vcanvas")||(l=s.createElement("span"),l.innerHTML="a",a.html(l),r=t(l).innerHeight()||t(l).height(),t(l).remove(),l=null):r=o.get("height"),o.get("disableInteraction")?u=!1:(u=t.data(this,"_jqs_mhandler"),u?o.get("composite")||u.reset():(u=new m(this,o),t.data(this,"_jqs_mhandler",u))),o.get("composite")&&!t.data(this,"_jqs_vcanvas"))return void(t.data(this,"_jqs_errnotify")||(alert("Attempted to attach a composite sparkline to an element with no existing sparkline"),t.data(this,"_jqs_errnotify",!0)));c=new(t.fn.sparkline[o.get("type")])(this,n,o,i,r),c.render(),u&&u.registerSparkline(c)},t(this).html()&&!o.get("disableHiddenCheck")&&t(this).is(":hidden")||!t(this).parents("body").length){if(!o.get("composite")&&t.data(this,"_jqs_pending"))for(r=P.length;r;r--)P[r-1][0]==this&&P.splice(r-1,1);P.push([this,i]),t.data(this,"_jqs_pending",!0)}else i.call(this)})},t.fn.sparkline.defaults=e(),t.sparkline_display_visible=function(){var e,n,i,r=[];for(n=0,i=P.length;n<i;n++)e=P[n][0],t(e).is(":visible")&&!t(e).parents().is(":hidden")?(P[n][1].call(e),t.data(P[n][0],"_jqs_pending",!1),r.push(n)):t(e).closest("html").length||t.data(e,"_jqs_pending")||(t.data(P[n][0],"_jqs_pending",!1),r.push(n));for(n=r.length;n;n--)P.splice(r[n-1],1)},t.fn.sparkline.options=n({init:function(e,n){var i,r,o,s;this.userOptions=n=n||{},this.tag=e,this.tagValCache={},r=t.fn.sparkline.defaults,o=r.common,this.tagOptionsPrefix=n.enableTagOptions&&(n.tagOptionsPrefix||o.tagOptionsPrefix),s=this.getTagSetting("type"),i=s===N?r[n.type||o.type]:r[s],this.mergedOptions=t.extend({},o,i,n)},getTagSetting:function(t){var e,n,i,r,o=this.tagOptionsPrefix;if(!1===o||void 0===o)return N;if(this.tagValCache.hasOwnProperty(t))e=this.tagValCache.key;else{if(void 0===(e=this.tag.getAttribute(o+t))||null===e)e=N;else if("["===e.substr(0,1))for(e=e.substr(1,e.length-2).split(","),n=e.length;n--;)e[n]=l(e[n].replace(/(^\s*)|(\s*$)/g,""));else if("{"===e.substr(0,1))for(i=e.substr(1,e.length-2).split(","),e={},n=i.length;n--;)r=i[n].split(":",2),e[r[0].replace(/(^\s*)|(\s*$)/g,"")]=l(r[1].replace(/(^\s*)|(\s*$)/g,""));else e=l(e);this.tagValCache.key=e}return e},get:function(t,e){var n,i=this.getTagSetting(t);return i!==N?i:void 0===(n=this.mergedOptions[t])?e:n}}),t.fn.sparkline._base=n({disabled:!1,init:function(e,n,i,r,o){this.el=e,this.$el=t(e),this.values=n,this.options=i,this.width=r,this.height=o,this.currentRegion=void 0},initTarget:function(){var t=!this.options.get("disableInteraction");(this.target=this.$el.simpledraw(this.width,this.height,this.options.get("composite"),t))?(this.canvasWidth=this.target.pixelWidth,this.canvasHeight=this.target.pixelHeight):this.disabled=!0},render:function(){return!this.disabled||(this.el.innerHTML="",!1)},getRegion:function(t,e){},setRegionHighlight:function(t,e,n){var i,r=this.currentRegion,o=!this.options.get("disableHighlight");return e>this.canvasWidth||n>this.canvasHeight||e<0||n<0?null:(i=this.getRegion(t,e,n),r!==i&&(void 0!==r&&o&&this.removeHighlight(),this.currentRegion=i,void 0!==i&&o&&this.renderHighlight(),!0))},clearRegionHighlight:function(){return void 0!==this.currentRegion&&(this.removeHighlight(),this.currentRegion=void 0,!0)},renderHighlight:function(){this.changeHighlight(!0)},removeHighlight:function(){this.changeHighlight(!1)},changeHighlight:function(t){},getCurrentRegionTooltip:function(){var e,n,r,o,s,a,l,u,c,h,d,p,f,g,v=this.options,m="",y=[];if(void 0===this.currentRegion)return"";if(e=this.getCurrentRegionFields(),d=v.get("tooltipFormatter"))return d(this,v,e);if(v.get("tooltipChartTitle")&&(m+='<div class="jqs jqstitle">'+v.get("tooltipChartTitle")+"</div>\n"),!(n=this.options.get("tooltipFormat")))return"";if(t.isArray(n)||(n=[n]),t.isArray(e)||(e=[e]),l=this.options.get("tooltipFormatFieldlist"),u=this.options.get("tooltipFormatFieldlistKey"),l&&u){for(c=[],a=e.length;a--;)h=e[a][u],-1!=(g=t.inArray(h,l))&&(c[g]=e[a]);e=c}for(r=n.length,f=e.length,a=0;a<r;a++)for(p=n[a],"string"==typeof p&&(p=new i(p)),o=p.fclass||"jqsfield",g=0;g<f;g++)e[g].isNull&&v.get("tooltipSkipNull")||(t.extend(e[g],{prefix:v.get("tooltipPrefix"),suffix:v.get("tooltipSuffix")}),s=p.render(e[g],v.get("tooltipValueLookups"),v),y.push('<div class="'+o+'">'+s+"</div>"));return y.length?m+y.join("\n"):""},getCurrentRegionFields:function(){},calcHighlightColor:function(t,e){var n,i,o,s,l=e.get("highlightColor"),u=e.get("highlightLighten");if(l)return l;if(u&&(n=/^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(t)||/^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(t))){for(o=[],i=4===t.length?16:1,s=0;s<3;s++)o[s]=r(a.round(parseInt(n[s+1],16)*i*u),0,255);return"rgb("+o.join(",")+")"}return t}}),b={changeHighlight:function(e){var n,i=this.currentRegion,r=this.target,o=this.regionShapes[i];o&&(n=this.renderRegion(i,e),t.isArray(n)||t.isArray(o)?(r.replaceWithShapes(o,n),this.regionShapes[i]=t.map(n,function(t){return t.id})):(r.replaceWithShape(o,n),this.regionShapes[i]=n.id))},render:function(){var e,n,i,r,o=this.values,s=this.target,a=this.regionShapes;if(this.cls._super.render.call(this)){for(i=o.length;i--;)if(e=this.renderRegion(i))if(t.isArray(e)){for(n=[],r=e.length;r--;)e[r].append(),n.push(e[r].id);a[i]=n}else e.append(),a[i]=e.id;else a[i]=null;s.render()}}},t.fn.sparkline.line=w=n(t.fn.sparkline._base,{type:"line",init:function(t,e,n,i,r){w._super.init.call(this,t,e,n,i,r),this.vertices=[],this.regionMap=[],this.xvalues=[],this.yvalues=[],this.yminmax=[],this.hightlightSpotId=null,this.lastShapeId=null,this.initTarget()},getRegion:function(t,e,n){var i,r=this.regionMap;for(i=r.length;i--;)if(null!==r[i]&&e>=r[i][0]&&e<=r[i][1])return r[i][2]},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:null===this.yvalues[t],x:this.xvalues[t],y:this.yvalues[t],color:this.options.get("lineColor"),fillColor:this.options.get("fillColor"),offset:t}},renderHighlight:function(){var t,e,n=this.currentRegion,i=this.target,r=this.vertices[n],o=this.options,s=o.get("spotRadius"),a=o.get("highlightSpotColor"),l=o.get("highlightLineColor");r&&(s&&a&&(t=i.drawCircle(r[0],r[1],s,void 0,a),this.highlightSpotId=t.id,i.insertAfterShape(this.lastShapeId,t)),l&&(e=i.drawLine(r[0],this.canvasTop,r[0],this.canvasTop+this.canvasHeight,l),this.highlightLineId=e.id,i.insertAfterShape(this.lastShapeId,e)))},removeHighlight:function(){var t=this.target;this.highlightSpotId&&(t.removeShapeId(this.highlightSpotId),this.highlightSpotId=null),this.highlightLineId&&(t.removeShapeId(this.highlightLineId),this.highlightLineId=null)},scanValues:function(){var t,e,n,i,r,o=this.values,s=o.length,l=this.xvalues,u=this.yvalues,c=this.yminmax;for(t=0;t<s;t++)e=o[t],n="string"==typeof o[t],i="object"==typeof o[t]&&o[t]instanceof Array,r=n&&o[t].split(":"),n&&2===r.length?(l.push(Number(r[0])),u.push(Number(r[1])),c.push(Number(r[1]))):i?(l.push(e[0]),u.push(e[1]),c.push(e[1])):(l.push(t),null===o[t]||"null"===o[t]?u.push(null):(u.push(Number(e)),c.push(Number(e))));this.options.get("xvalues")&&(l=this.options.get("xvalues")),this.maxy=this.maxyorg=a.max.apply(a,c),this.miny=this.minyorg=a.min.apply(a,c),this.maxx=a.max.apply(a,l),this.minx=a.min.apply(a,l),this.xvalues=l,this.yvalues=u,this.yminmax=c},processRangeOptions:function(){var t=this.options,e=t.get("normalRangeMin"),n=t.get("normalRangeMax");void 0!==e&&(e<this.miny&&(this.miny=e),n>this.maxy&&(this.maxy=n)),void 0!==t.get("chartRangeMin")&&(t.get("chartRangeClip")||t.get("chartRangeMin")<this.miny)&&(this.miny=t.get("chartRangeMin")),void 0!==t.get("chartRangeMax")&&(t.get("chartRangeClip")||t.get("chartRangeMax")>this.maxy)&&(this.maxy=t.get("chartRangeMax")),void 0!==t.get("chartRangeMinX")&&(t.get("chartRangeClipX")||t.get("chartRangeMinX")<this.minx)&&(this.minx=t.get("chartRangeMinX")),void 0!==t.get("chartRangeMaxX")&&(t.get("chartRangeClipX")||t.get("chartRangeMaxX")>this.maxx)&&(this.maxx=t.get("chartRangeMaxX"))},drawNormalRange:function(t,e,n,i,r){var o=this.options.get("normalRangeMin"),s=this.options.get("normalRangeMax"),l=e+a.round(n-n*((s-this.miny)/r)),u=a.round(n*(s-o)/r);this.target.drawRect(t,l,i,u,void 0,this.options.get("normalRangeColor")).append()},render:function(){var e,n,i,r,o,s,l,u,c,h,d,p,f,g,m,y,b,_,x,C,k,S,T,A,E,O=this.options,j=this.target,D=this.canvasWidth,M=this.canvasHeight,P=this.vertices,N=O.get("spotRadius"),R=this.regionMap;if(w._super.render.call(this)&&(this.scanValues(),this.processRangeOptions(),T=this.xvalues,A=this.yvalues,this.yminmax.length&&!(this.yvalues.length<2))){for(r=o=0,e=this.maxx-this.minx==0?1:this.maxx-this.minx,n=this.maxy-this.miny==0?1:this.maxy-this.miny,i=this.yvalues.length-1,N&&(D<4*N||M<4*N)&&(N=0),N&&(k=O.get("highlightSpotColor")&&!O.get("disableInteraction"),(k||O.get("minSpotColor")||O.get("spotColor")&&A[i]===this.miny)&&(M-=a.ceil(N)),(k||O.get("maxSpotColor")||O.get("spotColor")&&A[i]===this.maxy)&&(M-=a.ceil(N),r+=a.ceil(N)),(k||(O.get("minSpotColor")||O.get("maxSpotColor"))&&(A[0]===this.miny||A[0]===this.maxy))&&(o+=a.ceil(N),D-=a.ceil(N)),(k||O.get("spotColor")||O.get("minSpotColor")||O.get("maxSpotColor")&&(A[i]===this.miny||A[i]===this.maxy))&&(D-=a.ceil(N))),M--,void 0===O.get("normalRangeMin")||O.get("drawNormalOnTop")||this.drawNormalRange(o,r,M,D,n),l=[],u=[l],g=m=null,y=A.length,E=0;E<y;E++)c=T[E],d=T[E+1],h=A[E],p=o+a.round((c-this.minx)*(D/e)),f=E<y-1?o+a.round((d-this.minx)*(D/e)):D,m=p+(f-p)/2,R[E]=[g||0,m,E],g=m,null===h?E&&(null!==A[E-1]&&(l=[],u.push(l)),P.push(null)):(h<this.miny&&(h=this.miny),h>this.maxy&&(h=this.maxy),l.length||l.push([p,r+M]),s=[p,r+a.round(M-M*((h-this.miny)/n))],l.push(s),P.push(s));for(b=[],_=[],x=u.length,E=0;E<x;E++)l=u[E],l.length&&(O.get("fillColor")&&(l.push([l[l.length-1][0],r+M]),_.push(l.slice(0)),l.pop()),l.length>2&&(l[0]=[l[0][0],l[1][1]]),b.push(l));for(x=_.length,E=0;E<x;E++)j.drawShape(_[E],O.get("fillColor"),O.get("fillColor")).append();for(void 0!==O.get("normalRangeMin")&&O.get("drawNormalOnTop")&&this.drawNormalRange(o,r,M,D,n),x=b.length,E=0;E<x;E++)j.drawShape(b[E],O.get("lineColor"),void 0,O.get("lineWidth")).append();if(N&&O.get("valueSpots"))for(C=O.get("valueSpots"),void 0===C.get&&(C=new v(C)),E=0;E<y;E++)(S=C.get(A[E]))&&j.drawCircle(o+a.round((T[E]-this.minx)*(D/e)),r+a.round(M-M*((A[E]-this.miny)/n)),N,void 0,S).append();N&&O.get("spotColor")&&null!==A[i]&&j.drawCircle(o+a.round((T[T.length-1]-this.minx)*(D/e)),r+a.round(M-M*((A[i]-this.miny)/n)),N,void 0,O.get("spotColor")).append(),this.maxy!==this.minyorg&&(N&&O.get("minSpotColor")&&(c=T[t.inArray(this.minyorg,A)],j.drawCircle(o+a.round((c-this.minx)*(D/e)),r+a.round(M-M*((this.minyorg-this.miny)/n)),N,void 0,O.get("minSpotColor")).append()),N&&O.get("maxSpotColor")&&(c=T[t.inArray(this.maxyorg,A)],j.drawCircle(o+a.round((c-this.minx)*(D/e)),r+a.round(M-M*((this.maxyorg-this.miny)/n)),N,void 0,O.get("maxSpotColor")).append())),this.lastShapeId=j.getLastShapeId(),this.canvasTop=r,j.render()}}}),t.fn.sparkline.bar=_=n(t.fn.sparkline._base,b,{type:"bar",init:function(e,n,i,o,s){var h,d,p,f,g,m,y,b,w,x,C,k,S,T,A,E,O,j,D,M,P,N,R=parseInt(i.get("barWidth"),10),I=parseInt(i.get("barSpacing"),10),$=i.get("chartRangeMin"),L=i.get("chartRangeMax"),H=i.get("chartRangeClip"),F=1/0,q=-1/0;for(_._super.init.call(this,e,n,i,o,s),m=0,y=n.length;m<y;m++)M=n[m],((h="string"==typeof M&&M.indexOf(":")>-1)||t.isArray(M))&&(A=!0,h&&(M=n[m]=u(M.split(":"))),M=c(M,null),d=a.min.apply(a,M),p=a.max.apply(a,M),d<F&&(F=d),p>q&&(q=p));this.stacked=A,this.regionShapes={},this.barWidth=R,this.barSpacing=I,this.totalBarWidth=R+I,this.width=o=n.length*R+(n.length-1)*I,this.initTarget(),H&&(S=void 0===$?-1/0:$,T=void 0===L?1/0:L),g=[],f=A?[]:g;var W=[],B=[];for(m=0,y=n.length;m<y;m++)if(A)for(E=n[m],n[m]=D=[],W[m]=0,f[m]=B[m]=0,O=0,j=E.length;O<j;O++)null!==(M=D[O]=H?r(E[O],S,T):E[O])&&(M>0&&(W[m]+=M),F<0&&q>0?M<0?B[m]+=a.abs(M):f[m]+=M:f[m]+=a.abs(M-(M<0?q:F)),g.push(M));else M=H?r(n[m],S,T):n[m],null!==(M=n[m]=l(M))&&g.push(M);this.max=k=a.max.apply(a,g),this.min=C=a.min.apply(a,g),this.stackMax=q=A?a.max.apply(a,W):k,this.stackMin=F=A?a.min.apply(a,g):C,void 0!==i.get("chartRangeMin")&&(i.get("chartRangeClip")||i.get("chartRangeMin")<C)&&(C=i.get("chartRangeMin")),void 0!==i.get("chartRangeMax")&&(i.get("chartRangeClip")||i.get("chartRangeMax")>k)&&(k=i.get("chartRangeMax")),this.zeroAxis=w=i.get("zeroAxis",!0),x=C<=0&&k>=0&&w?0:0==w?C:C>0?C:k,this.xaxisOffset=x,b=A?a.max.apply(a,f)+a.max.apply(a,B):k-C,this.canvasHeightEf=w&&C<0?this.canvasHeight-2:this.canvasHeight-1,C<x?(N=A&&k>=0?q:k,(P=(N-x)/b*this.canvasHeight)!==a.ceil(P)&&(this.canvasHeightEf-=2,P=a.ceil(P))):P=this.canvasHeight,this.yoffset=P,t.isArray(i.get("colorMap"))?(this.colorMapByIndex=i.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=i.get("colorMap"),this.colorMapByValue&&void 0===this.colorMapByValue.get&&(this.colorMapByValue=new v(this.colorMapByValue))),this.range=b},getRegion:function(t,e,n){var i=a.floor(e/this.totalBarWidth);return i<0||i>=this.values.length?void 0:i},getCurrentRegionFields:function(){var t,e,n=this.currentRegion,i=f(this.values[n]),r=[];for(e=i.length;e--;)t=i[e],r.push({isNull:null===t,value:t,color:this.calcColor(e,t,n),offset:n});return r},calcColor:function(e,n,i){var r,o,s=this.colorMapByIndex,a=this.colorMapByValue,l=this.options;return r=this.stacked?l.get("stackedBarColor"):n<0?l.get("negBarColor"):l.get("barColor"),0===n&&void 0!==l.get("zeroColor")&&(r=l.get("zeroColor")),a&&(o=a.get(n))?r=o:s&&s.length>i&&(r=s[i]),t.isArray(r)?r[e%r.length]:r},renderRegion:function(e,n){var i,r,o,s,l,u,c,h,p,f,g=this.values[e],v=this.options,m=this.xaxisOffset,y=[],b=this.range,w=this.stacked,_=this.target,x=e*this.totalBarWidth,C=this.canvasHeightEf,k=this.yoffset;if(g=t.isArray(g)?g:[g],c=g.length,h=g[0],s=d(null,g),f=d(m,g,!0),s)return v.get("nullColor")?(o=n?v.get("nullColor"):this.calcHighlightColor(v.get("nullColor"),v),i=k>0?k-1:k,_.drawRect(x,i,this.barWidth-1,0,o,o)):void 0;for(l=k,u=0;u<c;u++){if(h=g[u],w&&h===m){if(!f||p)continue;p=!0}r=b>0?a.floor(C*(a.abs(h-m)/b))+1:1,h<m||h===m&&0===k?(i=l,l+=r):(i=k-r,k-=r),o=this.calcColor(u,h,e),n&&(o=this.calcHighlightColor(o,v)),y.push(_.drawRect(x,i,this.barWidth-1,r-1,o,o))}return 1===y.length?y[0]:y}}),t.fn.sparkline.tristate=x=n(t.fn.sparkline._base,b,{type:"tristate",init:function(e,n,i,r,o){var s=parseInt(i.get("barWidth"),10),a=parseInt(i.get("barSpacing"),10);x._super.init.call(this,e,n,i,r,o),this.regionShapes={},this.barWidth=s,this.barSpacing=a,this.totalBarWidth=s+a,this.values=t.map(n,Number),this.width=r=n.length*s+(n.length-1)*a,t.isArray(i.get("colorMap"))?(this.colorMapByIndex=i.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=i.get("colorMap"),this.colorMapByValue&&void 0===this.colorMapByValue.get&&(this.colorMapByValue=new v(this.colorMapByValue))),this.initTarget()},getRegion:function(t,e,n){return a.floor(e/this.totalBarWidth)},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],color:this.calcColor(this.values[t],t),offset:t}},calcColor:function(t,e){var n,i=this.values,r=this.options,o=this.colorMapByIndex,s=this.colorMapByValue;return s&&(n=s.get(t))?n:o&&o.length>e?o[e]:i[e]<0?r.get("negBarColor"):i[e]>0?r.get("posBarColor"):r.get("zeroBarColor")},renderRegion:function(t,e){var n,i,r,o,s,l,u=this.values,c=this.options,h=this.target;if(n=h.pixelHeight,r=a.round(n/2),o=t*this.totalBarWidth,u[t]<0?(s=r,i=r-1):u[t]>0?(s=0,i=r-1):(s=r-1,i=2),null!==(l=this.calcColor(u[t],t)))return e&&(l=this.calcHighlightColor(l,c)),h.drawRect(o,s,this.barWidth-1,i-1,l,l)}}),t.fn.sparkline.discrete=C=n(t.fn.sparkline._base,b,{type:"discrete",init:function(e,n,i,r,o){C._super.init.call(this,e,n,i,r,o),this.regionShapes={},this.values=n=t.map(n,Number),this.min=a.min.apply(a,n),this.max=a.max.apply(a,n),this.range=this.max-this.min,this.width=r="auto"===i.get("width")?2*n.length:this.width,this.interval=a.floor(r/n.length),this.itemWidth=r/n.length,void 0!==i.get("chartRangeMin")&&(i.get("chartRangeClip")||i.get("chartRangeMin")<this.min)&&(this.min=i.get("chartRangeMin")),void 0!==i.get("chartRangeMax")&&(i.get("chartRangeClip")||i.get("chartRangeMax")>this.max)&&(this.max=i.get("chartRangeMax")),this.initTarget(),this.target&&(this.lineHeight="auto"===i.get("lineHeight")?a.round(.3*this.canvasHeight):i.get("lineHeight"))},getRegion:function(t,e,n){return a.floor(e/this.itemWidth)},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],offset:t}},renderRegion:function(t,e){var n,i,o,s,l=this.values,u=this.options,c=this.min,h=this.max,d=this.range,p=this.interval,f=this.target,g=this.canvasHeight,v=this.lineHeight,m=g-v;return i=r(l[t],c,h),s=t*p,n=a.round(m-m*((i-c)/d)),o=u.get("thresholdColor")&&i<u.get("thresholdValue")?u.get("thresholdColor"):u.get("lineColor"),e&&(o=this.calcHighlightColor(o,u)),f.drawLine(s,n,s,n+v,o)}}),t.fn.sparkline.bullet=k=n(t.fn.sparkline._base,{type:"bullet",init:function(t,e,n,i,r){var o,s,l;k._super.init.call(this,t,e,n,i,r),this.values=e=u(e),l=e.slice(),l[0]=null===l[0]?l[2]:l[0],l[1]=null===e[1]?l[2]:l[1],o=a.min.apply(a,e),s=a.max.apply(a,e),o=void 0===n.get("base")?o<0?o:0:n.get("base"),this.min=o,this.max=s,this.range=s-o,this.shapes={},this.valueShapes={},this.regiondata={},this.width=i="auto"===n.get("width")?"4.0em":i,this.target=this.$el.simpledraw(i,r,n.get("composite")),e.length||(this.disabled=!0),this.initTarget()},getRegion:function(t,e,n){var i=this.target.getShapeAt(t,e,n);return void 0!==i&&void 0!==this.shapes[i]?this.shapes[i]:void 0},getCurrentRegionFields:function(){var t=this.currentRegion;return{fieldkey:t.substr(0,1),value:this.values[t.substr(1)],region:t}},changeHighlight:function(t){var e,n=this.currentRegion,i=this.valueShapes[n];switch(delete this.shapes[i],n.substr(0,1)){case"r":e=this.renderRange(n.substr(1),t);break;case"p":e=this.renderPerformance(t);break;case"t":e=this.renderTarget(t)}this.valueShapes[n]=e.id,this.shapes[e.id]=n,this.target.replaceWithShape(i,e)},renderRange:function(t,e){var n=this.values[t],i=a.round(this.canvasWidth*((n-this.min)/this.range)),r=this.options.get("rangeColors")[t-2];return e&&(r=this.calcHighlightColor(r,this.options)),this.target.drawRect(0,0,i-1,this.canvasHeight-1,r,r)},renderPerformance:function(t){var e=this.values[1],n=a.round(this.canvasWidth*((e-this.min)/this.range)),i=this.options.get("performanceColor");return t&&(i=this.calcHighlightColor(i,this.options)),this.target.drawRect(0,a.round(.3*this.canvasHeight),n-1,a.round(.4*this.canvasHeight)-1,i,i)},renderTarget:function(t){var e=this.values[0],n=a.round(this.canvasWidth*((e-this.min)/this.range)-this.options.get("targetWidth")/2),i=a.round(.1*this.canvasHeight),r=this.canvasHeight-2*i,o=this.options.get("targetColor");return t&&(o=this.calcHighlightColor(o,this.options)),this.target.drawRect(n,i,this.options.get("targetWidth")-1,r-1,o,o)},render:function(){var t,e,n=this.values.length,i=this.target;if(k._super.render.call(this)){for(t=2;t<n;t++)e=this.renderRange(t).append(),this.shapes[e.id]="r"+t,this.valueShapes["r"+t]=e.id;null!==this.values[1]&&(e=this.renderPerformance().append(),this.shapes[e.id]="p1",this.valueShapes.p1=e.id),null!==this.values[0]&&(e=this.renderTarget().append(),this.shapes[e.id]="t0",this.valueShapes.t0=e.id),i.render()}}}),t.fn.sparkline.pie=S=n(t.fn.sparkline._base,{type:"pie",init:function(e,n,i,r,o){var s,l=0;if(S._super.init.call(this,e,n,i,r,o),this.shapes={},this.valueShapes={},this.values=n=t.map(n,Number),"auto"===i.get("width")&&(this.width=this.height),n.length>0)for(s=n.length;s--;)l+=n[s];this.total=l,this.initTarget(),this.radius=a.floor(a.min(this.canvasWidth,this.canvasHeight)/2)},getRegion:function(t,e,n){var i=this.target.getShapeAt(t,e,n);return void 0!==i&&void 0!==this.shapes[i]?this.shapes[i]:void 0},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],percent:this.values[t]/this.total*100,color:this.options.get("sliceColors")[t%this.options.get("sliceColors").length],offset:t}},changeHighlight:function(t){var e=this.currentRegion,n=this.renderSlice(e,t),i=this.valueShapes[e];delete this.shapes[i],this.target.replaceWithShape(i,n),this.valueShapes[e]=n.id,this.shapes[n.id]=e},renderSlice:function(t,e){var n,i,r,o,s,l=this.target,u=this.options,c=this.radius,h=u.get("borderWidth"),d=u.get("offset"),p=2*a.PI,f=this.values,g=this.total,v=d?2*a.PI*(d/360):0;for(o=f.length,r=0;r<o;r++){if(n=v,i=v,g>0&&(i=v+p*(f[r]/g)),t===r)return s=u.get("sliceColors")[r%u.get("sliceColors").length],e&&(s=this.calcHighlightColor(s,u)),l.drawPieSlice(c,c,c-h,n,i,void 0,s);v=i}},render:function(){var t,e,n=this.target,i=this.values,r=this.options,o=this.radius,s=r.get("borderWidth");if(S._super.render.call(this)){for(s&&n.drawCircle(o,o,a.floor(o-s/2),r.get("borderColor"),void 0,s).append(),e=i.length;e--;)i[e]&&(t=this.renderSlice(e).append(),this.valueShapes[e]=t.id,this.shapes[t.id]=e);n.render()}}}),t.fn.sparkline.box=T=n(t.fn.sparkline._base,{type:"box",init:function(e,n,i,r,o){T._super.init.call(this,e,n,i,r,o),this.values=t.map(n,Number),this.width="auto"===i.get("width")?"4.0em":r,this.initTarget(),this.values.length||(this.disabled=1)},getRegion:function(){return 1},getCurrentRegionFields:function(){var t=[{field:"lq",value:this.quartiles[0]},{field:"med",value:this.quartiles[1]},{field:"uq",value:this.quartiles[2]}];return void 0!==this.loutlier&&t.push({field:"lo",value:this.loutlier}),void 0!==this.routlier&&t.push({field:"ro",value:this.routlier}),void 0!==this.lwhisker&&t.push({field:"lw",value:this.lwhisker}),void 0!==this.rwhisker&&t.push({field:"rw",value:this.rwhisker}),t},render:function(){var t,e,n,i,r,s,l,u,c,h,d,p=this.target,f=this.values,g=f.length,v=this.options,m=this.canvasWidth,y=this.canvasHeight,b=void 0===v.get("chartRangeMin")?a.min.apply(a,f):v.get("chartRangeMin"),w=void 0===v.get("chartRangeMax")?a.max.apply(a,f):v.get("chartRangeMax"),_=0;if(T._super.render.call(this)){if(v.get("raw"))v.get("showOutliers")&&f.length>5?(e=f[0],t=f[1],i=f[2],r=f[3],s=f[4],l=f[5],u=f[6]):(t=f[0],i=f[1],r=f[2],s=f[3],l=f[4]);else if(f.sort(function(t,e){return t-e}),i=o(f,1),r=o(f,2),s=o(f,3),n=s-i,v.get("showOutliers")){for(t=l=void 0,c=0;c<g;c++)void 0===t&&f[c]>i-n*v.get("outlierIQR")&&(t=f[c]),f[c]<s+n*v.get("outlierIQR")&&(l=f[c]);e=f[0],u=f[g-1]}else t=f[0],l=f[g-1];this.quartiles=[i,r,s],this.lwhisker=t,this.rwhisker=l,this.loutlier=e,this.routlier=u,d=m/(w-b+1),v.get("showOutliers")&&(_=a.ceil(v.get("spotRadius")),m-=2*a.ceil(v.get("spotRadius")),d=m/(w-b+1),e<t&&p.drawCircle((e-b)*d+_,y/2,v.get("spotRadius"),v.get("outlierLineColor"),v.get("outlierFillColor")).append(),u>l&&p.drawCircle((u-b)*d+_,y/2,v.get("spotRadius"),v.get("outlierLineColor"),v.get("outlierFillColor")).append()),p.drawRect(a.round((i-b)*d+_),a.round(.1*y),a.round((s-i)*d),a.round(.8*y),v.get("boxLineColor"),v.get("boxFillColor")).append(),p.drawLine(a.round((t-b)*d+_),a.round(y/2),a.round((i-b)*d+_),a.round(y/2),v.get("lineColor")).append(),p.drawLine(a.round((t-b)*d+_),a.round(y/4),a.round((t-b)*d+_),a.round(y-y/4),v.get("whiskerColor")).append(),p.drawLine(a.round((l-b)*d+_),a.round(y/2),a.round((s-b)*d+_),a.round(y/2),v.get("lineColor")).append(),p.drawLine(a.round((l-b)*d+_),a.round(y/4),a.round((l-b)*d+_),a.round(y-y/4),v.get("whiskerColor")).append(),p.drawLine(a.round((r-b)*d+_),a.round(.1*y),a.round((r-b)*d+_),a.round(.9*y),v.get("medianColor")).append(),v.get("target")&&(h=a.ceil(v.get("spotRadius")),p.drawLine(a.round((v.get("target")-b)*d+_),a.round(y/2-h),a.round((v.get("target")-b)*d+_),a.round(y/2+h),v.get("targetColor")).append(),p.drawLine(a.round((v.get("target")-b)*d+_-h),a.round(y/2),a.round((v.get("target")-b)*d+_+h),a.round(y/2),v.get("targetColor")).append()),p.render()}}}),O=n({init:function(t,e,n,i){this.target=t,this.id=e,this.type=n,this.args=i},append:function(){return this.target.appendShape(this),this}}),j=n({_pxregex:/(\d+)(px)?\s*$/i,init:function(e,n,i){e&&(this.width=e,this.height=n,this.target=i,this.lastShapeId=null,i[0]&&(i=i[0]),t.data(i,"_jqs_vcanvas",this))},drawLine:function(t,e,n,i,r,o){return this.drawShape([[t,e],[n,i]],r,o)},drawShape:function(t,e,n,i){return this._genShape("Shape",[t,e,n,i])},drawCircle:function(t,e,n,i,r,o){return this._genShape("Circle",[t,e,n,i,r,o])},drawPieSlice:function(t,e,n,i,r,o,s){return this._genShape("PieSlice",[t,e,n,i,r,o,s])},drawRect:function(t,e,n,i,r,o){return this._genShape("Rect",[t,e,n,i,r,o])},getElement:function(){return this.canvas},getLastShapeId:function(){return this.lastShapeId},reset:function(){alert("reset not implemented")},_insert:function(e,n){t(n).html(e)},_calculatePixelDims:function(e,n,i){var r;r=this._pxregex.exec(n),this.pixelHeight=r?r[1]:t(i).height(),r=this._pxregex.exec(e),this.pixelWidth=r?r[1]:t(i).width()},_genShape:function(t,e){var n=R++;return e.unshift(n),new 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Are you sure?":"Cela supprimera de manière permanente les données de votre historique. Êtes-vous certain?",Dataset:"Jeu de données",Annotation:"Annotation","This history is empty. Click 'Get Data' on the left tool menu to start":"Cet historique est vide. 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Use the "Resume Paused Jobs" in the history menu to resume':'Ce traitement est en pause. Utilisez le "Relancer les traitements en pause" dans le menu d\'historique pour le relancer',"An error occurred with this dataset":"Une erreur est survenue avec ce jeu de données","No data":"Aucune donnée","An error occurred setting the metadata for this dataset":"Une erreur est survenue pendant la récupération des métadonnées de ce jeu de données","There was an error getting the data for this dataset":"Il est survenu une erreur durant la récupération du contenu de ce jeu de données","This dataset has been deleted and removed from disk":"Ce jeu de données a été supprimé et effacé du disque","This dataset has been deleted":"Ce jeu de données a été supprimé","This dataset has been hidden":"Ce jeu de données a été caché",format:"format",database:"génome de référence","Edit attributes":"Editer les attributs","Cannot edit attributes of datasets removed from disk":"Impossible d'éditer les attributs de jeux de données effacés du disque","Undelete dataset to edit attributes":"Restaurer le jeu de données pour en éditer les attributs","This dataset must finish uploading before it can be edited":"Ce jeu de données doit être entièrement téléversé avant toute modification","This dataset is not yet editable":"Ce jeu de données n'est pas encore éditable",Delete:"Supprimer","Dataset is already deleted":"Le jeu de données est déjà supprimé","View or report this error":"Voir ou remonter cette erreur","Run this job again":"Exécuter ce traitement à nouveau",Visualize:"Visualiser","Visualize in":"Visualiser via","Undelete it":"Restaurer","Permanently remove it from disk":"Supprimer définitivement du disque","Unhide it":"Rendre visible","You may be able to":"Vous devriez être en mesure de","set it manually or retry auto-detection":"Traitez le manuellement ou retenter la détection automatique","Edit dataset tags":"Editer les mots-clés du jeu de données","Edit dataset annotation":"Editer les annotations du jeu de données",Tags:"Mots-clés","Edit annotation":"Editer les annotations"},__zh:{"This history is empty":"历史已空","No matching datasets found":"未找到匹配的数据集","Search datasets":"搜索数据集","You are currently viewing a deleted history!":"正在查看已删除的历史","You are over your disk quota":"您已超过磁盘配额",All:"皆",None:"一个也没有","For all selected":"为每个选定","Click to rename history":"单击要重命名的历史","Operations on multiple datasets":"编辑多个数据集","Permanently delete datasets":"永久删除数据集","This will permanently remove the data in your datasets. Are you sure?":"这将永久在你的数据集删除数据。你确定？",Dataset:"数据集","This history is empty. Click 'Get Data' on the left tool menu to start":"历史已空，请单击左边窗格中‘获取数据’","You must be logged in to create histories":"你必须登录后才能创建历史","View data":"数据",Download:"下载","Download dataset":"下载数据集","View details":"查看详情","This job is waiting to run":"等待运行的进程","This job is currently running":"正在运行的进程","An error occurred with this dataset":"进程运行时出错","No data":"没有数据","This dataset has been deleted":"此数据集已被删除","This dataset has been hidden":"此数据集已隐藏",format:"格式",database:"数据库","Edit attributes":"编辑属性",Delete:"删除","View or report this error":"报告错误","Run this job again":"重新运行",Visualize:"图形","Undelete it":"反删除","Permanently remove it from disk":"从磁盘中永久删除","Unhide it":"取消隐藏"}};n.init=function(t){t||(t=window._i18n&&window._i18n.locale?window._i18n.locale:document.documentElement.lang?document.documentElement.lang:"root");var e=this["__"+t]||this.__root;if(e)for(var n in e)this[n]=e[n]},n.init(),t.exports=n},3:function(t,e,n){"use strict";(function(t,i,r){function o(t){return'<iframe src="'+t+'" 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0,!0)},renderHighlight:function(){this.changeHighlight(!0)},removeHighlight:function(){this.changeHighlight(!1)},changeHighlight:function(t){},getCurrentRegionTooltip:function(){var e,n,r,o,s,a,l,u,c,h,d,p,f,g,v=this.options,m="",y=[];if(void 0===this.currentRegion)return"";if(e=this.getCurrentRegionFields(),d=v.get("tooltipFormatter"))return d(this,v,e);if(v.get("tooltipChartTitle")&&(m+='<div class="jqs jqstitle">'+v.get("tooltipChartTitle")+"</div>\n"),!(n=this.options.get("tooltipFormat")))return"";if(t.isArray(n)||(n=[n]),t.isArray(e)||(e=[e]),l=this.options.get("tooltipFormatFieldlist"),u=this.options.get("tooltipFormatFieldlistKey"),l&&u){for(c=[],a=e.length;a--;)h=e[a][u],-1!=(g=t.inArray(h,l))&&(c[g]=e[a]);e=c}for(r=n.length,f=e.length,a=0;a<r;a++)for(p=n[a],"string"==typeof p&&(p=new i(p)),o=p.fclass||"jqsfield",g=0;g<f;g++)e[g].isNull&&v.get("tooltipSkipNull")||(t.extend(e[g],{prefix:v.get("tooltipPrefix"),suffix:v.get("tooltipSuffix")}),s=p.render(e[g],v.get("tooltipValueLookups"),v),y.push('<div class="'+o+'">'+s+"</div>"));return y.length?m+y.join("\n"):""},getCurrentRegionFields:function(){},calcHighlightColor:function(t,e){var n,i,o,s,l=e.get("highlightColor"),u=e.get("highlightLighten");if(l)return l;if(u&&(n=/^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(t)||/^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(t))){for(o=[],i=4===t.length?16:1,s=0;s<3;s++)o[s]=r(a.round(parseInt(n[s+1],16)*i*u),0,255);return"rgb("+o.join(",")+")"}return t}}),b={changeHighlight:function(e){var n,i=this.currentRegion,r=this.target,o=this.regionShapes[i];o&&(n=this.renderRegion(i,e),t.isArray(n)||t.isArray(o)?(r.replaceWithShapes(o,n),this.regionShapes[i]=t.map(n,function(t){return t.id})):(r.replaceWithShape(o,n),this.regionShapes[i]=n.id))},render:function(){var e,n,i,r,o=this.values,s=this.target,a=this.regionShapes;if(this.cls._super.render.call(this)){for(i=o.length;i--;)if(e=this.renderRegion(i))if(t.isArray(e)){for(n=[],r=e.length;r--;)e[r].append(),n.push(e[r].id);a[i]=n}else e.append(),a[i]=e.id;else a[i]=null;s.render()}}},t.fn.sparkline.line=w=n(t.fn.sparkline._base,{type:"line",init:function(t,e,n,i,r){w._super.init.call(this,t,e,n,i,r),this.vertices=[],this.regionMap=[],this.xvalues=[],this.yvalues=[],this.yminmax=[],this.hightlightSpotId=null,this.lastShapeId=null,this.initTarget()},getRegion:function(t,e,n){var i,r=this.regionMap;for(i=r.length;i--;)if(null!==r[i]&&e>=r[i][0]&&e<=r[i][1])return r[i][2]},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:null===this.yvalues[t],x:this.xvalues[t],y:this.yvalues[t],color:this.options.get("lineColor"),fillColor:this.options.get("fillColor"),offset:t}},renderHighlight:function(){var t,e,n=this.currentRegion,i=this.target,r=this.vertices[n],o=this.options,s=o.get("spotRadius"),a=o.get("highlightSpotColor"),l=o.get("highlightLineColor");r&&(s&&a&&(t=i.drawCircle(r[0],r[1],s,void 0,a),this.highlightSpotId=t.id,i.insertAfterShape(this.lastShapeId,t)),l&&(e=i.drawLine(r[0],this.canvasTop,r[0],this.canvasTop+this.canvasHeight,l),this.highlightLineId=e.id,i.insertAfterShape(this.lastShapeId,e)))},removeHighlight:function(){var t=this.target;this.highlightSpotId&&(t.removeShapeId(this.highlightSpotId),this.highlightSpotId=null),this.highlightLineId&&(t.removeShapeId(this.highlightLineId),this.highlightLineId=null)},scanValues:function(){var t,e,n,i,r,o=this.values,s=o.length,l=this.xvalues,u=this.yvalues,c=this.yminmax;for(t=0;t<s;t++)e=o[t],n="string"==typeof o[t],i="object"==typeof o[t]&&o[t]instanceof Array,r=n&&o[t].split(":"),n&&2===r.length?(l.push(Number(r[0])),u.push(Number(r[1])),c.push(Number(r[1]))):i?(l.push(e[0]),u.push(e[1]),c.push(e[1])):(l.push(t),null===o[t]||"null"===o[t]?u.push(null):(u.push(Number(e)),c.push(Number(e))));this.options.get("xvalues")&&(l=this.options.get("xvalues")),this.maxy=this.maxyorg=a.max.apply(a,c),this.miny=this.minyorg=a.min.apply(a,c),this.maxx=a.max.apply(a,l),this.minx=a.min.apply(a,l),this.xvalues=l,this.yvalues=u,this.yminmax=c},processRangeOptions:function(){var t=this.options,e=t.get("normalRangeMin"),n=t.get("normalRangeMax");void 0!==e&&(e<this.miny&&(this.miny=e),n>this.maxy&&(this.maxy=n)),void 0!==t.get("chartRangeMin")&&(t.get("chartRangeClip")||t.get("chartRangeMin")<this.miny)&&(this.miny=t.get("chartRangeMin")),void 0!==t.get("chartRangeMax")&&(t.get("chartRangeClip")||t.get("chartRangeMax")>this.maxy)&&(this.maxy=t.get("chartRangeMax")),void 0!==t.get("chartRangeMinX")&&(t.get("chartRangeClipX")||t.get("chartRangeMinX")<this.minx)&&(this.minx=t.get("chartRangeMinX")),void 0!==t.get("chartRangeMaxX")&&(t.get("chartRangeClipX")||t.get("chartRangeMaxX")>this.maxx)&&(this.maxx=t.get("chartRangeMaxX"))},drawNormalRange:function(t,e,n,i,r){var o=this.options.get("normalRangeMin"),s=this.options.get("normalRangeMax"),l=e+a.round(n-n*((s-this.miny)/r)),u=a.round(n*(s-o)/r);this.target.drawRect(t,l,i,u,void 0,this.options.get("normalRangeColor")).append()},render:function(){var e,n,i,r,o,s,l,u,c,h,d,p,f,g,m,y,b,_,x,C,k,S,T,A,E,O=this.options,j=this.target,D=this.canvasWidth,M=this.canvasHeight,P=this.vertices,N=O.get("spotRadius"),R=this.regionMap;if(w._super.render.call(this)&&(this.scanValues(),this.processRangeOptions(),T=this.xvalues,A=this.yvalues,this.yminmax.length&&!(this.yvalues.length<2))){for(r=o=0,e=this.maxx-this.minx==0?1:this.maxx-this.minx,n=this.maxy-this.miny==0?1:this.maxy-this.miny,i=this.yvalues.length-1,N&&(D<4*N||M<4*N)&&(N=0),N&&(k=O.get("highlightSpotColor")&&!O.get("disableInteraction"),(k||O.get("minSpotColor")||O.get("spotColor")&&A[i]===this.miny)&&(M-=a.ceil(N)),(k||O.get("maxSpotColor")||O.get("spotColor")&&A[i]===this.maxy)&&(M-=a.ceil(N),r+=a.ceil(N)),(k||(O.get("minSpotColor")||O.get("maxSpotColor"))&&(A[0]===this.miny||A[0]===this.maxy))&&(o+=a.ceil(N),D-=a.ceil(N)),(k||O.get("spotColor")||O.get("minSpotColor")||O.get("maxSpotColor")&&(A[i]===this.miny||A[i]===this.maxy))&&(D-=a.ceil(N))),M--,void 0===O.get("normalRangeMin")||O.get("drawNormalOnTop")||this.drawNormalRange(o,r,M,D,n),l=[],u=[l],g=m=null,y=A.length,E=0;E<y;E++)c=T[E],d=T[E+1],h=A[E],p=o+a.round((c-this.minx)*(D/e)),f=E<y-1?o+a.round((d-this.minx)*(D/e)):D,m=p+(f-p)/2,R[E]=[g||0,m,E],g=m,null===h?E&&(null!==A[E-1]&&(l=[],u.push(l)),P.push(null)):(h<this.miny&&(h=this.miny),h>this.maxy&&(h=this.maxy),l.length||l.push([p,r+M]),s=[p,r+a.round(M-M*((h-this.miny)/n))],l.push(s),P.push(s));for(b=[],_=[],x=u.length,E=0;E<x;E++)l=u[E],l.length&&(O.get("fillColor")&&(l.push([l[l.length-1][0],r+M]),_.push(l.slice(0)),l.pop()),l.length>2&&(l[0]=[l[0][0],l[1][1]]),b.push(l));for(x=_.length,E=0;E<x;E++)j.drawShape(_[E],O.get("fillColor"),O.get("fillColor")).append();for(void 0!==O.get("normalRangeMin")&&O.get("drawNormalOnTop")&&this.drawNormalRange(o,r,M,D,n),x=b.length,E=0;E<x;E++)j.drawShape(b[E],O.get("lineColor"),void 0,O.get("lineWidth")).append();if(N&&O.get("valueSpots"))for(C=O.get("valueSpots"),void 0===C.get&&(C=new v(C)),E=0;E<y;E++)(S=C.get(A[E]))&&j.drawCircle(o+a.round((T[E]-this.minx)*(D/e)),r+a.round(M-M*((A[E]-this.miny)/n)),N,void 0,S).append();N&&O.get("spotColor")&&null!==A[i]&&j.drawCircle(o+a.round((T[T.length-1]-this.minx)*(D/e)),r+a.round(M-M*((A[i]-this.miny)/n)),N,void 0,O.get("spotColor")).append(),this.maxy!==this.minyorg&&(N&&O.get("minSpotColor")&&(c=T[t.inArray(this.minyorg,A)],j.drawCircle(o+a.round((c-this.minx)*(D/e)),r+a.round(M-M*((this.minyorg-this.miny)/n)),N,void 0,O.get("minSpotColor")).append()),N&&O.get("maxSpotColor")&&(c=T[t.inArray(this.maxyorg,A)],j.drawCircle(o+a.round((c-this.minx)*(D/e)),r+a.round(M-M*((this.maxyorg-this.miny)/n)),N,void 0,O.get("maxSpotColor")).append())),this.lastShapeId=j.getLastShapeId(),this.canvasTop=r,j.render()}}}),t.fn.sparkline.bar=_=n(t.fn.sparkline._base,b,{type:"bar",init:function(e,n,i,o,s){var h,d,p,f,g,m,y,b,w,x,C,k,S,T,A,E,O,j,D,M,P,N,R=parseInt(i.get("barWidth"),10),I=parseInt(i.get("barSpacing"),10),$=i.get("chartRangeMin"),L=i.get("chartRangeMax"),H=i.get("chartRangeClip"),F=1/0,q=-1/0;for(_._super.init.call(this,e,n,i,o,s),m=0,y=n.length;m<y;m++)M=n[m],((h="string"==typeof M&&M.indexOf(":")>-1)||t.isArray(M))&&(A=!0,h&&(M=n[m]=u(M.split(":"))),M=c(M,null),d=a.min.apply(a,M),p=a.max.apply(a,M),d<F&&(F=d),p>q&&(q=p));this.stacked=A,this.regionShapes={},this.barWidth=R,this.barSpacing=I,this.totalBarWidth=R+I,this.width=o=n.length*R+(n.length-1)*I,this.initTarget(),H&&(S=void 0===$?-1/0:$,T=void 0===L?1/0:L),g=[],f=A?[]:g;var W=[],B=[];for(m=0,y=n.length;m<y;m++)if(A)for(E=n[m],n[m]=D=[],W[m]=0,f[m]=B[m]=0,O=0,j=E.length;O<j;O++)null!==(M=D[O]=H?r(E[O],S,T):E[O])&&(M>0&&(W[m]+=M),F<0&&q>0?M<0?B[m]+=a.abs(M):f[m]+=M:f[m]+=a.abs(M-(M<0?q:F)),g.push(M));else M=H?r(n[m],S,T):n[m],null!==(M=n[m]=l(M))&&g.push(M);this.max=k=a.max.apply(a,g),this.min=C=a.min.apply(a,g),this.stackMax=q=A?a.max.apply(a,W):k,this.stackMin=F=A?a.min.apply(a,g):C,void 0!==i.get("chartRangeMin")&&(i.get("chartRangeClip")||i.get("chartRangeMin")<C)&&(C=i.get("chartRangeMin")),void 0!==i.get("chartRangeMax")&&(i.get("chartRangeClip")||i.get("chartRangeMax")>k)&&(k=i.get("chartRangeMax")),this.zeroAxis=w=i.get("zeroAxis",!0),x=C<=0&&k>=0&&w?0:0==w?C:C>0?C:k,this.xaxisOffset=x,b=A?a.max.apply(a,f)+a.max.apply(a,B):k-C,this.canvasHeightEf=w&&C<0?this.canvasHeight-2:this.canvasHeight-1,C<x?(N=A&&k>=0?q:k,(P=(N-x)/b*this.canvasHeight)!==a.ceil(P)&&(this.canvasHeightEf-=2,P=a.ceil(P))):P=this.canvasHeight,this.yoffset=P,t.isArray(i.get("colorMap"))?(this.colorMapByIndex=i.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=i.get("colorMap"),this.colorMapByValue&&void 0===this.colorMapByValue.get&&(this.colorMapByValue=new v(this.colorMapByValue))),this.range=b},getRegion:function(t,e,n){var i=a.floor(e/this.totalBarWidth);return i<0||i>=this.values.length?void 0:i},getCurrentRegionFields:function(){var t,e,n=this.currentRegion,i=f(this.values[n]),r=[];for(e=i.length;e--;)t=i[e],r.push({isNull:null===t,value:t,color:this.calcColor(e,t,n),offset:n});return r},calcColor:function(e,n,i){var r,o,s=this.colorMapByIndex,a=this.colorMapByValue,l=this.options;return r=this.stacked?l.get("stackedBarColor"):n<0?l.get("negBarColor"):l.get("barColor"),0===n&&void 0!==l.get("zeroColor")&&(r=l.get("zeroColor")),a&&(o=a.get(n))?r=o:s&&s.length>i&&(r=s[i]),t.isArray(r)?r[e%r.length]:r},renderRegion:function(e,n){var i,r,o,s,l,u,c,h,p,f,g=this.values[e],v=this.options,m=this.xaxisOffset,y=[],b=this.range,w=this.stacked,_=this.target,x=e*this.totalBarWidth,C=this.canvasHeightEf,k=this.yoffset;if(g=t.isArray(g)?g:[g],c=g.length,h=g[0],s=d(null,g),f=d(m,g,!0),s)return v.get("nullColor")?(o=n?v.get("nullColor"):this.calcHighlightColor(v.get("nullColor"),v),i=k>0?k-1:k,_.drawRect(x,i,this.barWidth-1,0,o,o)):void 0;for(l=k,u=0;u<c;u++){if(h=g[u],w&&h===m){if(!f||p)continue;p=!0}r=b>0?a.floor(C*(a.abs(h-m)/b))+1:1,h<m||h===m&&0===k?(i=l,l+=r):(i=k-r,k-=r),o=this.calcColor(u,h,e),n&&(o=this.calcHighlightColor(o,v)),y.push(_.drawRect(x,i,this.barWidth-1,r-1,o,o))}return 1===y.length?y[0]:y}}),t.fn.sparkline.tristate=x=n(t.fn.sparkline._base,b,{type:"tristate",init:function(e,n,i,r,o){var s=parseInt(i.get("barWidth"),10),a=parseInt(i.get("barSpacing"),10);x._super.init.call(this,e,n,i,r,o),this.regionShapes={},this.barWidth=s,this.barSpacing=a,this.totalBarWidth=s+a,this.values=t.map(n,Number),this.width=r=n.length*s+(n.length-1)*a,t.isArray(i.get("colorMap"))?(this.colorMapByIndex=i.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=i.get("colorMap"),this.colorMapByValue&&void 0===this.colorMapByValue.get&&(this.colorMapByValue=new v(this.colorMapByValue))),this.initTarget()},getRegion:function(t,e,n){return a.floor(e/this.totalBarWidth)},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],color:this.calcColor(this.values[t],t),offset:t}},calcColor:function(t,e){var n,i=this.values,r=this.options,o=this.colorMapByIndex,s=this.colorMapByValue;return s&&(n=s.get(t))?n:o&&o.length>e?o[e]:i[e]<0?r.get("negBarColor"):i[e]>0?r.get("posBarColor"):r.get("zeroBarColor")},renderRegion:function(t,e){var n,i,r,o,s,l,u=this.values,c=this.options,h=this.target;if(n=h.pixelHeight,r=a.round(n/2),o=t*this.totalBarWidth,u[t]<0?(s=r,i=r-1):u[t]>0?(s=0,i=r-1):(s=r-1,i=2),null!==(l=this.calcColor(u[t],t)))return e&&(l=this.calcHighlightColor(l,c)),h.drawRect(o,s,this.barWidth-1,i-1,l,l)}}),t.fn.sparkline.discrete=C=n(t.fn.sparkline._base,b,{type:"discrete",init:function(e,n,i,r,o){C._super.init.call(this,e,n,i,r,o),this.regionShapes={},this.values=n=t.map(n,Number),this.min=a.min.apply(a,n),this.max=a.max.apply(a,n),this.range=this.max-this.min,this.width=r="auto"===i.get("width")?2*n.length:this.width,this.interval=a.floor(r/n.length),this.itemWidth=r/n.length,void 0!==i.get("chartRangeMin")&&(i.get("chartRangeClip")||i.get("chartRangeMin")<this.min)&&(this.min=i.get("chartRangeMin")),void 0!==i.get("chartRangeMax")&&(i.get("chartRangeClip")||i.get("chartRangeMax")>this.max)&&(this.max=i.get("chartRangeMax")),this.initTarget(),this.target&&(this.lineHeight="auto"===i.get("lineHeight")?a.round(.3*this.canvasHeight):i.get("lineHeight"))},getRegion:function(t,e,n){return a.floor(e/this.itemWidth)},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],offset:t}},renderRegion:function(t,e){var n,i,o,s,l=this.values,u=this.options,c=this.min,h=this.max,d=this.range,p=this.interval,f=this.target,g=this.canvasHeight,v=this.lineHeight,m=g-v;return i=r(l[t],c,h),s=t*p,n=a.round(m-m*((i-c)/d)),o=u.get("thresholdColor")&&i<u.get("thresholdValue")?u.get("thresholdColor"):u.get("lineColor"),e&&(o=this.calcHighlightColor(o,u)),f.drawLine(s,n,s,n+v,o)}}),t.fn.sparkline.bullet=k=n(t.fn.sparkline._base,{type:"bullet",init:function(t,e,n,i,r){var o,s,l;k._super.init.call(this,t,e,n,i,r),this.values=e=u(e),l=e.slice(),l[0]=null===l[0]?l[2]:l[0],l[1]=null===e[1]?l[2]:l[1],o=a.min.apply(a,e),s=a.max.apply(a,e),o=void 0===n.get("base")?o<0?o:0:n.get("base"),this.min=o,this.max=s,this.range=s-o,this.shapes={},this.valueShapes={},this.regiondata={},this.width=i="auto"===n.get("width")?"4.0em":i,this.target=this.$el.simpledraw(i,r,n.get("composite")),e.length||(this.disabled=!0),this.initTarget()},getRegion:function(t,e,n){var i=this.target.getShapeAt(t,e,n);return void 0!==i&&void 0!==this.shapes[i]?this.shapes[i]:void 0},getCurrentRegionFields:function(){var t=this.currentRegion;return{fieldkey:t.substr(0,1),value:this.values[t.substr(1)],region:t}},changeHighlight:function(t){var e,n=this.currentRegion,i=this.valueShapes[n];switch(delete this.shapes[i],n.substr(0,1)){case"r":e=this.renderRange(n.substr(1),t);break;case"p":e=this.renderPerformance(t);break;case"t":e=this.renderTarget(t)}this.valueShapes[n]=e.id,this.shapes[e.id]=n,this.target.replaceWithShape(i,e)},renderRange:function(t,e){var n=this.values[t],i=a.round(this.canvasWidth*((n-this.min)/this.range)),r=this.options.get("rangeColors")[t-2];return e&&(r=this.calcHighlightColor(r,this.options)),this.target.drawRect(0,0,i-1,this.canvasHeight-1,r,r)},renderPerformance:function(t){var e=this.values[1],n=a.round(this.canvasWidth*((e-this.min)/this.range)),i=this.options.get("performanceColor");return t&&(i=this.calcHighlightColor(i,this.options)),this.target.drawRect(0,a.round(.3*this.canvasHeight),n-1,a.round(.4*this.canvasHeight)-1,i,i)},renderTarget:function(t){var e=this.values[0],n=a.round(this.canvasWidth*((e-this.min)/this.range)-this.options.get("targetWidth")/2),i=a.round(.1*this.canvasHeight),r=this.canvasHeight-2*i,o=this.options.get("targetColor");return t&&(o=this.calcHighlightColor(o,this.options)),this.target.drawRect(n,i,this.options.get("targetWidth")-1,r-1,o,o)},render:function(){var t,e,n=this.values.length,i=this.target;if(k._super.render.call(this)){for(t=2;t<n;t++)e=this.renderRange(t).append(),this.shapes[e.id]="r"+t,this.valueShapes["r"+t]=e.id;null!==this.values[1]&&(e=this.renderPerformance().append(),this.shapes[e.id]="p1",this.valueShapes.p1=e.id),null!==this.values[0]&&(e=this.renderTarget().append(),this.shapes[e.id]="t0",this.valueShapes.t0=e.id),i.render()}}}),t.fn.sparkline.pie=S=n(t.fn.sparkline._base,{type:"pie",init:function(e,n,i,r,o){var s,l=0;if(S._super.init.call(this,e,n,i,r,o),this.shapes={},this.valueShapes={},this.values=n=t.map(n,Number),"auto"===i.get("width")&&(this.width=this.height),n.length>0)for(s=n.length;s--;)l+=n[s];this.total=l,this.initTarget(),this.radius=a.floor(a.min(this.canvasWidth,this.canvasHeight)/2)},getRegion:function(t,e,n){var i=this.target.getShapeAt(t,e,n);return void 0!==i&&void 0!==this.shapes[i]?this.shapes[i]:void 0},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:void 0===this.values[t],value:this.values[t],percent:this.values[t]/this.total*100,color:this.options.get("sliceColors")[t%this.options.get("sliceColors").length],offset:t}},changeHighlight:function(t){var e=this.currentRegion,n=this.renderSlice(e,t),i=this.valueShapes[e];delete this.shapes[i],this.target.replaceWithShape(i,n),this.valueShapes[e]=n.id,this.shapes[n.id]=e},renderSlice:function(t,e){var n,i,r,o,s,l=this.target,u=this.options,c=this.radius,h=u.get("borderWidth"),d=u.get("offset"),p=2*a.PI,f=this.values,g=this.total,v=d?2*a.PI*(d/360):0;for(o=f.length,r=0;r<o;r++){if(n=v,i=v,g>0&&(i=v+p*(f[r]/g)),t===r)return s=u.get("sliceColors")[r%u.get("sliceColors").length],e&&(s=this.calcHighlightColor(s,u)),l.drawPieSlice(c,c,c-h,n,i,void 0,s);v=i}},render:function(){var t,e,n=this.target,i=this.values,r=this.options,o=this.radius,s=r.get("borderWidth");if(S._super.render.call(this)){for(s&&n.drawCircle(o,o,a.floor(o-s/2),r.get("borderColor"),void 0,s).append(),e=i.length;e--;)i[e]&&(t=this.renderSlice(e).append(),this.valueShapes[e]=t.id,this.shapes[t.id]=e);n.render()}}}),t.fn.sparkline.box=T=n(t.fn.sparkline._base,{type:"box",init:function(e,n,i,r,o){T._super.init.call(this,e,n,i,r,o),this.values=t.map(n,Number),this.width="auto"===i.get("width")?"4.0em":r,this.initTarget(),this.values.length||(this.disabled=1)},getRegion:function(){return 1},getCurrentRegionFields:function(){var t=[{field:"lq",value:this.quartiles[0]},{field:"med",value:this.quartiles[1]},{field:"uq",value:this.quartiles[2]}];return void 0!==this.loutlier&&t.push({field:"lo",value:this.loutlier}),void 0!==this.routlier&&t.push({field:"ro",value:this.routlier}),void 0!==this.lwhisker&&t.push({field:"lw",value:this.lwhisker}),void 0!==this.rwhisker&&t.push({field:"rw",value:this.rwhisker}),t},render:function(){var t,e,n,i,r,s,l,u,c,h,d,p=this.target,f=this.values,g=f.length,v=this.options,m=this.canvasWidth,y=this.canvasHeight,b=void 0===v.get("chartRangeMin")?a.min.apply(a,f):v.get("chartRangeMin"),w=void 0===v.get("chartRangeMax")?a.max.apply(a,f):v.get("chartRangeMax"),_=0;if(T._super.render.call(this)){if(v.get("raw"))v.get("showOutliers")&&f.length>5?(e=f[0],t=f[1],i=f[2],r=f[3],s=f[4],l=f[5],u=f[6]):(t=f[0],i=f[1],r=f[2],s=f[3],l=f[4]);else if(f.sort(function(t,e){return t-e}),i=o(f,1),r=o(f,2),s=o(f,3),n=s-i,v.get("showOutliers")){for(t=l=void 0,c=0;c<g;c++)void 0===t&&f[c]>i-n*v.get("outlierIQR")&&(t=f[c]),f[c]<s+n*v.get("outlierIQR")&&(l=f[c]);e=f[0],u=f[g-1]}else t=f[0],l=f[g-1];this.quartiles=[i,r,s],this.lwhisker=t,this.rwhisker=l,this.loutlier=e,this.routlier=u,d=m/(w-b+1),v.get("showOutliers")&&(_=a.ceil(v.get("spotRadius")),m-=2*a.ceil(v.get("spotRadius")),d=m/(w-b+1),e<t&&p.drawCircle((e-b)*d+_,y/2,v.get("spotRadius"),v.get("outlierLineColor"),v.get("outlierFillColor")).append(),u>l&&p.drawCircle((u-b)*d+_,y/2,v.get("spotRadius"),v.get("outlierLineColor"),v.get("outlierFillColor")).append()),p.drawRect(a.round((i-b)*d+_),a.round(.1*y),a.round((s-i)*d),a.round(.8*y),v.get("boxLineColor"),v.get("boxFillColor")).append(),p.drawLine(a.round((t-b)*d+_),a.round(y/2),a.round((i-b)*d+_),a.round(y/2),v.get("lineColor")).append(),p.drawLine(a.round((t-b)*d+_),a.round(y/4),a.round((t-b)*d+_),a.round(y-y/4),v.get("whiskerColor")).append(),p.drawLine(a.round((l-b)*d+_),a.round(y/2),a.round((s-b)*d+_),a.round(y/2),v.get("lineColor")).append(),p.drawLine(a.round((l-b)*d+_),a.round(y/4),a.round((l-b)*d+_),a.round(y-y/4),v.get("whiskerColor")).append(),p.drawLine(a.round((r-b)*d+_),a.round(.1*y),a.round((r-b)*d+_),a.round(.9*y),v.get("medianColor")).append(),v.get("target")&&(h=a.ceil(v.get("spotRadius")),p.drawLine(a.round((v.get("target")-b)*d+_),a.round(y/2-h),a.round((v.get("target")-b)*d+_),a.round(y/2+h),v.get("targetColor")).append(),p.drawLine(a.round((v.get("target")-b)*d+_-h),a.round(y/2),a.round((v.get("target")-b)*d+_+h),a.round(y/2),v.get("targetColor")).append()),p.render()}}}),O=n({init:function(t,e,n,i){this.target=t,this.id=e,this.type=n,this.args=i},append:function(){return this.target.appendShape(this),this}}),j=n({_pxregex:/(\d+)(px)?\s*$/i,init:function(e,n,i){e&&(this.width=e,this.height=n,this.target=i,this.lastShapeId=null,i[0]&&(i=i[0]),t.data(i,"_jqs_vcanvas",this))},drawLine:function(t,e,n,i,r,o){return this.drawShape([[t,e],[n,i]],r,o)},drawShape:function(t,e,n,i){return this._genShape("Shape",[t,e,n,i])},drawCircle:function(t,e,n,i,r,o){return this._genShape("Circle",[t,e,n,i,r,o])},drawPieSlice:function(t,e,n,i,r,o,s){return this._genShape("PieSlice",[t,e,n,i,r,o,s])},drawRect:function(t,e,n,i,r,o){return this._genShape("Rect",[t,e,n,i,r,o])},getElement:function(){return this.canvas},getLastShapeId:function(){return this.lastShapeId},reset:function(){alert("reset not implemented")},_insert:function(e,n){t(n).html(e)},_calculatePixelDims:function(e,n,i){var r;r=this._pxregex.exec(n),this.pixelHeight=r?r[1]:t(i).height(),r=this._pxregex.exec(e),this.pixelWidth=r?r[1]:t(i).width()},_genShape:function(t,e){var n=R++;return e.unshift(n),new O(this,n,t,e)},appendShape:function(t){alert("appendShape not implemented")},replaceWithShape:function(t,e){alert("replaceWithShape not implemented")},insertAfterShape:function(t,e){alert("insertAfterShape not implemented")},removeShapeId:function(t){alert("removeShapeId not implemented")},getShapeAt:function(t,e,n){alert("getShapeAt not implemented")},render:function(){alert("render not implemented")}}),D=n(j,{init:function(e,n,i,r){D._super.init.call(this,e,n,i),this.canvas=s.createElement("canvas"),i[0]&&(i=i[0]),t.data(i,"_jqs_vcanvas",this),t(this.canvas).css({display:"inline-block",width:e,height:n,verticalAlign:"top"}),this._insert(this.canvas,i),this._calculatePixelDims(e,n,this.canvas),this.canvas.width=this.pixelWidth,this.canvas.height=this.pixelHeight,this.interact=r,this.shapes={},this.shapeseq=[],this.currentTargetShapeId=void 0,t(this.canvas).css({width:this.pixelWidth,height:this.pixelHeight})},_getContext:function(t,e,n){var i=this.canvas.getContext("2d");return void 0!==t&&(i.strokeStyle=t),i.lineWidth=void 0===n?1:n,void 0!==e&&(i.fillStyle=e),i},reset:function(){this._getContext().clearRect(0,0,this.pixelWidth,this.pixelHeight),this.shapes={},this.shapeseq=[],this.currentTargetShapeId=void 0},_drawShape:function(t,e,n,i,r){var o,s,a=this._getContext(n,i,r);for(a.beginPath(),a.moveTo(e[0][0]+.5,e[0][1]+.5),o=1,s=e.length;o<s;o++)a.lineTo(e[o][0]+.5,e[o][1]+.5);void 0!==n&&a.stroke(),void 0!==i&&a.fill(),void 0!==this.targetX&&void 0!==this.targetY&&a.isPointInPath(this.targetX,this.targetY)&&(this.currentTargetShapeId=t)},_drawCircle:function(t,e,n,i,r,o,s){var l=this._getContext(r,o,s);l.beginPath(),l.arc(e,n,i,0,2*a.PI,!1),void 0!==this.targetX&&void 0!==this.targetY&&l.isPointInPath(this.targetX,this.targetY)&&(this.currentTargetShapeId=t),void 0!==r&&l.stroke(),void 0!==o&&l.fill()},_drawPieSlice:function(t,e,n,i,r,o,s,a){var l=this._getContext(s,a);l.beginPath(),l.moveTo(e,n),l.arc(e,n,i,r,o,!1),l.lineTo(e,n),l.closePath(),void 0!==s&&l.stroke(),a&&l.fill(),void 0!==this.targetX&&void 0!==this.targetY&&l.isPointInPath(this.targetX,this.targetY)&&(this.currentTargetShapeId=t)},_drawRect:function(t,e,n,i,r,o,s){return this._drawShape(t,[[e,n],[e+i,n],[e+i,n+r],[e,n+r],[e,n]],o,s)},appendShape:function(t){return this.shapes[t.id]=t,this.shapeseq.push(t.id),this.lastShapeId=t.id,t.id},replaceWithShape:function(t,e){var n,i=this.shapeseq;for(this.shapes[e.id]=e,n=i.length;n--;)i[n]==t&&(i[n]=e.id);delete this.shapes[t]},replaceWithShapes:function(t,e){var n,i,r,o=this.shapeseq,s={};for(i=t.length;i--;)s[t[i]]=!0;for(i=o.length;i--;)n=o[i],s[n]&&(o.splice(i,1),delete this.shapes[n],r=i);for(i=e.length;i--;)o.splice(r,0,e[i].id),this.shapes[e[i].id]=e[i]},insertAfterShape:function(t,e){var n,i=this.shapeseq;for(n=i.length;n--;)if(i[n]===t)return i.splice(n+1,0,e.id),void(this.shapes[e.id]=e)},removeShapeId:function(t){var e,n=this.shapeseq;for(e=n.length;e--;)if(n[e]===t){n.splice(e,1);break}delete this.shapes[t]},getShapeAt:function(t,e,n){return this.targetX=e,this.targetY=n,this.render(),this.currentTargetShapeId},render:function(){var t,e,n,i=this.shapeseq,r=this.shapes,o=i.length,s=this._getContext();for(s.clearRect(0,0,this.pixelWidth,this.pixelHeight),n=0;n<o;n++)t=i[n],e=r[t],this["_draw"+e.type].apply(this,e.args);this.interact||(this.shapes={},this.shapeseq=[])}}),M=n(j,{init:function(e,n,i){var r;M._super.init.call(this,e,n,i),i[0]&&(i=i[0]),t.data(i,"_jqs_vcanvas",this),this.canvas=s.createElement("span"),t(this.canvas).css({display:"inline-block",position:"relative",overflow:"hidden",width:e,height:n,margin:"0px",padding:"0px",verticalAlign:"top"}),this._insert(this.canvas,i),this._calculatePixelDims(e,n,this.canvas),this.canvas.width=this.pixelWidth,this.canvas.height=this.pixelHeight,r='<v:group coordorigin="0 0" coordsize="'+this.pixelWidth+" "+this.pixelHeight+'" style="position:absolute;top:0;left:0;width:'+this.pixelWidth+"px;height="+this.pixelHeight+'px;"></v:group>',this.canvas.insertAdjacentHTML("beforeEnd",r),this.group=t(this.canvas).children()[0],this.rendered=!1,this.prerender=""},_drawShape:function(t,e,n,i,r){var o,s,a,l,u,c,h=[];for(c=0,u=e.length;c<u;c++)h[c]=e[c][0]+","+e[c][1];return o=h.splice(0,1),r=void 0===r?1:r,s=void 0===n?' stroked="false" ':' strokeWeight="'+r+'px" strokeColor="'+n+'" ',a=void 0===i?' filled="false"':' fillColor="'+i+'" filled="true" ',l=h[0]===h[h.length-1]?"x ":"",'<v:shape coordorigin="0 0" coordsize="'+this.pixelWidth+" "+this.pixelHeight+'"  id="jqsshape'+t+'" '+s+a+' style="position:absolute;left:0px;top:0px;height:'+this.pixelHeight+"px;width:"+this.pixelWidth+'px;padding:0px;margin:0px;"  path="m '+o+" l "+h.join(", ")+" "+l+'e"> </v:shape>'},_drawCircle:function(t,e,n,i,r,o,s){var a,l;return e-=i,n-=i,a=void 0===r?' stroked="false" ':' strokeWeight="'+s+'px" strokeColor="'+r+'" ',l=void 0===o?' filled="false"':' fillColor="'+o+'" filled="true" ','<v:oval  id="jqsshape'+t+'" '+a+l+' style="position:absolute;top:'+n+"px; left:"+e+"px; width:"+2*i+"px; height:"+2*i+'px"></v:oval>'},_drawPieSlice:function(t,e,n,i,r,o,s,l){var u,c,h,d,p,f,g;if(r===o)return"";if(o-r==2*a.PI&&(r=0,o=2*a.PI),c=e+a.round(a.cos(r)*i),h=n+a.round(a.sin(r)*i),d=e+a.round(a.cos(o)*i),p=n+a.round(a.sin(o)*i),c===d&&h===p){if(o-r<a.PI)return"";c=d=e+i,h=p=n}return c===d&&h===p&&o-r<a.PI?"":(u=[e-i,n-i,e+i,n+i,c,h,d,p],f=void 0===s?' stroked="false" ':' strokeWeight="1px" strokeColor="'+s+'" ',g=void 0===l?' filled="false"':' fillColor="'+l+'" filled="true" ','<v:shape coordorigin="0 0" coordsize="'+this.pixelWidth+" "+this.pixelHeight+'"  id="jqsshape'+t+'" '+f+g+' style="position:absolute;left:0px;top:0px;height:'+this.pixelHeight+"px;width:"+this.pixelWidth+'px;padding:0px;margin:0px;"  path="m '+e+","+n+" wa "+u.join(", ")+' x e"> </v:shape>')},_drawRect:function(t,e,n,i,r,o,s){return this._drawShape(t,[[e,n],[e,n+r],[e+i,n+r],[e+i,n],[e,n]],o,s)},reset:function(){this.group.innerHTML=""},appendShape:function(t){var e=this["_draw"+t.type].apply(this,t.args);return this.rendered?this.group.insertAdjacentHTML("beforeEnd",e):this.prerender+=e,this.lastShapeId=t.id,t.id},replaceWithShape:function(e,n){var i=t("#jqsshape"+e),r=this["_draw"+n.type].apply(this,n.args);i[0].outerHTML=r},replaceWithShapes:function(e,n){var i,r=t("#jqsshape"+e[0]),o="",s=n.length;for(i=0;i<s;i++)o+=this["_draw"+n[i].type].apply(this,n[i].args);for(r[0].outerHTML=o,i=1;i<e.length;i++)t("#jqsshape"+e[i]).remove()},insertAfterShape:function(e,n){var i=t("#jqsshape"+e),r=this["_draw"+n.type].apply(this,n.args);i[0].insertAdjacentHTML("afterEnd",r)},removeShapeId:function(e){var n=t("#jqsshape"+e);this.group.removeChild(n[0])},getShapeAt:function(t,e,n){return t.id.substr(8)},render:function(){this.rendered||(this.group.innerHTML=this.prerender,this.rendered=!0)}})})}(document,Math)},231:function(t,e,n){(function(t){!function(){function e(){var t="{}";if("userDataBehavior"==C){_.load("jStorage");try{t=_.getAttribute("jStorage")}catch(t){}try{T=_.getAttribute("jStorage_update")}catch(t){}w.jStorage=t}a(),c(),h()}function n(){"localStorage"==C||"globalStorage"==C?"addEventListener"in window?window.addEventListener("storage",i,!1):document.attachEvent("onstorage",i):"userDataBehavior"==C&&setInterval(i,1e3)}function i(){var t;clearTimeout(S),S=setTimeout(function(){if("localStorage"==C||"globalStorage"==C)t=w.jStorage_update;else if("userDataBehavior"==C){_.load("jStorage");try{t=_.getAttribute("jStorage_update")}catch(t){}}t&&t!=T&&(T=t,r())},25)}function r(){var t,n=m.parse(m.stringify(b.__jstorage_meta.CRC32));e(),t=m.parse(m.stringify(b.__jstorage_meta.CRC32));var i,r=[],s=[];for(i in 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workflows":!1,"Analysis home view":!1,"History Lists":!1,"Histories Shared with Me":!1,"Current History":!1,"Create New":!1,"Copy History":!1,"Share or Publish":!1,"Show Structure":!1,"Extract Workflow":!1,"Delete Permanently":!1,"Dataset Actions":!1,"Copy Datasets":!1,"Dataset Security":!1,"Resume Paused Jobs":!1,"Collapse Expanded Datasets":!1,"Unhide Hidden Datasets":!1,"Delete Hidden Datasets":!1,"Purge Deleted Datasets":!1,Downloads:!1,"Export Tool Citations":!1,"Export History to File":!1,"Other Actions":!1,"Import from File":!1,Webhooks:!1,"This history is empty":!1,"No matching datasets found":!1,"An error occurred while getting updates from the server":!1,"Please contact a Galaxy administrator if the problem persists":!1,"search datasets":!1,"You are currently viewing a deleted history!":!1,"You are over your disk quota":!1,"Tool execution is on hold until your disk usage drops below your allocated quota":!1,All:!1,None:!1,"For all selected":!1,"Edit history tags":!1,"Edit history Annotation":!1,"Click to rename history":!1,"Operations on multiple datasets":!1,"Hide datasets":!1,"Unhide datasets":!1,"Delete datasets":!1,"Undelete datasets":!1,"Permanently delete datasets":!1,"This will permanently remove the data in your datasets. Are you sure?":!1,Dataset:!1,Annotation:!1,"This history is empty. Click 'Get Data' on the left tool menu to start":!1,"You must be logged in to create histories":!1,"Unable to purge dataset":!1,"Cannot display datasets removed from disk":!1,"This dataset must finish uploading before it can be viewed":!1,"This dataset is not yet viewable":!1,"View data":!1,Download:!1,"Download dataset":!1,"Additional files":!1,"View details":!1,"This is a new dataset and not all of its data are available yet":!1,"You do not have permission to view this dataset":!1,"The job creating this dataset was cancelled before completion":!1,"This job is waiting to run":!1,"This dataset is currently uploading":!1,"Metadata is being auto-detected":!1,"This job is currently running":!1,'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':!1,"An error occurred with this dataset":!1,"No data":!1,"An error occurred setting the metadata for this dataset":!1,"There was an error getting the data for this dataset":!1,"This dataset has been deleted and removed from disk":!1,"This dataset has been deleted":!1,"This dataset has been hidden":!1,format:!1,database:!1,"Edit attributes":!1,"Cannot edit attributes of datasets removed from disk":!1,"Undelete dataset to edit attributes":!1,"This dataset must finish uploading before it can be edited":!1,"This dataset is not yet editable":!1,Delete:!1,"Dataset is already deleted":!1,"View or report this error":!1,"Run this job again":!1,Visualize:!1,"Visualize in":!1,"Undelete it":!1,"Permanently remove it from disk":!1,"Unhide it":!1,"You may be able to":!1,"set it manually or retry auto-detection":!1,"Edit dataset tags":!1,"Edit dataset annotation":!1,"Tool Help":!1,"Search Tool Shed":!1,"Monitor installing repositories":!1,"Manage installed tools":!1,"Reset metadata":!1,"Download local tool":!1,"Tool lineage":!1,"Reload a tool's configuration":!1,"Review tool migration stages":!1,"View Tool Error Logs":!1,"Manage Display Whitelist":!1,"Manage Tool Dependencies":!1,Users:!1,Groups:!1,"API keys":!1,"Impersonate a user":!1,Data:!1,Quotas:!1,Roles:!1,"Local data":!1,"Form Definitions":!1,"Enable/Disable Scratchbook":!1,"Show/Hide Scratchbook":!1,Tags:!1,"Edit annotation":!1},__ja:{"Analyze Data":"データ解析",Workflow:"ワークフロー","Shared Data":"共有データ","Data Libraries":"データライブラリ",Histories:"ヒストリー",Workflows:"ワークフロー",Visualizations:"可視化",Pages:"ページ",Visualization:"可視化","New Track Browser":"新しい Track Browser","Saved Visualizations":"保存された可視化","Interactive Environments":"インタラクティブ環境",Admin:"管理者",Help:"ヘルプ",Support:"サポート",Search:"検索","Mailing Lists":"メーリングリスト",Videos:"動画","How to Cite Galaxy":"Galaxy を引用する方法","Interactive Tours":"インタラクティブツアー",User:"ユーザー",Login:"ログイン",Register:"登録","Login or Register":"ログイン/登録",Preferences:"設定","Custom Builds":"カスタムビルド",Logout:"ログアウト","Saved Histories":"保存されたヒストリ","Saved Datasets":"保存されたデータセット","Saved Pages":"保存されたページ","Account and saved data":"アカウントと保存されたデータ","Account registration or login":"アカウントの登録またはログイン","Support, contact, and community":"サポート、コンタクト、コミュニティ","Administer this Galaxy":"この Galaxy の管理者","Visualize datasets":"データセットの可視化","Access published resources":"パブリッシュされたリソースへアクセス","Chain tools into workflows":"ツールとワークフローの連携","Analysis home view":"解析ホーム","History Lists":"ヒストリーリスト","Histories Shared with Me":"私と共有されているヒストリー","Current History":"現在のヒストリー","Create New":"新しく作成","Copy History":"ヒストリーをコピーする","Share or Publish":"共有またはパブリッシュ","Show Structure":"構造を見る","Extract Workflow":"ワークフローを抽出","Delete Permanently":"永久に削除","Dataset Actions":"データセットの操作","Copy Datasets":"データセットをコピー","Dataset Security":"データセットのセキュリティ","Resume Paused Jobs":"一時停止したジョブの再開","Collapse Expanded Datasets":"展開されたデータセットを畳む","Unhide Hidden Datasets":"隠されたデータセットを表示する","Delete Hidden Datasets":"隠されたデータセットを削除する","Purge Deleted Datasets":"削除されたデータセットを永久に削除",Downloads:"ダウンロード","Export Tool Citations":"ツールの引用をエクスポート","Export History to File":"ヒストリーをファイルへエクスポート","Other Actions":"その他のアクション","Import from File":"ファイルからの読み込み",Webhooks:"Webhooks","This history is empty":"ヒストリーは空です","No matching datasets found":"一致するデータセットが見つかりませんでした","Search datasets":"データセットを検索する","You are currently viewing a deleted history!":"消去したヒストリーをみています。","You are over your disk quota":"あなたはディスククォータを超えている",All:"一式",None:"なし","For all selected":"各項目を","Edit history tags":"ヒストリーのタグを編集","Edit history annotation":"ヒストリーのアノテーションを編集","Click to rename history":"ヒストリーの名前を変更するにはクリック","Operations on multiple datasets":"複数のデータセットに対する操作","Permanently delete datasets":"永久にデータセットを削除","This will permanently remove the data in your datasets. Are you sure?":"これは永久にあなたのデータセット内のデータを削除します。本当に？",Dataset:"データセット","This history is empty. Click 'Get Data' on the left tool menu to start":"ヒストリーは空です。解析をはじめるには、左パネルの 'データ取得' をクリック","You must be logged in to create histories":"ヒストリーを作成するためにはログインする必要があります","View data":"データを表示",Download:"ダウンロード","Download dataset":"データセットをダウンロード","View details":"細部を表示","This job is waiting to run":"ジョブは実行待ちです","This job is currently running":"ジョブは実行中です","An error occurred with this dataset":"このジョブの実行中に発生したエラー","No data":"データ無し","This dataset has been deleted and removed from disk":"このデータセットは、永続的にディスクから削除されました","This dataset has been deleted":"このデータセットは削除されました","This dataset has been hidden":"このデータセットは、非表示にされた",format:"フォーマット",database:"データベース","Edit attributes":"変数を編集する",Delete:"削除する","View or report this error":"このエラーを届け出る","Run this job again":"もう一度このジョブを実行する",Visualize:"可視化する","Undelete it":"復元する","Permanently remove it from disk":"永久にディスクから削除","Unhide it":"非表示解除する","Search Tool Shed":"Tool Shed で探す","Search Tool Shed (Beta)":"Tool Shed (Beta) で探す","Monitor installing repositories":"インストールレポジトリのモニタ","Manage installed tools":"インストールしたツールの管理","Reset metadata":"メタデータのリセット","Download local tool":"ローカルツールのダウンロード","Tool lineage":"ツール系統","Reload a tool's configuration":"ツールのコンフィグのリロード","Review tool migration stages":"ツール移行ステージのレビュー","View Tool Error Logs":"ツールのエラーログ","Manage Display Whitelist":"表示ホワイトリストの管理","Manage Tool Dependencies":"ツール依存関係の管理",Users:"ユーザー",Groups:"グループ","API keys":"API キー","Impersonate a user":"ユーザー偽装",Data:"データ",Quotas:"クォータ",Roles:"ロール","Local data":"ローカルデータ","Form definitions":"フォーム定義",Administration:"管理",Server:"サーバー","Tools and Tool Shed":"ツールと Tool Shed","User Management":"ユーザ管理","Form Definitions":"フォーム定義"},__fr:{"Analyze Data":"Analyse de données",Workflow:"Workflow","Shared Data":"Données partagées","Data Libraries":"Bibliothèque de données",Histories:"Historiques",Workflows:"Workflows",Visualizations:"Visualisations",Pages:"Pages",Visualization:"Visualisation","New Track Browser":"Nouveau Navigateur de Tracks/Pistes","Saved Visualizations":"Visualisations sauvegardées","Interactive Environments":"Environnements interactifs",Admin:"Admin",Help:"Aide",Support:"Assistance",Search:"Recherche","Mailing Lists":"Liste de diffusion",Videos:"Vidéos",Wiki:"Documentations","How to Cite Galaxy":"Comment citer Galaxy","Interactive Tours":"Guides interactifs",User:"Utilisateur",Login:"Authentification",Register:"Enregistrement","Login or Register":"Authentification et Enregistrement","Logged in as":"Authentifié en tant que",Preferences:"Préférences","Custom Builds":"Mes génomes Builds de référence",Logout:"Déconnexion","Saved Histories":"Historiques sauvegardés","Saved Datasets":"Jeux de données sauvegardés","Saved Pages":"Pages sauvegardées","Account and saved data":"Compte et données sauvegardées","Account registration or login":"Enregistrement ou authentification","Support, contact, and community":"Support,contact et communauté","Administer this Galaxy":"Outils Admin","Visualize datasets":"Visualiser les jeux de données","Access published resources":"Accéder aux données partagées","Chain tools into workflows":"Relier outils dans un workflow","Analysis home view":"Accueil analyse de données","History Lists":"Tableaux des historiques","Histories Shared with Me":"Historiques partagés avec moi","Current History":"Cet Historique","Create New":"Créer un nouveau","Copy History":"Copier l'Historique","Share or Publish":"Partager et publier","Show Structure":"Montrer la structure","Extract Workflow":"Extraire un Workflow","Delete Permanently":"Supprimer définitivement","Dataset Actions":"Actions sur les jeux de données","Copy Datasets":"Copier des jeux de données","Dataset Security":"Permissions/Sécurité","Resume Paused Jobs":"Reprendre les processus en pause","Collapse Expanded Datasets":"Réduire les données étendues","Unhide Hidden Datasets":"Afficher les données cachées","Delete Hidden Datasets":"Supprimer les données cachées","Purge Deleted Datasets":"Purger les données supprimées",Downloads:"Télécharger","Export Tool Citations":"Exporter les citations des outils","Export History to File":"Exporter l'Historique dans un fichier","Other Actions":"Autres actions","Import from File":"Importer depuis un fichier",Webhooks:"Webhooks","This history is empty":"Cet historique est vide","No matching datasets found":"Aucunes données correspondantes n'ont été trouvées","An error occurred while getting updates from the server":"Une erreur s'est produite lors de la réception des données depuis le serveur","Please contact a Galaxy administrator if the problem persists":"Veuillez contacter un administrateur de l'instance Galaxy si ce problème persiste","search datasets":"Rechercher des données","You are currently viewing a deleted history!":"Vous consultez actuellement un historique supprimé!","You are over your disk quota":"Vous avez dépassé votre quota d'espace disque","Tool execution is on hold until your disk usage drops below your allocated quota":"L'exécution de l'outil est en attente tant que votre utilisation d'espace disque dépasse le quota attribué",All:"Tout",None:"Aucun","For all selected":"Pour toute la sélection","Edit history tags":"Editer les mots-clés de l'historique","Edit history Annotation":"Editer l'annotation de l'historique","Click to rename history":"Cliquer pour renommer l'historique","Operations on multiple datasets":"Opérer sur plusieurs jeux de données en même temps","Hide datasets":"Cacher les jeux de données","Unhide datasets":"Afficher les jeux de données cachés","Delete datasets":"Supprimer les jeux de données","Undelete datasets":"Restaurer les jeux de données supprimés","Permanently delete datasets":"Supprimer définitivement les jeux de données","This will permanently remove the data in your datasets. Are you sure?":"Cela supprimera de manière permanente les données de votre historique. Êtes-vous certain?",Dataset:"Jeu de données",Annotation:"Annotation","This history is empty. Click 'Get Data' on the left tool menu to start":"Cet historique est vide. Cliquer sur 'Get Data' au niveau du menu d'outils à gauche pour démarrer","You must be logged in to create histories":"Vous devez être connecté pour créer un historique","load your own data":"Charger vos propres données","get data from an external source":"Charger des données depuis une source externe","Include Deleted Datasets":"Inclure les jeux de données supprimés","Include Hidden Datasets":"Inclure les jeux de données cachés","Unable to purge dataset":"Impossible de purger le jeu de données","Cannot display datasets removed from disk":"Impossible de visualiser les jeux de données supprimés du disque","This dataset must finish uploading before it can be viewed":"Le jeu de données doit être totalement téléversé avant de pouvoir être visualiser","This dataset is not yet viewable":"Ce jeu de données n'est pas visualisable","View data":"Voir les données",Download:"Télécharger","Download dataset":"Télécharger le jeu de données","Additional files":"Fichiers additionnels","View details":"Voir les détails","This is a new dataset and not all of its data are available yet":"Il s'agit d'un nouveau jeu de données et seule une partie des données est accessible pour le moment","You do not have permission to view this dataset":"Vous n'avez pas la permission de voir ce jeu de données","The job creating this dataset was cancelled before completion":"Le processus à l'origine de ce jeu de données a été annulé prématurément","This job is waiting to run":"Ce calcul est en attente de traitement","This dataset is currently uploading":"Ce jeu de données est en cours de téléversement","Metadata is being auto-detected":"Les métadonnées sont auto-détectées","This job is currently running":"Le traitement est en cours",'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':'Ce traitement est en pause. Utilisez le "Relancer les traitements en pause" dans le menu d\'historique pour le relancer',"An error occurred with this dataset":"Une erreur est survenue avec ce jeu de données","No data":"Aucune donnée","An error occurred setting the metadata for this dataset":"Une erreur est survenue pendant la récupération des métadonnées de ce jeu de données","There was an error getting the data for this dataset":"Il est survenu une erreur durant la récupération du contenu de ce jeu de données","This dataset has been deleted and removed from disk":"Ce jeu de données a été supprimé et effacé du disque","This dataset has been deleted":"Ce jeu de données a été supprimé","This dataset has been hidden":"Ce jeu de données a été caché",format:"format",database:"génome de référence","Edit attributes":"Editer les attributs","Cannot edit attributes of datasets removed from disk":"Impossible d'éditer les attributs de jeux de données effacés du disque","Undelete dataset to edit attributes":"Restaurer le jeu de données pour en éditer les attributs","This dataset must finish uploading before it can be edited":"Ce jeu de données doit être entièrement téléversé avant toute modification","This dataset is not yet editable":"Ce jeu de données n'est pas encore éditable",Delete:"Supprimer","Dataset is already deleted":"Le jeu de données est déjà supprimé","View or report this error":"Voir ou remonter cette erreur","Run this job again":"Exécuter ce traitement à nouveau",Visualize:"Visualiser","Visualize in":"Visualiser via","Undelete it":"Restaurer","Permanently remove it from disk":"Supprimer définitivement du disque","Unhide it":"Rendre visible","You may be able to":"Vous devriez être en mesure de","set it manually or retry auto-detection":"Traitez le manuellement ou retenter la détection automatique","Edit dataset tags":"Editer les mots-clés du jeu de données","Edit dataset annotation":"Editer les annotations du jeu de données",Tags:"Mots-clés","Edit annotation":"Editer les annotations"},__zh:{"This history is empty":"历史已空","No matching datasets found":"未找到匹配的数据集","Search datasets":"搜索数据集","You are currently viewing a deleted history!":"正在查看已删除的历史","You are over your disk quota":"您已超过磁盘配额",All:"皆",None:"一个也没有","For all selected":"为每个选定","Click to rename history":"单击要重命名的历史","Operations on multiple datasets":"编辑多个数据集","Permanently delete datasets":"永久删除数据集","This will permanently remove the data in your datasets. Are you sure?":"这将永久在你的数据集删除数据。你确定？",Dataset:"数据集","This history is empty. 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diff --git a/static/scripts/bundled/login.bundled.js b/static/scripts/bundled/login.bundled.js
index 08f0fc29e29..a95acbc746e 100644
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d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. 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Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){o.append(n("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],o=this.form.data.match(a),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==r)return this.form.highlight(o),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],o=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,o=n-r,s=0;o<=0&&(o=1,s=r-(n-o));var l,d=r+s,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td 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f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var o=t.columns[r];if("advanced"==o.filterable){var s=o.key,l=i[s],d=e[s];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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class="text-filter-form" column_key="'+r+'" action="'+e.url+'" method="get" >';for(u in e.columns){var s=e.columns[u],l=n[s.key];l&&"All"!=l&&(s.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+s.key+'" name="f-'+s.key+'" value="'+l+'"/>')}o+='<span id="'+r+'-filtering-criteria">';var d=n[r];if(d){var c=t.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(r,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(r,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+r+'-filter" name="f-'+r+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+r+'-filtering-criteria">';var m=!1;for(var g in e.categorical_filters[r]){var v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],s.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(D.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var q=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),D.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(q.prototype,j.prototype,D.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){D.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){D.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(D.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),D.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){D.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(D.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new q(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new q(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:q,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:q,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),D=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>D)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,D-j,$),void 0!==v&&k>x&&!(j>b||D<v)){var q=Math.max(j,v),I=Math.min(D,b);t.fillRect(q,d+1,I-q,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),q+14<I&&(q+=2,I-=2),t.fillRect(q,d+1,I-q,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,D,d),z=j,R=D}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],D=P[1],q=d+g;if(p=f(q),_=f(q+D),o([q,q+D],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=D;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+D):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,q-a),Math.min(q-a+D,s-a)));for(var L=Math.max(q,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=D),g+=D;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=D;break;case"D":$.draw_deletion(p,S,D),g+=D;break;case"I":var V=p-b;if(o([q,q+D],m)){var G=h.slice(v,v+D);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([q,q+D],m)){case 1003:G=G.slice(a-q);break;case 1004:G=G.slice(0,q-s);break;case 1005:break;case 1002:G=G.slice(a-q,q-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(q+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=D}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,D),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,D)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var D=P[5];S.test(D)&&(j.itemRgb="rgb("+D+")")}if(P.length>A-3&&E)for(var q=A-3;q<P.length;++q)j[E.fields[q+3].name]=P[q];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var 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Uint8Array(t.buffer,t.byteOffset+e,a),i,n):s(t,e,i,n,a)}}function s(t,e,i,n,a){for(var r=0;r<a;++r)i[n+r]=t[e+r]}function l(t,e,i){e.set(t,i)}function d(e,i,n,a){e=i?n?new Uint8Array(e,i,n):new Uint8Array(e,i,e.byteLength-i):new Uint8Array(e);var r=new t;r.inflateInit(c,!0),r.next_in=e,r.next_in_index=0,r.avail_in=e.length;for(var s=[],l=0;;){var d=new Uint8Array(32e3);r.next_out=d,r.next_out_index=0,r.avail_out=d.length;var u=r.inflate(h);if(u!=f&&u!=p&&u!=_)throw r.msg;if(0!=r.avail_out){var m=new Uint8Array(d.length-r.avail_out);o(d,0,m,0,d.length-r.avail_out),d=m}if(s.push(d),l+=d.length,u==p||u==_)break}if(a&&(a[0]=(i||0)+r.next_in_index),1==s.length)return s[0].buffer;for(var g=new Uint8Array(l),v=0,b=0;b<s.length;++b){var w=s[b];o(w,0,g,v,w.length),v+=w.length}return g.buffer}var c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),s=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+s,d=e+":"+i+l,c=null,u=null,h='<iframe 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e=this;o.each(o.keys(t),function(i){e.set_input_value(i,t[i])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(t){var e=o.extend({tool_id:this.id,inputs:this.get_inputs_dict()},t),i=n.Deferred(),a=new l.default.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return n.when(a.go()).then(function(t){i.resolve(new c.default.DatasetCollection(t))}),i}});o.extend(b.prototype,h);var w=(t.View.extend({}),t.Collection.extend({model:b})),y=t.Model.extend(h),x=t.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){o.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var e,i=!0;o.each(this.attributes.elems,function(n){n instanceof y?(e=n,e.hide()):n instanceof b&&n.apply_search_results(t)&&(i=!1,e&&e.show())}),i?this.hide():(this.show(),this.set("open",!0))}});o.extend(x.prototype,h);var k=t.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length<this.attributes.min_chars_for_search)return void this.set("results",null);var e=t;this.timer&&clearTimeout(this.timer),n("#search-clear-btn").hide(),n("#search-spinner").show();var i=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"?q="+e),n.get(i.urlRoot,{q:e},function(t){i.set("results",t),n("#search-spinner").hide(),n("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});o.extend(k.prototype,h);var C=t.Model.extend({initialize:function(e){this.attributes.tool_search=e.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=e.tools,this.attributes.layout=new t.Collection(this.parse(e.layout))},parse:function(t){var e=this,i=function t(i){var n=i.model_class;if(n.indexOf("Tool")===n.length-4)return e.attributes.tools.get(i.id);if("ToolSection"===n){var a=o.map(i.elems,t);return i.elems=a,new x(i)}return"ToolSectionLabel"===n?new y(i):void 0};return o.map(t,i)},clear_search_results:function(){this.get("layout").each(function(t){t instanceof x?t.clear_search_results():t.show()})},apply_search_results:function(){var t=this.get("tool_search").get("results");if(null===t)return void this.clear_search_results();var e=null;this.get("layout").each(function(i){i instanceof y?(e=i,e.hide()):i instanceof b?i.apply_search_results(t)&&e&&e.show():(e=null,i.apply_search_results(t))})}}),S=t.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),$=S.extend({tagName:"div",render:function(){var t=n("<div/>");t.append(z.tool_link(this.model.toJSON()));var e=this.model.get("form_style",null);if("upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("regular"===e){var i=this;t.find("a").on("click",function(t){t.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(t),this}}),T=S.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(n("<span/>").text(this.model.attributes.text)),this}}),M=S.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){S.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(z.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return o.each(this.model.attributes.elems,function(e){if(e instanceof b){var i=new $({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof y){var n=new T({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),O=t.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(z.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),n("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){if(this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which)return this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),A=t.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new O({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof x){var i=new M({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof b){var n=new $({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var a=new T({model:e});a.render(),t.$el.append(a.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=n(this).attr("class").split(/\s+/)[0],a=t.model.get("tools").get(i);t.trigger("tool_link_click",e,a)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?n("#search-no-results").show():n("#search-no-results").hide()}}),E=t.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(z.tool_form(this.model.toJSON()))}}),z=(t.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new A({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" ','placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />','<a id="search-clear-btn" title="clear search (esc)"> </a>','<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>'].join("")),panel_section:o.template(['<div class="toolSectionTitle" id="title_<%- id %>">','<a href="javascript:void(0)"><span><%- name %></span></a>',"</div>",'<div id="<%- id %>" class="toolSectionBody" style="display: none;">','<div class="toolSectionBg"></div>',"<div>"].join("")),tool_link:o.template(['<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">','<span class="labels">',"<% _.each( labels, function( label ){ %>",'<span class="label label-default label-<%- label %>">',"<%- label %>","</span>","<% }); %>","</span>",'<span class="tool-old-link">',"<%- name %>","</span>"," <%- description %>","</a>"].join("")),tool_form:o.template(['<div class="toolFormTitle"><%- tool.name %> (version <%- tool.version %>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});e.default={ToolParameter:f,IntegerToolParameter:m,SelectToolParameter:v,Tool:b,ToolCollection:w,ToolSearch:k,ToolPanel:C,ToolPanelView:A,ToolFormView:E}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(9),u=r(c),h=i(63),f=r(h),p=i(40),_=r(p),m=t.View.extend({initialize:function(t){var e=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(s.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(t,i){var a=i.model.attributes,r="",o={},l=a.job_id;l?r=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),s.default.get({url:r,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),e._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),t.resolve()},error:function(e,r){var o=e&&e.err_msg||"Uncaught error.";401==r?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},postchange:function(t,e){var i={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:n.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),s.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:i,success:function(i){e.update(i),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(t){var e=this,i=t.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var i=this,r={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(r))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){o.append(n("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],o=this.form.data.match(a),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==r)return this.form.highlight(o),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],o=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,o=n-r,s=0;o<=0&&(o=1,s=r-(n-o));var l,d=r+s,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(e+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var u=o;u<c+1;u++)u==t.cur_page_num?e+='<span class="page-link inactive-link" id="page-link-'+u+'">'+u+"</span>":e+='<span class="page-link" id="page-link-'+u+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+u+'">'+u+"</a></span>";c<a&&(e+='...<span class="page-link" id="page-link-'+a+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+a+'">'+a+"</a></span>"),e+="</span>",e+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(t.show_item_checkboxes){e+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var h in t.operations){var f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var o=t.columns[r];if("advanced"==o.filterable){var s=o.key,l=i[s],d=e[s];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],s.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(D.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var q=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),D.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(q.prototype,j.prototype,D.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){D.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){D.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(D.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),D.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){D.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(D.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new q(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new q(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:q,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:q,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),D=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>D)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,D-j,$),void 0!==v&&k>x&&!(j>b||D<v)){var q=Math.max(j,v),I=Math.min(D,b);t.fillRect(q,d+1,I-q,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),q+14<I&&(q+=2,I-=2),t.fillRect(q,d+1,I-q,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,D,d),z=j,R=D}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],D=P[1],q=d+g;if(p=f(q),_=f(q+D),o([q,q+D],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=D;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+D):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,q-a),Math.min(q-a+D,s-a)));for(var L=Math.max(q,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=D),g+=D;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=D;break;case"D":$.draw_deletion(p,S,D),g+=D;break;case"I":var V=p-b;if(o([q,q+D],m)){var G=h.slice(v,v+D);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([q,q+D],m)){case 1003:G=G.slice(a-q);break;case 1004:G=G.slice(0,q-s);break;case 1005:break;case 1002:G=G.slice(a-q,q-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(q+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=D}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,D),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,D)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new 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g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data 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i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var D=P[5];S.test(D)&&(j.itemRgb="rgb("+D+")")}if(P.length>A-3&&E)for(var q=A-3;q<P.length;++q)j[E.fields[q+3].name]=P[q];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&(S<0||x>$)&&(S=k,$=i<0?x:w,i<0?y:b),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&s.push(l[d]);return a(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return r.topLevelReductionCache=o,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=i>0?0:3e8;t.fromRef&&(s=e);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>s)return a(u)}else u.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<s)return a(u)}else u.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(s+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(o(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=r.exec(n);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};n=n.substring(s[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return t(null);this.data.slice(this.extHeaderOffset,64).fetch(function(i){if(!i)return t(null,"Couldn't fetch extension header");var n=new Uint8Array(i),a=new Int16Array(i),r=(new Int32Array(i),a[0],a[1]),o=s(n,4);if(0==r)return t(null);e.data.slice(o,20*r).fetch(function(i){if(!i)return t(null,"Couldn't fetch index info");for(var n=new Uint8Array(i),a=new Int16Array(i),o=(new Int32Array(i),[]),l=0;l<r;++l){var d=a[10*l],c=a[10*l+1],h=s(n,20*l+4),f=a[10*l+8],p=new u(e,d,c,h,f);o.push(p)}t(o)})})},u.prototype.lookup=function(t,e){var i=this;this.bbi.data.slice(this.offset,32).fetch(function(n){function a(n){i.bbi.data.slice(n,4+d*(c+u)).fetch(function(n){var o=new Uint8Array(n),l=new Uint16Array(n),d=(new Uint32Array(n),o[0]),h=l[1],f=4;if(0!=d){for(var p=0;p<h;++p){for(var _="",m=0;m<c;++m){var g=o[f++];0!=g&&(_+=String.fromCharCode(g))}if(_==t){var v=s(o,f),b=r(o,f+8);return i.bbi.getUnzoomedView().fetchFeatures(function(e,n,a,r){if(r&&r.length>i.field-3)return r[i.field-3]==t},[{offset:v,size:b}],e)}f+=u}return e([])}for(var w=null,p=0;p<h;++p){for(var _="",m=0;m<c;++m){var g=o[f++];0!=g&&(_+=String.fromCharCode(g))}var y=s(o,f);if(f+=8,t.localeCompare(_)<0&&w)return void a(w);w=y}a(w)})}var o=new Uint8Array(n),l=(new Int16Array(n),new Int32Array(n)),d=(l[0],l[1]),c=l[2],u=l[3];s(o,16);a(i.offset+32)})},{makeBwg:c}}.apply(e,a))&&(t.exports=r)}).call(e,i(0))},function(t,e,i){var n,a;n=[],void 0!==(a=function(){"use strict";function t(t,e){if("number"!=typeof t||"number"!=typeof e)throw"Bad range "+t+","+e;this._min=t,this._max=e}function e(t){var e=t.sort(o),i=[],n=e.shift();e.forEach(function(t){t._min<=n._max?t._max>n._max&&(n._max=t._max):(i.push(n),n=t)}),i.push(n),this._ranges=i}function i(t,i){return t instanceof e||(t instanceof Array||(t=[t]),t=new e(t)),i&&t.insertRange(i),t}function n(i,n){for(var a=i.ranges(),r=n.ranges(),o=a.length,s=r.length,l=0,d=0,c=[];l<o&&d<s;){var i=a[l],n=r[d],u=Math.max(i.min(),n.min()),h=Math.min(i.max(),n.max());h>=u&&c.push(new t(u,h)),i.max()>n.max()?++d:++l}return 0==c.length?null:1==c.length?c[0]:new e(c)}function a(t){for(var e=0,i=t.ranges(),n=0;n<i.length;++n){var a=i[n];e+=a.max()-a.min()+1}return e}function r(t,e){return t.min()<e.min()?-1:t.min()>e.min()?1:t.max()<e.max()?-1:e.max()>t.max()?1:0}function o(t,e){return t._min<e._min?-1:t._min>e._min?1:t._max<e._max?-1:e._max>t._max?1:0}return t.prototype.min=function(){return this._min},t.prototype.max=function(){return this._max},t.prototype.contains=function(t){return t>=this._min&&t<=this._max},t.prototype.isContiguous=function(){return!0},t.prototype.ranges=function(){return[this]},t.prototype._pushRanges=function(t){t.push(this)},t.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},e.prototype.min=function(){return this._ranges[0].min()},e.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},e.prototype.lower_bound=function(t){var e=this.ranges();if(t>this.max())return e.length;if(t<this.min())return 0;for(var i=0,n=e.length-1;i<=n;){var a=Math.floor((i+n)/2);if(t>e[a]._max)i=a+1;else{if(!(t<e[a]._min))return a;n=a-1}}return i},e.prototype.contains=function(t){var e=this.lower_bound(t);return!!(e<this._ranges.length&&this._ranges[e].contains(t))},e.prototype.insertRange=function(t){var e=this.lower_bound(t._min);if(e===this._ranges.length)return void this._ranges.push(t);var i=this.ranges();if(t._max<i[e]._min)return void this._ranges.splice(e,0,t);i[e]._min<t._min&&(t._min=i[e]._min);for(var n=e+1;n<i.length&&i[n]._min<=t._max;)n++;n--,i[n]._max>t._max&&(t._max=i[n]._max),this._ranges.splice(e,n-e+1,t)},e.prototype.isContiguous=function(){return this._ranges.length>1},e.prototype.ranges=function(){return this._ranges},e.prototype._pushRanges=function(t){for(var e=0;e<this._ranges.length;++e)t.push(this._ranges[e])},e.prototype.toString=function(){for(var t="",e=0;e<this._ranges.length;++e)e>0&&(t+=","),t+=this._ranges[e].toString();return t},{Range:t,union:i,intersection:n,coverage:a,rangeOver:r,_rangeOrder:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){var n,a;n=[],void 0!==(a=function(){function t(){}function e(){this.was=[0]}function i(t,e,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=e,this.mode=g,this.reset(t,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function r(t,e,i,n,a){return t[0]=v,e[0]=b,i[0]=w,n[0]=y,f}function o(t,e,i,n,a){if(0!=a){if(!t)throw"Undef src";if(!i)throw"Undef dest";0==e&&a==t.length?l(t,i,n):O?l(t.subarray(e,e+a),i,n):1==t.BYTES_PER_ELEMENT&&a>100?l(new 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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e.default=t,e}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=(a(r),i(1)),s=a(o),l=i(8),d=n(l),c=i(7),u=n(c),h=s.Model.extend(d.default.LoggableMixin).extend({_logNamespace:"user",urlRoot:function(){return Galaxy.root+"api/users"},defaults:{id:null,username:"("+(0,u.default)("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(t){this.log("User.initialize:",t),this.on("loaded",function(t,e){this.log(this+" has loaded:",t,e)}),this.on("change",function(t,e){this.log(this+" has changed:",t,e.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(t,e){t=t||h.CURRENT_ID_STR,e=e||{};var i=this,n=e.success;return e.success=function(t,e){i.trigger("loaded",t,e),n&&n(t,e)},t===h.CURRENT_ID_STR&&(e.url=this.urlRoot+"/"+h.CURRENT_ID_STR),s.Model.prototype.fetch.call(this,e)},clearSessionStorage:function(){for(var t in sessionStorage)0===t.indexOf("history:")?sessionStorage.removeItem(t):"history-panel"===t&&sessionStorage.removeItem(t)},toString:function(){var t=[this.get("username")];return this.get("id")&&(t.unshift(this.get("id")),t.push(this.get("email"))),"User("+t.join(":")+")"}});h.CURRENT_ID_STR="current",h.getCurrentUserFromApi=function(t){var e=new h;return e.loadFromApi(h.CURRENT_ID_STR,t),e};s.Collection.extend(d.default.LoggableMixin).extend({model:h,urlRoot:function(){return Galaxy.root+"api/users"}});e.default={User:h}},,function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=(a(r),i(161)),s=a(o),l=i(163),d=a(l),c=i(164),u=a(c),h=t.View.extend({initialize:function(t){var e=this;this.options=t,this.setElement(this._template()),this.$navbarBrandLink=this.$(".navbar-brand-link"),this.$navbarBrandImage=this.$(".navbar-brand-image"),this.$navbarBrandTitle=this.$(".navbar-brand-title"),this.$navbarTabs=this.$(".navbar-tabs"),this.$quoteMeter=this.$(".quota-meter-container"),this.collection=new s.default.Collection,this.collection.on("add",function(t){e.$navbarTabs.append(new s.default.Tab({model:t}).render().$el)}).on("reset",function(){e.$navbarTabs.empty()}).on("dispatch",function(t){e.collection.each(function(e){t(e)})}).fetch(this.options),Galaxy.frame=this.frame=new d.default({collection:this.collection}),Galaxy.quotaMeter=this.quotaMeter=new u.default.UserQuotaMeter({model:Galaxy.user,el:this.$quoteMeter}),n(window).on("click",function(t){var e=n(t.target).closest("a[download]");1==e.length&&(0===n("iframe[id=download]").length&&n("body").append(n("<iframe/>").attr("id","download").hide()),n("iframe[id=download]").attr("src",e.attr("href")),t.preventDefault())}).on("beforeunload",function(){var t="";if(e.collection.each(function(e){var i=e.get("onbeforeunload")&&e.get("onbeforeunload")();i&&(t+=i+" ")}),""!==t)return t})},render:function(){return this.$navbarBrandTitle.html("Galaxy "+(this.options.brand&&"/ "+this.options.brand||"")),this.$navbarBrandLink.attr("href",this.options.logo_url),this.$navbarBrandImage.attr("src",this.options.logo_src),this.quotaMeter.render(),this},_template:function(){return'<div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div class="navbar-header"><div class="navbar-tabs"/></div><div class="navbar-brand"><a class="navbar-brand-link"><img class="navbar-brand-image"/><span class="navbar-brand-title"/></a></div><div class="quota-meter-container"/><div 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Libraries"),url:"library/list"},{title:(0,h.default)("Histories"),url:"histories/list_published"},{title:(0,h.default)("Workflows"),url:"workflows/list_published"},{title:(0,h.default)("Visualizations"),url:"visualizations/list_published"},{title:(0,h.default)("Pages"),url:"pages/list_published"}]}),this.add({id:"visualization",title:(0,h.default)("Visualization"),url:"visualizations/list",tooltip:(0,h.default)("Visualize datasets"),disabled:!Galaxy.user.id,menu:[{title:(0,h.default)("New Track Browser"),url:"visualization/trackster",target:"_frame"},{title:(0,h.default)("Saved Visualizations"),url:"visualizations/list",target:"_frame"},{title:(0,h.default)("Interactive Environments"),url:"visualization/gie_list",target:"galaxy_main"}]}),c.default.add({url:"api/webhooks/masthead/all",callback:function(t){n(document).ready(function(){n.each(t.models,function(t,e){var i=e.toJSON();if(i.activate){var n={id:i.name,icon:i.config.icon,url:i.config.url,tooltip:i.config.tooltip,onclick:i.config.function&&new Function(i.config.function)};Galaxy.page?Galaxy.page.masthead.collection.add(n):Galaxy.masthead&&Galaxy.masthead.collection.add(n),p.default.appendScriptStyle(i)}})})}}),Galaxy.user.get("is_admin")&&this.add({id:"admin",title:(0,h.default)("Admin"),url:"admin",tooltip:(0,h.default)("Administer this Galaxy"),cls:"admin-only"});var i={id:"help",title:(0,h.default)("Help"),tooltip:(0,h.default)("Support, contact, and community"),menu:[{title:(0,h.default)("Support"),url:t.support_url,target:"_blank"},{title:(0,h.default)("Search"),url:t.search_url,target:"_blank"},{title:(0,h.default)("Mailing Lists"),url:t.mailing_lists,target:"_blank"},{title:(0,h.default)("Videos"),url:t.screencasts_url,target:"_blank"},{title:(0,h.default)("Wiki"),url:t.wiki_url,target:"_blank"},{title:(0,h.default)("How to Cite Galaxy"),url:t.citation_url,target:"_blank"},{title:(0,h.default)("Interactive Tours"),url:"tours"}]};t.terms_url&&i.menu.push({title:(0,h.default)("Terms and Conditions"),url:t.terms_url,target:"_blank"}),t.biostar_url&&i.menu.unshift({title:(0,h.default)("Ask a question"),url:"biostar/biostar_question_redirect",target:"_blank"}),t.biostar_url&&i.menu.unshift({title:(0,h.default)("Galaxy Biostar"),url:t.biostar_url_redirect,target:"_blank"}),this.add(i);var r={};r=Galaxy.user.id?{id:"user",title:(0,h.default)("User"),cls:"loggedin-only",tooltip:(0,h.default)("Account and saved data"),menu:[{title:(0,h.default)("Logged in as")+" "+Galaxy.user.get("email")},{title:(0,h.default)("Preferences"),url:"user"},{title:(0,h.default)("Custom Builds"),url:"custom_builds"},{title:(0,h.default)("Logout"),url:"user/logout?session_csrf_token="+Galaxy.session_csrf_token,target:"_top",divider:!0},{title:(0,h.default)("Saved Histories"),url:"histories/list",target:"_top"},{title:(0,h.default)("Saved Datasets"),url:"datasets/list",target:"_top"},{title:(0,h.default)("Saved Pages"),url:"pages/list",target:"_top"}]}:t.allow_user_creation?{id:"user",title:(0,h.default)("Login or Register"),cls:"loggedout-only",tooltip:(0,h.default)("Account registration or login"),menu:[{title:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},{title:(0,h.default)("Register"),url:"user/create",target:"galaxy_main",noscratchbook:!0}]}:{id:"user",title:(0,h.default)("Login"),cls:"loggedout-only",tooltip:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},this.add(r);var o=this.get(t.active_view);return o&&o.set("active",!0),(new a.Deferred).resolve().promise()}}),m=t.View.extend({initialize:function(t){this.model=t.model,this.setElement(this._template()),this.$dropdown=this.$(".dropdown"),this.$toggle=this.$(".dropdown-toggle"),this.$menu=this.$(".dropdown-menu"),this.$note=this.$(".dropdown-note"),this.listenTo(this.model,"change",this.render,this)},events:{"click .dropdown-toggle":"_toggleClick"},render:function(){var t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa "+this.model.get("icon")).addClass(this.model.get("toggle")&&"toggle").attr("target",this.model.get("target")).attr("href",this.model.get("url")).attr("title",this.model.get("tooltip")).tooltip("destroy"),this.model.get("tooltip")&&this.$toggle.tooltip({placement:"bottom"}),this.$dropdown.removeClass().addClass("dropdown").addClass(this.model.get("disabled")&&"disabled").addClass(this.model.get("active")&&"active"),this.model.get("menu")&&this.model.get("show_menu")?(this.$menu.show(),n("#dd-helper").show().off().on("click",function(){n("#dd-helper").hide(),t.model.set("show_menu",!1)})):(t.$menu.hide(),n("#dd-helper").hide()),this.$menu.empty().removeClass("dropdown-menu"),this.model.get("menu")&&(r.each(this.model.get("menu"),function(e){t.$menu.append(t._buildMenuItem(e)),e.divider&&t.$menu.append(n("<li/>").addClass("divider"))}),t.$menu.addClass("dropdown-menu"),t.$toggle.append(n("<b/>").addClass("caret"))),this},_buildMenuItem:function(t){var e=this;return t=r.defaults(t||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),t.url=e._formatUrl(t.url),n("<li/>").append(n("<a/>").attr("href",t.url).attr("target",t.target).html(t.title).on("click",function(i){i.preventDefault(),e.model.set("show_menu",!1),t.onclick?t.onclick():Galaxy.frame.add(t)}))},_toggleClick:function(t){var e=this,i=this.model;if(t.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(t){i.id!==t.id&&t.get("menu")&&t.set("show_menu",!1)}),i.get("disabled")){var a=function(t,e){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+e).html(t)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){e.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),s=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+s,d=e+":"+i+l,c=null,u=null,h='<iframe 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a={container:e,name:i.get("title"),id:i.id,dbkey:i.get("dbkey"),stand_alone:!1},r=i.get("latest_revision"),o=r.config.view.drawables;n.each(o,function(t){t.dataset={hda_ldda:t.hda_ldda,id:t.dataset_id}}),view=t.create_visualization(a,r.config.viewport,r.config.view.drawables,r.config.bookmarks,!1)}};e.add(a)})},add:function(t){if("_blank"==t.target)window.open(t.url);else if("_top"==t.target||"_parent"==t.target||"_self"==t.target)window.location=t.url;else if(!this.active||t.noscratchbook){var e=a(window.parent.document).find("#galaxy_main");"galaxy_main"==t.target||"center"==t.target?0===e.length?window.location=t.url+(-1==t.url.indexOf("?")?"?":"&")+"use_panels=True":e.attr("src",t.url):window.location=t.url}else this.frames.add(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(8),s=r(o),l=i(7),d=r(l),c=t.View.extend(s.default.LoggableMixin).extend({_logNamespace:"user",options:{warnAtPercent:85,errorAtPercent:100},initialize:function(t){this.log(this+".initialize:",t),n.extend(this.options,t),this.listenTo(this.model,"change:quota_percent change:total_disk_usage",this.render)},update:function(t){return this.log(this+" updating user data...",t),this.model.loadFromApi(this.model.get("id"),t),this},isOverQuota:function(){return null!==this.model.get("quota_percent")&&this.model.get("quota_percent")>=this.options.errorAtPercent},_render_quota:function(){var t=this.model.toJSON(),e=t.quota_percent,i=a(this._templateQuotaMeter(t)),n=i.find(".progress-bar");return this.isOverQuota()?(n.attr("class","progress-bar progress-bar-danger"),i.find(".quota-meter-text").css("color","white"),this.trigger("quota:over",t)):e>=this.options.warnAtPercent?(n.attr("class","progress-bar progress-bar-warning"),this.trigger("quota:under 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o=i(2),s=a(o),l=i(1),d=a(l),c=i(8),u=n(c),h=i(158),f=n(h),p=i(178),_=n(p),m=i(62),g=n(m),v=i(7),b=n(v);(0,g.default)(r,"GalaxyApp");var w="galaxy:debug:namespaces",y=!1;try{y="true"==localStorage.getItem("galaxy:debug")}catch(t){console.log((0,b.default)("localStorage not available for debug flag retrieval"))}r.prototype._init=function(t,e){var i=this;return s.extend(i,d.Events),y&&(i.logger=console,console.debug("debugging galaxy:","options:",t,"bootstrapped:",e)),i._processOptions(t),i.root=t.root||"/",i.params=t.params||{},i.session_csrf_token=t.session_csrf_token||null,i._initConfig(t.config||{}),i._patchGalaxy(window.Galaxy),i._initLogger(i.options.loggerOptions||{}),i.debug("GalaxyApp.options: ",i.options),i.debug("GalaxyApp.config: ",i.config),i.debug("GalaxyApp.logger: ",i.logger),i._initLocale(),i.debug("GalaxyApp.localize: ",i.localize),i.config=t.config||{},i.debug("GalaxyApp.config: ",i.config),i._initUser(t.user||{}),i.debug("GalaxyApp.user: 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_.default.MetricsLogger(t),e.emit={},["log","debug","info","warn","error","metric"].map(function(t){e.emit[t]=function(i){e.logger.emit(t,arguments[0],Array.prototype.slice.call(arguments,1))}}),e.config.debug&&(u.default.LoggableMixin.logger=e.logger),e},r.prototype._initLocale=function(t){var e=this;return e.debug("_initLocale:",t),e.localize=b.default,window._l=e.localize,e},r.prototype._initUser=function(t){var e=this;return e.debug("_initUser:",t),e.user=new f.default.User(t),e.user.logger=e.logger,e},r.prototype._setUpListeners=function(){var e=this;return e.lastAjax={},t(document).bind("ajaxSend",function(t,i,n){var a=n.data;try{a=JSON.parse(a)}catch(t){}e.lastAjax={url:location.href.slice(0,-1)+n.url,data:a}}),e},r.prototype.debugging=function(t){var e=this;try{if(void 0===t)return"true"===localStorage.getItem("galaxy:debug");if(t)return localStorage.setItem("galaxy:debug",!0),!0;localStorage.removeItem("galaxy:debug"),e.debuggingNamespaces(null)}catch(t){console.log((0,b.default)("localStorage not available for debug flag retrieval"))}return!1},r.prototype.debuggingNamespaces=function(t){var e=this;try{if(void 0===t){var i=localStorage.getItem(w);return"string"==typeof i?i.split(","):[]}null===t?localStorage.removeItem(w):localStorage.setItem(w,t);var n=e.debuggingNamespaces();return e.logger&&(e.logger.options.consoleNamespaceWhitelist=n),n}catch(t){console.log((0,b.default)("localStorage not available for debug namespace retrieval"))}},r.prototype.toString=function(){return"GalaxyApp("+(this.user?this.user.get("email")||"(anonymous)":"uninitialized")+")"},e.default={GalaxyApp:r}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t){t=t||{};var e=this;return 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e=this;e.options={};for(var n in i.defaultOptions)i.defaultOptions.hasOwnProperty(n)&&(e.options[n]=t.hasOwnProperty(n)?t[n]:i.defaultOptions[n]);return e.options.logLevel=e._parseLevel(e.options.logLevel),e.options.consoleLevel=e._parseLevel(e.options.consoleLevel),e._sending=!1,e._waiting=null,e._postSize=e.options.postSize,e._initCache(),e},i.prototype._initCache=function(){try{this.cache=new a({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(t){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",t]),this.options.logLevel=i.NONE}},i.prototype._parseLevel=function(t){var e=void 0===t?"undefined":r(t);if("number"===e)return t;if("string"===e){var n=t.toUpperCase();if(i.hasOwnProperty(n))return i[n]}throw new Error("Unknown log level: "+t)},i.prototype.emit=function(t,e,i){var n=this;return e=e||n.options.defaultNamespace,t&&i?(t=n._parseLevel(t),t>=n.options.logLevel&&n._addToCache(t,e,i),n.consoleLogger&&t>=n.options.consoleLevel&&n._emitToConsole(t,e,i),n):n},i.prototype._addToCache=function(t,e,i){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var n=this;try{n.cache.add(n._buildEntry(t,e,i))>=n._postSize&&n._postCache()}catch(t){n._emitToConsole("warn","MetricsLogger",["Metrics logger could not stringify logArguments:",e,i]),n._emitToConsole("error","MetricsLogger",[t])}return n},i.prototype._buildEntry=function(t,e,i){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var n={level:t,namespace:this.options.clientPrefix+e,args:i};return this.options.addTime&&(n.time=(new Date).toISOString()),n},i.prototype._postCache=function(e){if(e=e||{},this._emitToConsole("info","MetricsLogger",["_postCache",e,this._postSize]),!this.options.postUrl||this._sending)return t.when({});var i=this,n=e.count||i._postSize,a=i.cache.get(n),r=a.length,o="function"==typeof i.options.getPingData?i.options.getPingData():{};return o.metrics=JSON.stringify(a),i._sending=!0,t.post(i.options.postUrl,o).always(function(){i._sending=!1}).fail(function(t,e,n){i._postSize=i.options.maxCacheSize,i.emit("error","MetricsLogger",["_postCache error:",t.readyState,t.status,t.responseJSON||t.responseText])}).done(function(t){"function"==typeof i.options.onServerResponse&&i.options.onServerResponse(t),i.cache.remove(r),i._postSize=i.options.postSize})},i.prototype._delayPost=function(){var t=this;t._waiting=setTimeout(function(){t._waiting=null},t.options.delayPostInMs)},i.prototype._emitToConsole=function(t,e,a){var r=this,o=r.options.consoleNamespaceWhitelist;if(!r.consoleLogger)return r;if(o&&-1===o.indexOf(e))return r;var s=Array.prototype.slice.call(a,0);return s.unshift(e),r.options.consoleFlattenMessages&&(s=[s.map(n).join(" ")]),t>=i.METRIC&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof r.consoleLogger.log&&r.consoleLogger.log.apply(r.consoleLogger,s),r)},i.prototype.log=function(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.debug=function(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.info=function(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.warn=function(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.error=function(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.metric=function(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},a.defaultOptions={maxSize:5e3},a.prototype._init=function(t){if(!this._hasStorage())throw new Error("LoggingCache needs localStorage");if(!t.key)throw new Error("LoggingCache needs key for localStorage");return this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return localStorage.setItem(this.key,"[]"),this},a.prototype.stringify=function(t){return JSON.stringify(this.get(t))},a.prototype.print=function(){console.log(JSON.stringify(this._fetchAndParse(),null,"  "))},e.default={MetricsLogger:i,LoggingCache:a}}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(160),s=r(o),l=i(176),d=r(l),c=i(9),u=r(c),h=i(3),f=r(h),p=t.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(e){var i=this;this.config=n.defaults(e.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(t){t.title?(f.default.setWindowTitle(t.title),t.allow_title_display=!1):(f.default.setWindowTitle(),t.allow_title_display=!0),i.center.display(t)},Galaxy.router=this.router=e.Router&&new e.Router(i,e),this.masthead=new s.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(t){var n=t.charAt(0).toUpperCase()+t.slice(1),a=e[n];if(a){var r=new a(i,e);i[r.toString()]=r,i.panels[t]=new d.default.SidePanel({id:t,el:i.$("#"+t),view:r})}}),this.render(),this.router&&t.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var t=this.config.message_box_content||"",e=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+e+"-message").html(t).toggle(!!t).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var t=this.config.inactivity_box_content||"",e=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(t+" ").append(e).toggle(!!t).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var t=this;return n.each(this._panelids,function(e){var i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var t=window.Galaxy.config.communication_server_host,e=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:t+":"+e}).success(function(t){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(t){n.css("visibility","hidden")}):n.css("visibility","hidden")}});e.default={View:p}}).call(e,i(1),i(2),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,i){"use strict";(function(t,e){function n(t){return t&&t.__esModule?t:{default:t}}var a=i(0),r=n(a),o=i(177),s=n(o),l=i(7),d=n(l),c=i(179),u=n(c),h=r.default;window.app=function(i,n){window.Galaxy=new s.default.GalaxyApp(i,n),Galaxy.debug("login app");var a=encodeURI(i.redirect);if(!i.show_welcome_with_login){var o=r.default.param({use_panels:"True",redirect:a});return void(window.location.href=Galaxy.root+"user/login?"+o)}var l=t.View.extend({initialize:function(e){this.page=e,this.model=new t.Model({title:(0,d.default)("Login required")}),this.setElement(this._template())},render:function(){this.page.$("#galaxy_main").prop("src",i.welcome_url)},_template:function(){return'<iframe src="'+i.root+"user/login?"+h.param({redirect:a})+'" frameborder="0" style="width: 100%; height: 100%;"/>'}});h(function(){Galaxy.page=new u.default.View(e.extend(i,{Right:l}))})}}).call(e,i(1),i(2))}],[237]);
\ No newline at end of file
diff --git a/static/scripts/bundled/masthead.bundled.js b/static/scripts/bundled/masthead.bundled.js
index d33f8be8763..ffa9fe8b756 100644
--- a/static/scripts/bundled/masthead.bundled.js
+++ b/static/scripts/bundled/masthead.bundled.js
@@ -4,4 +4,4 @@ webpackJsonp([3],[,,,,function(t,e,i){"use strict";(function(t,n,a){function r(t
  * @author   Feross Aboukhadijeh <feross@feross.org> <http://feross.org>
  * @license  MIT
  */
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e=this;s.each(s.keys(t),function(i){e.set_input_value(i,t[i])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(t){var e=s.extend({tool_id:this.id,inputs:this.get_inputs_dict()},t),i=n.Deferred(),a=new l.default.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return n.when(a.go()).then(function(t){i.resolve(new c.default.DatasetCollection(t))}),i}});s.extend(b.prototype,h);var w=(t.View.extend({}),t.Collection.extend({model:b})),y=t.Model.extend(h),x=t.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){s.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var e,i=!0;s.each(this.attributes.elems,function(n){n instanceof y?(e=n,e.hide()):n instanceof b&&n.apply_search_results(t)&&(i=!1,e&&e.show())}),i?this.hide():(this.show(),this.set("open",!0))}});s.extend(x.prototype,h);var k=t.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length<this.attributes.min_chars_for_search)return void this.set("results",null);var e=t;this.timer&&clearTimeout(this.timer),n("#search-clear-btn").hide(),n("#search-spinner").show();var i=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"?q="+e),n.get(i.urlRoot,{q:e},function(t){i.set("results",t),n("#search-spinner").hide(),n("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});s.extend(k.prototype,h);var C=t.Model.extend({initialize:function(e){this.attributes.tool_search=e.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=e.tools,this.attributes.layout=new t.Collection(this.parse(e.layout))},parse:function(t){var e=this,i=function t(i){var n=i.model_class;if(n.indexOf("Tool")===n.length-4)return e.attributes.tools.get(i.id);if("ToolSection"===n){var a=s.map(i.elems,t);return i.elems=a,new x(i)}return"ToolSectionLabel"===n?new y(i):void 0};return s.map(t,i)},clear_search_results:function(){this.get("layout").each(function(t){t instanceof x?t.clear_search_results():t.show()})},apply_search_results:function(){var t=this.get("tool_search").get("results");if(null===t)return void this.clear_search_results();var e=null;this.get("layout").each(function(i){i instanceof y?(e=i,e.hide()):i instanceof b?i.apply_search_results(t)&&e&&e.show():(e=null,i.apply_search_results(t))})}}),$=t.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),T=$.extend({tagName:"div",render:function(){var t=n("<div/>");t.append(z.tool_link(this.model.toJSON()));var e=this.model.get("form_style",null);if("upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("regular"===e){var i=this;t.find("a").on("click",function(t){t.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(t),this}}),S=$.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(n("<span/>").text(this.model.attributes.text)),this}}),M=$.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){$.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(z.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return s.each(this.model.attributes.elems,function(e){if(e instanceof b){var i=new T({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof y){var n=new S({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),O=t.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(z.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),n("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){if(this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which)return this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),A=t.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new O({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof x){var i=new M({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof b){var n=new T({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var a=new S({model:e});a.render(),t.$el.append(a.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=n(this).attr("class").split(/\s+/)[0],a=t.model.get("tools").get(i);t.trigger("tool_link_click",e,a)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?n("#search-no-results").show():n("#search-no-results").hide()}}),E=t.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(z.tool_form(this.model.toJSON()))}}),z=(t.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new A({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:s.template(['<input id="tool-search-query" class="search-query parent-width" name="query" ','placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />','<a id="search-clear-btn" title="clear search (esc)"> </a>','<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>'].join("")),panel_section:s.template(['<div class="toolSectionTitle" id="title_<%- id %>">','<a href="javascript:void(0)"><span><%- name %></span></a>',"</div>",'<div id="<%- id %>" class="toolSectionBody" style="display: none;">','<div class="toolSectionBg"></div>',"<div>"].join("")),tool_link:s.template(['<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">','<span class="labels">',"<% _.each( labels, function( label ){ %>",'<span class="label label-default label-<%- label %>">',"<%- label %>","</span>","<% }); %>","</span>",'<span class="tool-old-link">',"<%- name %>","</span>"," <%- description %>","</a>"].join("")),tool_form:s.template(['<div class="toolFormTitle"><%- tool.name %> (version <%- tool.version %>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});e.default={ToolParameter:f,IntegerToolParameter:m,SelectToolParameter:g,Tool:b,ToolCollection:w,ToolSearch:k,ToolPanel:C,ToolPanelView:A,ToolFormView:E}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(4),d=r(l),c=i(9),u=r(c),h=i(63),f=r(h),p=i(40),_=r(p),m=t.View.extend({initialize:function(t){var e=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(o.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(t,i){var a=i.model.attributes,r="",s={},l=a.job_id;l?r=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+a.id+"/build",s=n.extend({},Galaxy.params),s.tool_id&&delete s.tool_id),a.version&&(s.tool_version=a.version),o.default.get({url:r,data:s,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),e._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),t.resolve()},error:function(e,r){var s=e&&e.err_msg||"Uncaught error.";401==r?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},postchange:function(t,e){var i={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:n.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),o.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:i,success:function(i){e.update(i),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(t){var e=this,i=t.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var i=this,r={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(r))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var s=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){s.append(n("<input/>").attr({name:e,value:t}))}),s.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),o.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var s in a){i.form.highlight(s,a[s]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],s=this.form.data.match(a),o=this.form.field_list[s],l=this.form.input_list[s];if(s&&l&&o){if(!l.optional&&null==r)return this.form.highlight(s),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(s,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(s,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],s=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+s+'" id="'+s+'" class="grid-row-select-checkbox" /></td>');for(var o in e.columns){var l=e.columns[o];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+s+'" for="'+s+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,s=n-r,o=0;s<=0&&(s=1,o=r-(n-s));var l,d=r+o,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(s-=l)<1&&(s=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td colspan="100"><span id="page-link-container">Page:',s>1&&(e+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var u=s;u<c+1;u++)u==t.cur_page_num?e+='<span class="page-link inactive-link" id="page-link-'+u+'">'+u+"</span>":e+='<span class="page-link" id="page-link-'+u+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+u+'">'+u+"</a></span>";c<a&&(e+='...<span class="page-link" id="page-link-'+a+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+a+'">'+a+"</a></span>"),e+="</span>",e+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(t.show_item_checkboxes){e+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var h in t.operations){var f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var s=t.columns[r];if("advanced"==s.filterable){var o=s.key,l=i[o],d=e[o];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div id="standard-search" style="display: '+c+';"><table><tr><td style="padding: 0;"><table>';for(var r in t.columns){var s=t.columns[r];"standard"==s.filterable&&(u+=this.grid_column_filter(t,s))}u+="</table></td></tr><tr><td>",a&&(u+='<a href="" class="advanced-search-toggle">Advanced Search</a>'),u+="</td></tr></table></div>",u+='<div id="advanced-search" style="display: '+n+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var r in t.columns){var s=t.columns[r];"advanced"==s.filterable&&(u+=this.grid_column_filter(t,s))}return u+="</table></div>"},grid_column_filter:function(e,i){var n=(e.default_filter_dict,e.filters),a=i.label,r=i.key;"advanced"==i.filterable&&(a=a.toLowerCase());var s="<tr>";if("advanced"==i.filterable&&(s+='<td align="left" style="padding-left: 10px">'+a+":</td>"),s+='<td style="padding-bottom: 1px;">',i.is_text){s+='<form class="text-filter-form" column_key="'+r+'" action="'+e.url+'" method="get" >';for(u in e.columns){var o=e.columns[u],l=n[o.key];l&&"All"!=l&&(o.is_text&&(l=JSON.stringify(l)),s+='<input type="hidden" id="'+o.key+'" name="f-'+o.key+'" value="'+l+'"/>')}s+='<span id="'+r+'-filtering-criteria">';var d=n[r];if(d){var c=t.type(d);if("string"==c&&"All"!=d&&(s+=this.filter_element(r,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),s+=this.filter_element(r,h)}}s+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}s+='<span class="search-box"><input class="search-box-input" id="input-'+r+'-filter" name="f-'+r+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{s+='<span id="'+r+'-filtering-criteria">';var m=!1;for(var v in e.categorical_filters[r]){var g=e.categorical_filters[r][v],b="",w="";for(var y in g)b=y,w=g[y];m&&(s+=" | "),m=!0;var h=n[r];h&&g[r]&&h==w?s+='<span class="categorical-filter '+r+'-filter current-filter">'+v+"</span>":s+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+v+"</a></span>"}s+="</span>"}return s+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=i(146),l=a(o),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),v=i(3),g=a(v);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){g.default.cssLoadFile("static/style/jquery.rating.css"),g.default.cssLoadFile("static/style/autocomplete_tagging.css"),g.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),g.default.cssLoadFile("static/style/library.css"),g.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){s.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),s=n("<div/>").addClass("position").appendTo(r),o=(n("<a href=''/>").text(t).appendTo(s).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);o.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var o=this,d=new l.default.TracksterView(s.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,s=e.start,c=e.end,u=e.overview;n&&void 0!==s&&c?d.change_chrom(n,s,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],o.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&s.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function s(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var o=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(o),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),v=i(149),g=a(v),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),T=a($),S=i(151),M=a(S);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,s,o,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){s=r.position().top,o=s+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<s)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>o)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),s=a.position().top,o=s+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=s&&i.offsetY<=o)return i.offsetY-s<o-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=T.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new T.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),s=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&s++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),s>1&&s===this.drawables.length){var o,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],l[o.name]=[o];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],o.name in l&&l[o.name].push(o);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===s&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var B=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=T.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,s=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(s),n.current_height=e.clientY,n.current_x=n.offsetX;var o=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(o)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,s=i.high-i.low,o=i.viewport_container.width();i.update_location(Math.round(a/o*s)+i.low,Math.round(r/o*s)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),s=i.high-i.low,o=i.viewport_container.width(),l=i.low;i.low=Math.round(a/o*s)+l,i.high=Math.round(r/o*s)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(B.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,s=i.chrom_data.length;r<s;r++){var o=i.chrom_data[r].chrom,l=t("<option>");l.text(o),l.val(o),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var s=0,o=a.drawables.length;s<o;s++){var l=a.drawables[s];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var V=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),N=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new I({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,s=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var o=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,o,!1);o.container_div.insertBefore(r.view.content_div.children()[l]),o.add_drawable(r),r.container_div.appendTo(o.content_div),t=o}else t=r.container;var d=new r.constructor(view,t,{name:s,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),L=function(t,e){g.default.Scaler.call(this,e),this.filter=t};L.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,s,o,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=o,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),s=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?s:[r].concat(s),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new V(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new N({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),s=this.view.resolution_px_b,o=1/s;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,s=r/(view.max_high-view.max_low),o=1/s),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*o),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,s,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,s,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",s="max"===e?"max":"min",o="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(o),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(o,r(e,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,s=1/i,o=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:o.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&o.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,s,o.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,s,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return o.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),s=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return o.tile_cache.set_elt(c,void 0),void t.when(o.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=s[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,v=o.view.canvas_manager.new_canvas(),g=e.get("start"),b=e.get("end"),w=Math.ceil((b-g)*i)+o.left_offset,y=l.max(_);v.width=w,v.height=n.height||y;var x=v.getContext("2d");x.translate(o.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(s[n],x,u[n],e,i,a)}),void 0!==m&&(o.tile_cache.set_elt(c,m),o.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new g.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,s=this.view.container.width(),o=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*s);o.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(o)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var s=t[a].html_elt.find("canvas").height();s>r&&(r=s)}for(a=0;a<t.length;a++){var o=t[a];o.html_elt.find("canvas").height()!==r&&(this.draw_helper(o.region,i,{force:!0,height:r}),o.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),s=r.data,o=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=s.length;l<d;l++)e.fillStyle=this.view.get_base_color(s[l]),e.fillText(s[l],Math.floor(l*a),10);return new G(this,n,a,o,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(s(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new g.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=g.default.ArcLinkedFeaturePainter:this.painter=g.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,s=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var o={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){o[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(o,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(s.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,o)}})}if(s.filters_manager){var c,u=s.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}s.filters_available!==p&&(s.filters_available=p,s.filters_available||s.filters_manager.hide(),s.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,s){var o=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,v=t.data.length;m<v;m++){for(var g,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(g=_[y],g.update_attrs(b),!g.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new L(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return o.view.get_base_color(t)}),T=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var S=$.draw(e,l.width,l.height,a,f);T=S.feature_mapper,incomplete_features=S.incomplete_features,T.translation=-u}return s?void 0:new F(o,n,a,l,t.data,i,t.message,p,T,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=g.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),s=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&s&&s.length>1){var o;if(0===this.container_div.find(".yaxislabel.variant").length&&(o=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":o+"px",top:(this.config.get_value("summary_height")-o)/2+"px"})),this.config.get_value("show_sample_data"))){var d=s.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}o=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":o,"line-height":o}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=g.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:B,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,s){var o=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(o.model)}).appendTo(this.icons_div),s&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var s=i.display_modes[a];n[s]=function(t){return function(){i.change_mode(t)}}(s)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t,e){this.slot=t,this.feature=e},o=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(o.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var s=0,o=r.length;s<o;s++){var l=r[s];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,o=0,l=t.length;o<l;o++){e=t[o],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(o)}for(var o=0,l=a.length;o<l;o++){e=t[a[o]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new s(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:o}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},s=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},o=function(t,e,i,n,a,r){void 0===r&&(r=4);var s,o=n-e,l=a-i,d=Math.floor(Math.sqrt(o*o+l*l)/r),c=o/d,u=l/d;for(s=0;s<d;s++,e+=c,i+=u)s%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,s=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,s),t.lineTo(r,s),t.lineTo(e,i),t.lineTo(a,s),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,s=this.prefs.min_value,o=this.prefs.max_value,l=o-s,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+s/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var v,g=this.prefs.block_color||this.prefs.color,b=parseInt(g.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,$=0,T=h.length;$<T;$++)if(t.fillStyle=t.strokeStyle=g,k=C=!1,v=m[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(_=h[$][1])){if(_<s?(C=!0,_=s):_>o&&(k=!0,_=o),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,v,-_);else if("Intensity"===u){var S=(_-s)/l,M=Math.round(w+(255-w)*(1-S)),O=Math.round(y+(255-y)*(1-S)),A=Math.round(x+(255-x)*(1-S));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,v,d)}else _=Math.round(d-(_-s)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=v:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=g}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,s){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=s||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,s=this.view_start,o=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],v=m[0],g=m[1],b=m[2],w=a&&void 0!==a[v]?a[v].slot:null;("Dense"===this.mode||null!==w)&&g<o&&b>s&&(l=this.draw_element(t,this.mode,m,w,s,o,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(g<s||b>o)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,s,o,l){return[0,0]}});var _=function(t,e,i,n,a,r,s){p.call(this,t,e,i,n,a,r,s),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,s,o,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*s)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*s))),m=p,v=_,d=("Dense"===e?0:0+n)*o+this.get_top_padding(l),g=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(g=Math.floor(Math.max(0,(x-a)*s)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*s))));var T,S;if("Squish"===e?(T=1,S=3,$=!1):(T=5,S=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=S):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*s)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*s)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(S-T)/2+1,q-j,T),void 0!==g&&k>x&&!(j>b||q<g)){var D=Math.max(j,g),B=Math.min(q,b);t.fillRect(D,d+1,B-D,S),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<B&&(D+=2,B-=2),t.fillRect(D,d+1,B-D,S))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var V=this.height_scaler.gen_val(i),I=Math.ceil(S*V),N=Math.round((S-I)/2);1!==V&&(t.fillRect(p,M+1,_-p,N),t.fillRect(p,M+S-N+1,_-p,N))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,S),f&&$&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,S));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),v+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,v]}});var m=function(t,e,i,n,a,r,s,o,l){p.call(this,t,e,i,n,a,r,s),this.ref_seq=o?o.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,s=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),s=t.slice(-1);return"N"===s?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(s)&&(n[1]+=a,r+=a),[e.indexOf(s),a]});return{blocks:i,cigar:s}},draw_read:function(t,e,i,n,a,o,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,o],v=0,g=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,$=n+1,T=new x(t,C,i,e),S=[],M=[],O=this._parse_cigar(c);c=O.cigar,S=O.blocks;for(var A=0;A<S.length;A++){var E=S[A];s([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,$,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+v;if(p=f(D),_=f(D+q),s([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var B="";"X"===j?B=h.slice(g,g+q):this.ref_seq&&(B=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,o-a)));for(var V=Math.max(D,a),I=0;I<B.length;I++)if(B&&!this.prefs.show_differences||"X"===j){var N=Math.floor(Math.max(0,(V+I-a)*i));t.fillStyle=this.base_color_fn(B[I]),k&&i>w?t.fillText(B[I],N,n+9):i>.05&&t.fillRect(N-b,$,Math.max(1,Math.round(i)),C)}"X"===j&&(g+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,$+(C-1)/2,_-p,1),v+=q;break;case"D":T.draw_deletion(p,$,q),v+=q;break;case"I":var L=p-b;if(s([D,D+q],m)){var G=h.slice(g,g+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[L,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-o);break;case 1005:break;case 1002:G=G.slice(a-D,D-o)}for(var I=0,F=G.length;I<F;I++){var N=Math.floor(Math.max(0,(D+I-a)*i));t.fillText(G[I],N-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,L,n+9]})}g+=q}else v=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(v,j,q),g=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(g,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,s,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*s,(c-a-.5)*s)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*s))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var v=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,s,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):v=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,s,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):v=!1;var g=Math.ceil(Math.min(d,Math.max(-.5*s,(i[4][1]-a-.5)*s))),b=Math.floor(Math.max(-.5*s,(i[5][0]-a-.5)*s));if(v&&b>g){t.fillStyle="#ccc";var w=_+1+(m-1)/2;o(t,g,w,b,w)}}else this.draw_read(t,e,s,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,i,n,a,r,s){_.call(this,t,e,i,n,a,r,s),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var s=(i+n)/2,o=n-s;Math.PI;o>0&&(t.beginPath(),t.arc(s,r,n-s,Math.PI,0),t.stroke())}});var g=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};g.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,s=Math.max(i,n,a),o=Math.min(i,n,a),l=(s+o)/2,d=s-o;if(s===o)t=e=0;else{switch(e=l>.5?d/(2-s-o):d/(s+o),s){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,s=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,o=1-s,l=[i.rgb[0]*s+t.rgb[0]*o,i.rgb[1]*s+t.rgb[1]*o,i.rgb[2]*s+t.rgb[2]*o],d=i.alpha*n+t.alpha*(1-n);return new g(l,d)}};var b=function(t,e,i,n){this.start_color=new g(t),this.end_color=new g(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new 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v=0,g=f.length;v<g;v++)a=f[v],r=m(a[1]),s=m(a[2]),o=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,o,s-r,l-o);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,s,o,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,s=null;return"-"===e?(s="deletion",r=t.length):0===t.indexOf(e)&&i>n?(s="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(s="insertion",r=n-i,a=n),null!==s?{type:s,start:a,len:r}:{}},v=Math.max(1,Math.floor(n)),g=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===g&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],s=r[1],o=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(o,t);return a.extend(e,i)}),!(s<this.view_start||s>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(s+l[_].start,n),t.fillRect(h,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var $=c/d.length,T=Math.ceil(this.prefs.summary_height*$);t.fillRect(h,f-T,v,T),f-=T}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(s+u.start,n),"snp"===u.type){var S=u.value;t.fillStyle=this.base_color_fn(S),k.draw_details?t.fillText(S,this.get_draw_pos(s,n),f+b):t.fillRect(h,f+1,v,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(s.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var o=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){s.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,s=!1,o=t(this).parents(".slider-row");o.addClass("input"),n.slider("option","values")&&(r=2*r+1,s=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),o.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(s){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(s?"values":"value",l),o.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=o("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=o("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=s.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),s=i.filters,o=0;o<s.length;o++)"number"===s[o].type?(n=new l(s[o]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var s=[];for(var o in a)s[s.length]=[o,a[o]];!function e(i,n){var a=n[0],r=a[0],s=a[1],o="("+s.join(") and (")+")",l={cond:o,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,s)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var o=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(s.makeBwg(o)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:o}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function s(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function o(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(s(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),s=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==v)i.type="bigwig";else{if(d!=b)return d==g||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=s[2],i.numZoomLevels=s[3],i.chromTreeOffset=o(r,8),i.unzoomedDataOffset=o(r,16),i.unzoomedIndexOffset=o(r,24),i.fieldCount=s[16],i.definedFieldCount=s[17],i.asOffset=o(r,36),i.totalSummaryOffset=o(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=o(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=o(r,24*c+72),f=o(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,v=2291137574,g=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(s(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),s=(a[3],o(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=o(i,e);e+=8,c-=t.chromTreeOffset,s(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});s(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(s(a.bwg.url,this.cirTreeOffset,48)).then(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,s){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,s=4+32*a.cirBlockSize,o=0;o<t.length;++o){var u=new h(t[o],t[o]+s);i=i?f(i,u):u}for(var m=i.ranges(),v=0;v<m.length;++v){var g=m[v];p(t,g,e)}},p=function(t,e,i,o){e.max(),e.min();n.when(s(a.bwg.url,e.min(),e.max()-e.min())).then(function(s){for(var o=0;o<t.length;++o)e.contains(t[o])&&(_(s,t[o]-e.min(),i),t[o]-a.cirTreeOffset==48&&t[o]-e.min()==0&&(a.cachedCirRoot=s),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var s=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=s[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16),y=o(s,a+24);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var o=[],l=function(t,e,n,r){r||(r={});var s=new i;s._chromId=t,s.segment=a.bwg.idsToChroms[t],s.min=e,s.max=n,s.type=a.bwg.type;for(var l in r)s[l]=r[l];o.push(s)},d=function(){if(0===e.length){Date.now();return r.resolve(o)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(s(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,s=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,s.size-2);else{var o=new Uint8Array(s.size);m(new Uint8Array(t,i,s.size),0,o,0,s.size),r=o.buffer}s.data=r,i+=s.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=o[8*c],_=o[8*c+1],m=o[8*c+2],v=o[8*c+3],g=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/v,maxScore:g};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),u=o[0],y=o[1],x=(o[2],o[3]),k=o[4],C=r[20],d=s[11];if(3==C)for(var c=0;c<d;++c){var T=l[c+6],S=y+c*x+1,M=y+c*x+k;i(u,S,M)&&e(u,S,M,{score:T})}else if(2==C)for(var c=0;c<d;++c){var _=o[2*c+6]+1,m=_+k-1,T=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:T})}else if(1==C)for(var c=0;c<d;++c){var _=o[3*c+6]+1,m=o[3*c+7],T=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:T})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var T=parseInt(P[1]);isNaN(T)||(j.score=T)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];$.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var B=0|P[3],V=0|P[4],I=0|P[6],N=P[7].split(","),L=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<I;++W){var K=(0|L[W])+_,Z=K+(0|N[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(V>B){var at="+"==j.orientation?new h(B,V+3):new h(B-3,V),rt=p(tt,at);if(rt){j.type="translation";for(var st=rt.ranges(),ot=0,lt=0;st[0].min()>et[lt].max();)lt++;for(var it=0;it<st.length;++it){var dt=it;"-"==j.orientation&&(dt=st.length-it-1);var nt=st[dt];if(j.readframe=ot,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();ot=(ot+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,s=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var s=new h(t[r],t[r]+n);i=i?f(i,s):s}for(var o=i.ranges(),l=0;l<o.length;++l){var c=o[l];u(t,c,e)}}),u=function(s,o,l,c){o.max(),o.min();a.bwg.data.slice(o.min(),o.max()-o.min()).fetch(function(c){for(var u=0;u<s.length;++u)if(o.contains(s[u])&&(p(c,s[u]-o.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,s){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,s=0;s<t.length;++s){var o=t[s],l=o._chromId,d=o.min,c=o.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=o,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=o(h,d+16),C=o(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>s||y==s&&x>l)||i>0&&(b<s||b==s&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,s=i<0?y:b)),d+=32}else{for(var $=-1,T=-1,v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=p[g+4]<<32|p[g+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&($<0||x>T)&&($=k,T=i<0?x:w,i<0?y:b),d+=24}$>=0&&c([$],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var s;return s=t<0?this.getUnzoomedView():this.getZoomedView(t),s.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var o=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&o.push(l[d]);return a(o)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(s){return r.topLevelReductionCache=s,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];s._tsFetch(t.zoom,t.chr,t.min,t.max,function(s){var o=i>0?0:3e8;t.fromRef&&(o=e);for(var d=0;d<s.length;++d){var c,u=s[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>o)return a(u)}else u.max>o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<o)return a(u)}else u.min<o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var s=this,o=this.chromsToIDs[t],l=[{chrOrd:0,chr:o,zoom:s.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(o+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:s.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(s(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,s=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,o=r.exec(n);if(o){var l={declType:o[1],name:o[2],comment:o[4],fields:[]};n=n.substring(o[0]);for(var d=s.exec(n);null!=d;d=s.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return t(null);this.data.slice(this.extHeaderOffset,64).fetch(function(i){if(!i)return t(null,"Couldn't fetch extension header");var n=new Uint8Array(i),a=new Int16Array(i),r=(new Int32Array(i),a[0],a[1]),s=o(n,4);if(0==r)return t(null);e.data.slice(s,20*r).fetch(function(i){if(!i)return t(null,"Couldn't fetch index info");for(var n=new Uint8Array(i),a=new Int16Array(i),s=(new Int32Array(i),[]),l=0;l<r;++l){var d=a[10*l],c=a[10*l+1],h=o(n,20*l+4),f=a[10*l+8],p=new u(e,d,c,h,f);s.push(p)}t(s)})})},u.prototype.lookup=function(t,e){var i=this;this.bbi.data.slice(this.offset,32).fetch(function(n){function a(n){i.bbi.data.slice(n,4+d*(c+u)).fetch(function(n){var s=new Uint8Array(n),l=new Uint16Array(n),d=(new Uint32Array(n),s[0]),h=l[1],f=4;if(0!=d){for(var p=0;p<h;++p){for(var _="",m=0;m<c;++m){var v=s[f++];0!=v&&(_+=String.fromCharCode(v))}if(_==t){var g=o(s,f),b=r(s,f+8);return i.bbi.getUnzoomedView().fetchFeatures(function(e,n,a,r){if(r&&r.length>i.field-3)return r[i.field-3]==t},[{offset:g,size:b}],e)}f+=u}return e([])}for(var w=null,p=0;p<h;++p){for(var _="",m=0;m<c;++m){var v=s[f++];0!=v&&(_+=String.fromCharCode(v))}var y=o(s,f);if(f+=8,t.localeCompare(_)<0&&w)return void a(w);w=y}a(w)})}var s=new Uint8Array(n),l=(new Int16Array(n),new Int32Array(n)),d=(l[0],l[1]),c=l[2],u=l[3];o(s,16);a(i.offset+32)})},{makeBwg:c}}.apply(e,a))&&(t.exports=r)}).call(e,i(0))},function(t,e,i){var n,a;n=[],void 0!==(a=function(){"use strict";function t(t,e){if("number"!=typeof t||"number"!=typeof e)throw"Bad range "+t+","+e;this._min=t,this._max=e}function e(t){var e=t.sort(s),i=[],n=e.shift();e.forEach(function(t){t._min<=n._max?t._max>n._max&&(n._max=t._max):(i.push(n),n=t)}),i.push(n),this._ranges=i}function i(t,i){return t instanceof e||(t instanceof Array||(t=[t]),t=new e(t)),i&&t.insertRange(i),t}function n(i,n){for(var a=i.ranges(),r=n.ranges(),s=a.length,o=r.length,l=0,d=0,c=[];l<s&&d<o;){var i=a[l],n=r[d],u=Math.max(i.min(),n.min()),h=Math.min(i.max(),n.max());h>=u&&c.push(new t(u,h)),i.max()>n.max()?++d:++l}return 0==c.length?null:1==c.length?c[0]:new e(c)}function a(t){for(var e=0,i=t.ranges(),n=0;n<i.length;++n){var a=i[n];e+=a.max()-a.min()+1}return e}function r(t,e){return t.min()<e.min()?-1:t.min()>e.min()?1:t.max()<e.max()?-1:e.max()>t.max()?1:0}function s(t,e){return t._min<e._min?-1:t._min>e._min?1:t._max<e._max?-1:e._max>t._max?1:0}return t.prototype.min=function(){return this._min},t.prototype.max=function(){return this._max},t.prototype.contains=function(t){return t>=this._min&&t<=this._max},t.prototype.isContiguous=function(){return!0},t.prototype.ranges=function(){return[this]},t.prototype._pushRanges=function(t){t.push(this)},t.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},e.prototype.min=function(){return this._ranges[0].min()},e.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},e.prototype.lower_bound=function(t){var e=this.ranges();if(t>this.max())return e.length;if(t<this.min())return 0;for(var i=0,n=e.length-1;i<=n;){var a=Math.floor((i+n)/2);if(t>e[a]._max)i=a+1;else{if(!(t<e[a]._min))return a;n=a-1}}return i},e.prototype.contains=function(t){var e=this.lower_bound(t);return!!(e<this._ranges.length&&this._ranges[e].contains(t))},e.prototype.insertRange=function(t){var e=this.lower_bound(t._min);if(e===this._ranges.length)return void this._ranges.push(t);var i=this.ranges();if(t._max<i[e]._min)return void this._ranges.splice(e,0,t);i[e]._min<t._min&&(t._min=i[e]._min);for(var n=e+1;n<i.length&&i[n]._min<=t._max;)n++;n--,i[n]._max>t._max&&(t._max=i[n]._max),this._ranges.splice(e,n-e+1,t)},e.prototype.isContiguous=function(){return this._ranges.length>1},e.prototype.ranges=function(){return this._ranges},e.prototype._pushRanges=function(t){for(var e=0;e<this._ranges.length;++e)t.push(this._ranges[e])},e.prototype.toString=function(){for(var t="",e=0;e<this._ranges.length;++e)e>0&&(t+=","),t+=this._ranges[e].toString();return t},{Range:t,union:i,intersection:n,coverage:a,rangeOver:r,_rangeOrder:s}}.apply(e,n))&&(t.exports=a)},function(t,e,i){var n,a;n=[],void 0!==(a=function(){function t(){}function e(){this.was=[0]}function i(t,e,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=e,this.mode=v,this.reset(t,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function r(t,e,i,n,a){return t[0]=g,e[0]=b,i[0]=w,n[0]=y,f}function s(t,e,i,n,a){if(0!=a){if(!t)throw"Undef src";if(!i)throw"Undef dest";0==e&&a==t.length?l(t,i,n):O?l(t.subarray(e,e+a),i,n):1==t.BYTES_PER_ELEMENT&&a>100?l(new 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],v=0,g=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],$=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var T=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==T[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var S=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,o,l,d,c;for(o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case v:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],g=[];r(u,h,_,g,t),this.codes.init(u[0],h[0],_[0],0,g[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),s(t.next_in,o,this.window,d,i),o+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:v;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}this.blens[S[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[S[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),g=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,g,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,g[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){s(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,s){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,s,o,l,d,c=0,u=0,h=0;for(h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o;;)switch(this.mode){case 0:if(l>=258&&s>=10&&(t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=o-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);t.window[o++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,t.window[o++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,s++,h--),t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,o,l){var d,c,u,h,_,v,g,b,w,y,x,k,C,$,T,S;g=l.next_in_index,b=l.avail_in,_=o.bitb,v=o.bitk,w=o.write,y=w<o.read?o.read-w-1:o.end-w,x=m[t],k=m[e];do{for(;v<20;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if(d=_&x,c=i,u=n,S=3*(u+d),0!=(h=c[S]))for(;;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15,C=c[S+2]+(_&m[h]),_>>=h,v-=h;v<15;)b--,_|=(255&l.next_in[g++])<<v,v+=8;for(d=_&k,c=a,u=r,S=3*(u+d),h=c[S];;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15;v<h;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if($=c[S+2]+(_&m[h]),_>>=h,v-=h,y-=C,w>=$)T=w-$,o.window[w++]=o.window[T++],o.window[w++]=o.window[T++],C-=2;else{T=w-$;do{T+=o.end}while(T<0);if(h=o.end-T,C>h){if(C-=h,w-T>0&&h>w-T)do{o.window[w++]=o.window[T++]}while(0!=--h);else s(o.window,T,o.window,w,h),w+=h,T+=h,h=0;T=0}}do{o.window[w++]=o.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3;d+=c[S+2],d+=_&m[h],S=3*(u+d),h=c[S]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3);if(d+=c[S+2],d+=_&m[h],S=3*(u+d),0==(h=c[S])){_>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--;break}}else _>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,o,l,d,c,h){var p,m,v,g,b,w,y,x,k,C,$,T,S,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return o[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(v=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,S=2;0!=--b;)this.x[S]=w+=this.c[C],S++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[v],this.x[0]=b=0,C=0,g=-1,T=-x,this.u[0]=0,$=0,O=0;y<=v;y++)for(p=this.c[y];0!=p--;){for(;y>T+x;){if(g++,T+=x,O=v-T,O=O>x?x:O,(m=1<<(w=y-T))>p+1&&(m-=p+1,S=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++S]);)m-=this.c[S];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[g]=$=this.hn[0],this.hn[0]+=O,0!=g?(this.x[g]=b,this.r[0]=w,this.r[1]=x,w=b>>>T-x,this.r[2]=$-this.u[g-1]-w,s(this.r,0,d,3*(this.u[g-1]+w),3)):o[0]=$}for(this.r[1]=y-T,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-T,w=b>>>T;w<O;w+=m)s(this.r,0,d,3*($+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<T)-1;(b&k)!=this.x[g];)g--,T-=x,k=(1<<T)-1}return 0!=M&&1!=v?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,s,o,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,o,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,$,s,a,o,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;s(this.c,0,this.u,0,15),s(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:s}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,s;!function(n,o){r=[i(0)],a=o,void 0!==(s="function"==typeof a?a.apply(e,r):a)&&(t.exports=s)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},s={},o=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in s)s[t]()}),i.cors=!!o&&"withCredentials"in o,i.ajax=o=!!o,t.ajaxTransport("native",function(t){var e;if(i.cors||o&&!t.crossDomain)return{send:function(i,n){var o,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(o in 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e.default=t,e}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=(a(r),i(1)),o=a(s),l=i(8),d=n(l),c=i(7),u=n(c),h=o.Model.extend(d.default.LoggableMixin).extend({_logNamespace:"user",urlRoot:function(){return Galaxy.root+"api/users"},defaults:{id:null,username:"("+(0,u.default)("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(t){this.log("User.initialize:",t),this.on("loaded",function(t,e){this.log(this+" has loaded:",t,e)}),this.on("change",function(t,e){this.log(this+" has changed:",t,e.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(t,e){t=t||h.CURRENT_ID_STR,e=e||{};var i=this,n=e.success;return e.success=function(t,e){i.trigger("loaded",t,e),n&&n(t,e)},t===h.CURRENT_ID_STR&&(e.url=this.urlRoot+"/"+h.CURRENT_ID_STR),o.Model.prototype.fetch.call(this,e)},clearSessionStorage:function(){for(var t in sessionStorage)0===t.indexOf("history:")?sessionStorage.removeItem(t):"history-panel"===t&&sessionStorage.removeItem(t)},toString:function(){var t=[this.get("username")];return this.get("id")&&(t.unshift(this.get("id")),t.push(this.get("email"))),"User("+t.join(":")+")"}});h.CURRENT_ID_STR="current",h.getCurrentUserFromApi=function(t){var e=new h;return e.loadFromApi(h.CURRENT_ID_STR,t),e};o.Collection.extend(d.default.LoggableMixin).extend({model:h,urlRoot:function(){return Galaxy.root+"api/users"}});e.default={User:h}},,function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=(a(r),i(161)),o=a(s),l=i(163),d=a(l),c=i(164),u=a(c),h=t.View.extend({initialize:function(t){var e=this;this.options=t,this.setElement(this._template()),this.$navbarBrandLink=this.$(".navbar-brand-link"),this.$navbarBrandImage=this.$(".navbar-brand-image"),this.$navbarBrandTitle=this.$(".navbar-brand-title"),this.$navbarTabs=this.$(".navbar-tabs"),this.$quoteMeter=this.$(".quota-meter-container"),this.collection=new o.default.Collection,this.collection.on("add",function(t){e.$navbarTabs.append(new o.default.Tab({model:t}).render().$el)}).on("reset",function(){e.$navbarTabs.empty()}).on("dispatch",function(t){e.collection.each(function(e){t(e)})}).fetch(this.options),Galaxy.frame=this.frame=new d.default({collection:this.collection}),Galaxy.quotaMeter=this.quotaMeter=new u.default.UserQuotaMeter({model:Galaxy.user,el:this.$quoteMeter}),n(window).on("click",function(t){var e=n(t.target).closest("a[download]");1==e.length&&(0===n("iframe[id=download]").length&&n("body").append(n("<iframe/>").attr("id","download").hide()),n("iframe[id=download]").attr("src",e.attr("href")),t.preventDefault())}).on("beforeunload",function(){var t="";if(e.collection.each(function(e){var i=e.get("onbeforeunload")&&e.get("onbeforeunload")();i&&(t+=i+" ")}),""!==t)return t})},render:function(){return this.$navbarBrandTitle.html("Galaxy "+(this.options.brand&&"/ "+this.options.brand||"")),this.$navbarBrandLink.attr("href",this.options.logo_url),this.$navbarBrandImage.attr("src",this.options.logo_src),this.quotaMeter.render(),this},_template:function(){return'<div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div class="navbar-header"><div class="navbar-tabs"/></div><div class="navbar-brand"><a class="navbar-brand-link"><img class="navbar-brand-image"/><span class="navbar-brand-title"/></a></div><div class="quota-meter-container"/><div class="navbar-icons"/></div>'}});e.default={View:h}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a,r){function s(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(162),l=s(o),d=i(40),c=s(d),u=i(7),h=s(u),f=i(3),p=s(f),_=t.Collection.extend({model:t.Model.extend({defaults:{visible:!0,target:"_parent"}}),fetch:function(t){t=t||{},this.reset();var e=new l.default.GenericNavView;this.add(e.render()),this.add({id:"analysis",title:(0,h.default)("Analyze Data"),url:"",tooltip:(0,h.default)("Analysis home view")}),this.add({id:"workflow",title:(0,h.default)("Workflow"),tooltip:(0,h.default)("Chain tools into workflows"),disabled:!Galaxy.user.id,url:"workflows/list"}),this.add({id:"shared",title:(0,h.default)("Shared Data"),url:"library/index",tooltip:(0,h.default)("Access published resources"),menu:[{title:(0,h.default)("Data Libraries"),url:"library/list"},{title:(0,h.default)("Histories"),url:"histories/list_published"},{title:(0,h.default)("Workflows"),url:"workflows/list_published"},{title:(0,h.default)("Visualizations"),url:"visualizations/list_published"},{title:(0,h.default)("Pages"),url:"pages/list_published"}]}),this.add({id:"visualization",title:(0,h.default)("Visualization"),url:"visualizations/list",tooltip:(0,h.default)("Visualize datasets"),disabled:!Galaxy.user.id,menu:[{title:(0,h.default)("New Track Browser"),url:"visualization/trackster",target:"_frame"},{title:(0,h.default)("Saved Visualizations"),url:"visualizations/list",target:"_frame"},{title:(0,h.default)("Interactive Environments"),url:"visualization/gie_list",target:"galaxy_main"}]}),c.default.add({url:"api/webhooks/masthead/all",callback:function(t){n(document).ready(function(){n.each(t.models,function(t,e){var i=e.toJSON();if(i.activate){var n={id:i.name,icon:i.config.icon,url:i.config.url,tooltip:i.config.tooltip,onclick:i.config.function&&new Function(i.config.function)};Galaxy.page?Galaxy.page.masthead.collection.add(n):Galaxy.masthead&&Galaxy.masthead.collection.add(n),p.default.appendScriptStyle(i)}})})}}),Galaxy.user.get("is_admin")&&this.add({id:"admin",title:(0,h.default)("Admin"),url:"admin",tooltip:(0,h.default)("Administer this Galaxy"),cls:"admin-only"});var i={id:"help",title:(0,h.default)("Help"),tooltip:(0,h.default)("Support, contact, and community"),menu:[{title:(0,h.default)("Support"),url:t.support_url,target:"_blank"},{title:(0,h.default)("Search"),url:t.search_url,target:"_blank"},{title:(0,h.default)("Mailing Lists"),url:t.mailing_lists,target:"_blank"},{title:(0,h.default)("Videos"),url:t.screencasts_url,target:"_blank"},{title:(0,h.default)("Wiki"),url:t.wiki_url,target:"_blank"},{title:(0,h.default)("How to Cite Galaxy"),url:t.citation_url,target:"_blank"},{title:(0,h.default)("Interactive Tours"),url:"tours"}]};t.terms_url&&i.menu.push({title:(0,h.default)("Terms and Conditions"),url:t.terms_url,target:"_blank"}),t.biostar_url&&i.menu.unshift({title:(0,h.default)("Ask a question"),url:"biostar/biostar_question_redirect",target:"_blank"}),t.biostar_url&&i.menu.unshift({title:(0,h.default)("Galaxy Biostar"),url:t.biostar_url_redirect,target:"_blank"}),this.add(i);var r={};r=Galaxy.user.id?{id:"user",title:(0,h.default)("User"),cls:"loggedin-only",tooltip:(0,h.default)("Account and saved data"),menu:[{title:(0,h.default)("Logged in as")+" "+Galaxy.user.get("email")},{title:(0,h.default)("Preferences"),url:"user"},{title:(0,h.default)("Custom Builds"),url:"custom_builds"},{title:(0,h.default)("Logout"),url:"user/logout?session_csrf_token="+Galaxy.session_csrf_token,target:"_top",divider:!0},{title:(0,h.default)("Saved Histories"),url:"histories/list",target:"_top"},{title:(0,h.default)("Saved Datasets"),url:"datasets/list",target:"_top"},{title:(0,h.default)("Saved Pages"),url:"pages/list",target:"_top"}]}:t.allow_user_creation?{id:"user",title:(0,h.default)("Login or Register"),cls:"loggedout-only",tooltip:(0,h.default)("Account registration or login"),menu:[{title:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},{title:(0,h.default)("Register"),url:"user/create",target:"galaxy_main",noscratchbook:!0}]}:{id:"user",title:(0,h.default)("Login"),cls:"loggedout-only",tooltip:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},this.add(r);var s=this.get(t.active_view);return s&&s.set("active",!0),(new a.Deferred).resolve().promise()}}),m=t.View.extend({initialize:function(t){this.model=t.model,this.setElement(this._template()),this.$dropdown=this.$(".dropdown"),this.$toggle=this.$(".dropdown-toggle"),this.$menu=this.$(".dropdown-menu"),this.$note=this.$(".dropdown-note"),this.listenTo(this.model,"change",this.render,this)},events:{"click .dropdown-toggle":"_toggleClick"},render:function(){var t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa "+this.model.get("icon")).addClass(this.model.get("toggle")&&"toggle").attr("target",this.model.get("target")).attr("href",this.model.get("url")).attr("title",this.model.get("tooltip")).tooltip("destroy"),this.model.get("tooltip")&&this.$toggle.tooltip({placement:"bottom"}),this.$dropdown.removeClass().addClass("dropdown").addClass(this.model.get("disabled")&&"disabled").addClass(this.model.get("active")&&"active"),this.model.get("menu")&&this.model.get("show_menu")?(this.$menu.show(),n("#dd-helper").show().off().on("click",function(){n("#dd-helper").hide(),t.model.set("show_menu",!1)})):(t.$menu.hide(),n("#dd-helper").hide()),this.$menu.empty().removeClass("dropdown-menu"),this.model.get("menu")&&(r.each(this.model.get("menu"),function(e){t.$menu.append(t._buildMenuItem(e)),e.divider&&t.$menu.append(n("<li/>").addClass("divider"))}),t.$menu.addClass("dropdown-menu"),t.$toggle.append(n("<b/>").addClass("caret"))),this},_buildMenuItem:function(t){var e=this;return t=r.defaults(t||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),t.url=e._formatUrl(t.url),n("<li/>").append(n("<a/>").attr("href",t.url).attr("target",t.target).html(t.title).on("click",function(i){i.preventDefault(),e.model.set("show_menu",!1),t.onclick?t.onclick():Galaxy.frame.add(t)}))},_toggleClick:function(t){var e=this,i=this.model;if(t.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(t){i.id!==t.id&&t.get("menu")&&t.set("show_menu",!1)}),i.get("disabled")){var a=function(t,e){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+e).html(t)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){e.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),o=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+o,d=e+":"+i+l,c=null,u=null,h='<iframe class="f-iframe fade in communication-iframe" src="'+d+'"> </iframe>';return n(".chat-modal").length>0&&n(".chat-modal").remove(),s.modal=new r.default.View({body:h,height:350,width:600,closing_events:!0,title_separator:!1,cls:"ui-modal chat-modal"}),s.modal.show(),c=n(".chat-modal .modal-header"),u=n(".chat-modal .modal-body"),c.addClass("modal-header-body"),u.addClass("modal-header-body"),c.find("h4").remove(),c.removeAttr("min-height padding border"),c.append('<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i><i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i><i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>'),n(".close-modal").click(function(t){n(".chat-modal").css("display","none")}),n(".expand-compress-modal").click(function(t){n(".expand-compress-modal").hasClass("fa-expand")?(n(".chat-modal .modal-dialog").width("1000px"),n(".chat-modal 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No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. 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g=e.categorical_filters[r][v],b="",w="";for(var y in g)b=y,w=g[y];m&&(s+=" | "),m=!0;var h=n[r];h&&g[r]&&h==w?s+='<span class="categorical-filter '+r+'-filter current-filter">'+v+"</span>":s+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+v+"</a></span>"}s+="</span>"}return s+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=i(146),l=a(o),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),v=i(3),g=a(v);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){g.default.cssLoadFile("static/style/jquery.rating.css"),g.default.cssLoadFile("static/style/autocomplete_tagging.css"),g.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),g.default.cssLoadFile("static/style/library.css"),g.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){s.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),s=n("<div/>").addClass("position").appendTo(r),o=(n("<a href=''/>").text(t).appendTo(s).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);o.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var o=this,d=new l.default.TracksterView(s.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,s=e.start,c=e.end,u=e.overview;n&&void 0!==s&&c?d.change_chrom(n,s,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function s(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var o=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(o),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),v=i(149),g=a(v),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),T=a($),S=i(151),M=a(S);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,s,o,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){s=r.position().top,o=s+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<s)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>o)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),s=a.position().top,o=s+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=s&&i.offsetY<=o)return i.offsetY-s<o-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=T.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new T.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),s=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&s++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),s>1&&s===this.drawables.length){var o,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],l[o.name]=[o];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],o.name in l&&l[o.name].push(o);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===s&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var B=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=T.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,s=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(s),n.current_height=e.clientY,n.current_x=n.offsetX;var o=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(o)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,s=i.high-i.low,o=i.viewport_container.width();i.update_location(Math.round(a/o*s)+i.low,Math.round(r/o*s)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),s=i.high-i.low,o=i.viewport_container.width(),l=i.low;i.low=Math.round(a/o*s)+l,i.high=Math.round(r/o*s)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(B.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,s=i.chrom_data.length;r<s;r++){var o=i.chrom_data[r].chrom,l=t("<option>");l.text(o),l.val(o),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var s=0,o=a.drawables.length;s<o;s++){var l=a.drawables[s];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var V=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),N=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new I({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,s=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var o=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,o,!1);o.container_div.insertBefore(r.view.content_div.children()[l]),o.add_drawable(r),r.container_div.appendTo(o.content_div),t=o}else t=r.container;var d=new r.constructor(view,t,{name:s,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),L=function(t,e){g.default.Scaler.call(this,e),this.filter=t};L.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,s,o,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=o,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),s=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?s:[r].concat(s),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new V(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new N({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),s=this.view.resolution_px_b,o=1/s;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,s=r/(view.max_high-view.max_low),o=1/s),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*o),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,s,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,s,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",s="max"===e?"max":"min",o="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(o),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(o,r(e,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,s=1/i,o=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:o.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&o.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,s,o.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,s,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return o.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),s=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return o.tile_cache.set_elt(c,void 0),void t.when(o.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=s[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,v=o.view.canvas_manager.new_canvas(),g=e.get("start"),b=e.get("end"),w=Math.ceil((b-g)*i)+o.left_offset,y=l.max(_);v.width=w,v.height=n.height||y;var x=v.getContext("2d");x.translate(o.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(s[n],x,u[n],e,i,a)}),void 0!==m&&(o.tile_cache.set_elt(c,m),o.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new g.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,s=this.view.container.width(),o=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*s);o.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(o)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var s=t[a].html_elt.find("canvas").height();s>r&&(r=s)}for(a=0;a<t.length;a++){var o=t[a];o.html_elt.find("canvas").height()!==r&&(this.draw_helper(o.region,i,{force:!0,height:r}),o.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),s=r.data,o=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=s.length;l<d;l++)e.fillStyle=this.view.get_base_color(s[l]),e.fillText(s[l],Math.floor(l*a),10);return new G(this,n,a,o,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(s(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new g.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=g.default.ArcLinkedFeaturePainter:this.painter=g.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,s=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var o={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){o[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(o,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(s.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,o)}})}if(s.filters_manager){var c,u=s.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}s.filters_available!==p&&(s.filters_available=p,s.filters_available||s.filters_manager.hide(),s.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,s){var o=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,v=t.data.length;m<v;m++){for(var g,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(g=_[y],g.update_attrs(b),!g.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new L(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return o.view.get_base_color(t)}),T=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var S=$.draw(e,l.width,l.height,a,f);T=S.feature_mapper,incomplete_features=S.incomplete_features,T.translation=-u}return s?void 0:new F(o,n,a,l,t.data,i,t.message,p,T,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=g.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),s=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&s&&s.length>1){var o;if(0===this.container_div.find(".yaxislabel.variant").length&&(o=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":o+"px",top:(this.config.get_value("summary_height")-o)/2+"px"})),this.config.get_value("show_sample_data"))){var d=s.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}o=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":o,"line-height":o}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=g.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:B,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,s){var o=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(o.model)}).appendTo(this.icons_div),s&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var s=i.display_modes[a];n[s]=function(t){return function(){i.change_mode(t)}}(s)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t,e){this.slot=t,this.feature=e},o=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(o.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var s=0,o=r.length;s<o;s++){var l=r[s];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,o=0,l=t.length;o<l;o++){e=t[o],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(o)}for(var o=0,l=a.length;o<l;o++){e=t[a[o]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new s(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:o}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},s=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},o=function(t,e,i,n,a,r){void 0===r&&(r=4);var s,o=n-e,l=a-i,d=Math.floor(Math.sqrt(o*o+l*l)/r),c=o/d,u=l/d;for(s=0;s<d;s++,e+=c,i+=u)s%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,s=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,s),t.lineTo(r,s),t.lineTo(e,i),t.lineTo(a,s),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,s=this.prefs.min_value,o=this.prefs.max_value,l=o-s,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+s/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var v,g=this.prefs.block_color||this.prefs.color,b=parseInt(g.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,$=0,T=h.length;$<T;$++)if(t.fillStyle=t.strokeStyle=g,k=C=!1,v=m[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(_=h[$][1])){if(_<s?(C=!0,_=s):_>o&&(k=!0,_=o),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,v,-_);else if("Intensity"===u){var S=(_-s)/l,M=Math.round(w+(255-w)*(1-S)),O=Math.round(y+(255-y)*(1-S)),A=Math.round(x+(255-x)*(1-S));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,v,d)}else _=Math.round(d-(_-s)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=v:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=g}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,s){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=s||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,s=this.view_start,o=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],v=m[0],g=m[1],b=m[2],w=a&&void 0!==a[v]?a[v].slot:null;("Dense"===this.mode||null!==w)&&g<o&&b>s&&(l=this.draw_element(t,this.mode,m,w,s,o,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(g<s||b>o)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,s,o,l){return[0,0]}});var _=function(t,e,i,n,a,r,s){p.call(this,t,e,i,n,a,r,s),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,s,o,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*s)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*s))),m=p,v=_,d=("Dense"===e?0:0+n)*o+this.get_top_padding(l),g=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(g=Math.floor(Math.max(0,(x-a)*s)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*s))));var T,S;if("Squish"===e?(T=1,S=3,$=!1):(T=5,S=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=S):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*s)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*s)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(S-T)/2+1,q-j,T),void 0!==g&&k>x&&!(j>b||q<g)){var D=Math.max(j,g),B=Math.min(q,b);t.fillRect(D,d+1,B-D,S),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<B&&(D+=2,B-=2),t.fillRect(D,d+1,B-D,S))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var V=this.height_scaler.gen_val(i),I=Math.ceil(S*V),N=Math.round((S-I)/2);1!==V&&(t.fillRect(p,M+1,_-p,N),t.fillRect(p,M+S-N+1,_-p,N))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,S),f&&$&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,S));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),v+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,v]}});var m=function(t,e,i,n,a,r,s,o,l){p.call(this,t,e,i,n,a,r,s),this.ref_seq=o?o.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,s=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),s=t.slice(-1);return"N"===s?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(s)&&(n[1]+=a,r+=a),[e.indexOf(s),a]});return{blocks:i,cigar:s}},draw_read:function(t,e,i,n,a,o,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,o],v=0,g=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,$=n+1,T=new x(t,C,i,e),S=[],M=[],O=this._parse_cigar(c);c=O.cigar,S=O.blocks;for(var A=0;A<S.length;A++){var E=S[A];s([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,$,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+v;if(p=f(D),_=f(D+q),s([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var B="";"X"===j?B=h.slice(g,g+q):this.ref_seq&&(B=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,o-a)));for(var V=Math.max(D,a),I=0;I<B.length;I++)if(B&&!this.prefs.show_differences||"X"===j){var N=Math.floor(Math.max(0,(V+I-a)*i));t.fillStyle=this.base_color_fn(B[I]),k&&i>w?t.fillText(B[I],N,n+9):i>.05&&t.fillRect(N-b,$,Math.max(1,Math.round(i)),C)}"X"===j&&(g+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,$+(C-1)/2,_-p,1),v+=q;break;case"D":T.draw_deletion(p,$,q),v+=q;break;case"I":var L=p-b;if(s([D,D+q],m)){var G=h.slice(g,g+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[L,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-o);break;case 1005:break;case 1002:G=G.slice(a-D,D-o)}for(var I=0,F=G.length;I<F;I++){var N=Math.floor(Math.max(0,(D+I-a)*i));t.fillText(G[I],N-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,L,n+9]})}g+=q}else v=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(v,j,q),g=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(g,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,s,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*s,(c-a-.5)*s)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*s))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var v=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,s,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):v=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,s,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):v=!1;var g=Math.ceil(Math.min(d,Math.max(-.5*s,(i[4][1]-a-.5)*s))),b=Math.floor(Math.max(-.5*s,(i[5][0]-a-.5)*s));if(v&&b>g){t.fillStyle="#ccc";var w=_+1+(m-1)/2;o(t,g,w,b,w)}}else this.draw_read(t,e,s,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,i,n,a,r,s){_.call(this,t,e,i,n,a,r,s),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var s=(i+n)/2,o=n-s;Math.PI;o>0&&(t.beginPath(),t.arc(s,r,n-s,Math.PI,0),t.stroke())}});var g=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};g.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,s=Math.max(i,n,a),o=Math.min(i,n,a),l=(s+o)/2,d=s-o;if(s===o)t=e=0;else{switch(e=l>.5?d/(2-s-o):d/(s+o),s){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,s=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,o=1-s,l=[i.rgb[0]*s+t.rgb[0]*o,i.rgb[1]*s+t.rgb[1]*o,i.rgb[2]*s+t.rgb[2]*o],d=i.alpha*n+t.alpha*(1-n);return new g(l,d)}};var b=function(t,e,i,n){this.start_color=new g(t),this.end_color=new g(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,s;if(void 0===this.prefs.min_value){var o=1/0;for(r=0,s=this.data.length;r<s;r++)o=Math.min(o,this.data[r][6]);this.prefs.min_value=o}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,s=this.data.length;r<s;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,s,o,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,g=f.length;v<g;v++)a=f[v],r=m(a[1]),s=m(a[2]),o=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,o,s-r,l-o);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,s,o,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,s=null;return"-"===e?(s="deletion",r=t.length):0===t.indexOf(e)&&i>n?(s="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(s="insertion",r=n-i,a=n),null!==s?{type:s,start:a,len:r}:{}},v=Math.max(1,Math.floor(n)),g=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===g&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],s=r[1],o=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(o,t);return a.extend(e,i)}),!(s<this.view_start||s>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(s+l[_].start,n),t.fillRect(h,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var $=c/d.length,T=Math.ceil(this.prefs.summary_height*$);t.fillRect(h,f-T,v,T),f-=T}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(s+u.start,n),"snp"===u.type){var S=u.value;t.fillStyle=this.base_color_fn(S),k.draw_details?t.fillText(S,this.get_draw_pos(s,n),f+b):t.fillRect(h,f+1,v,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(s.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var o=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){s.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,s=!1,o=t(this).parents(".slider-row");o.addClass("input"),n.slider("option","values")&&(r=2*r+1,s=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),o.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(s){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(s?"values":"value",l),o.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=o("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=o("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=s.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),s=i.filters,o=0;o<s.length;o++)"number"===s[o].type?(n=new l(s[o]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var s=[];for(var o in a)s[s.length]=[o,a[o]];!function e(i,n){var a=n[0],r=a[0],s=a[1],o="("+s.join(") and (")+")",l={cond:o,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,s)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var o=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(s.makeBwg(o)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:o}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function s(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function o(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(s(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),s=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==v)i.type="bigwig";else{if(d!=b)return d==g||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=s[2],i.numZoomLevels=s[3],i.chromTreeOffset=o(r,8),i.unzoomedDataOffset=o(r,16),i.unzoomedIndexOffset=o(r,24),i.fieldCount=s[16],i.definedFieldCount=s[17],i.asOffset=o(r,36),i.totalSummaryOffset=o(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=o(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=o(r,24*c+72),f=o(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,v=2291137574,g=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(s(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),s=(a[3],o(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=o(i,e);e+=8,c-=t.chromTreeOffset,s(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});s(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(s(a.bwg.url,this.cirTreeOffset,48)).then(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,s){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,s=4+32*a.cirBlockSize,o=0;o<t.length;++o){var u=new h(t[o],t[o]+s);i=i?f(i,u):u}for(var m=i.ranges(),v=0;v<m.length;++v){var g=m[v];p(t,g,e)}},p=function(t,e,i,o){e.max(),e.min();n.when(s(a.bwg.url,e.min(),e.max()-e.min())).then(function(s){for(var o=0;o<t.length;++o)e.contains(t[o])&&(_(s,t[o]-e.min(),i),t[o]-a.cirTreeOffset==48&&t[o]-e.min()==0&&(a.cachedCirRoot=s),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var s=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=s[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16),y=o(s,a+24);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var o=[],l=function(t,e,n,r){r||(r={});var s=new i;s._chromId=t,s.segment=a.bwg.idsToChroms[t],s.min=e,s.max=n,s.type=a.bwg.type;for(var l in r)s[l]=r[l];o.push(s)},d=function(){if(0===e.length){Date.now();return r.resolve(o)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(s(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,s=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,s.size-2);else{var o=new Uint8Array(s.size);m(new Uint8Array(t,i,s.size),0,o,0,s.size),r=o.buffer}s.data=r,i+=s.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=o[8*c],_=o[8*c+1],m=o[8*c+2],v=o[8*c+3],g=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/v,maxScore:g};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),u=o[0],y=o[1],x=(o[2],o[3]),k=o[4],C=r[20],d=s[11];if(3==C)for(var c=0;c<d;++c){var T=l[c+6],S=y+c*x+1,M=y+c*x+k;i(u,S,M)&&e(u,S,M,{score:T})}else if(2==C)for(var c=0;c<d;++c){var _=o[2*c+6]+1,m=_+k-1,T=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:T})}else if(1==C)for(var c=0;c<d;++c){var _=o[3*c+6]+1,m=o[3*c+7],T=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:T})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var T=parseInt(P[1]);isNaN(T)||(j.score=T)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];$.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var B=0|P[3],V=0|P[4],I=0|P[6],N=P[7].split(","),L=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<I;++W){var K=(0|L[W])+_,Z=K+(0|N[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(V>B){var at="+"==j.orientation?new h(B,V+3):new h(B-3,V),rt=p(tt,at);if(rt){j.type="translation";for(var st=rt.ranges(),ot=0,lt=0;st[0].min()>et[lt].max();)lt++;for(var it=0;it<st.length;++it){var dt=it;"-"==j.orientation&&(dt=st.length-it-1);var nt=st[dt];if(j.readframe=ot,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();ot=(ot+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,s=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var s=new h(t[r],t[r]+n);i=i?f(i,s):s}for(var o=i.ranges(),l=0;l<o.length;++l){var c=o[l];u(t,c,e)}}),u=function(s,o,l,c){o.max(),o.min();a.bwg.data.slice(o.min(),o.max()-o.min()).fetch(function(c){for(var u=0;u<s.length;++u)if(o.contains(s[u])&&(p(c,s[u]-o.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,s){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,s=0;s<t.length;++s){var o=t[s],l=o._chromId,d=o.min,c=o.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=o,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=o(h,d+16),C=o(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>s||y==s&&x>l)||i>0&&(b<s||b==s&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,s=i<0?y:b)),d+=32}else{for(var $=-1,T=-1,v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=p[g+4]<<32|p[g+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&($<0||x>T)&&($=k,T=i<0?x:w,i<0?y:b),d+=24}$>=0&&c([$],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var s;return s=t<0?this.getUnzoomedView():this.getZoomedView(t),s.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var o=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&o.push(l[d]);return a(o)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(s){return r.topLevelReductionCache=s,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];s._tsFetch(t.zoom,t.chr,t.min,t.max,function(s){var o=i>0?0:3e8;t.fromRef&&(o=e);for(var d=0;d<s.length;++d){var c,u=s[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>o)return a(u)}else u.max>o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<o)return a(u)}else u.min<o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var s=this,o=this.chromsToIDs[t],l=[{chrOrd:0,chr:o,zoom:s.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(o+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:s.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(s(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,s=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,o=r.exec(n);if(o){var l={declType:o[1],name:o[2],comment:o[4],fields:[]};n=n.substring(o[0]);for(var d=s.exec(n);null!=d;d=s.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var T=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==T[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var S=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,o,l,d,c;for(o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case v:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],g=[];r(u,h,_,g,t),this.codes.init(u[0],h[0],_[0],0,g[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),s(t.next_in,o,this.window,d,i),o+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:v;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}this.blens[S[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[S[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),g=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,g,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,g[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){s(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,s){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,s,o,l,d,c=0,u=0,h=0;for(h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o;;)switch(this.mode){case 0:if(l>=258&&s>=10&&(t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=o-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);t.window[o++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,t.window[o++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,s++,h--),t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,o,l){var d,c,u,h,_,v,g,b,w,y,x,k,C,$,T,S;g=l.next_in_index,b=l.avail_in,_=o.bitb,v=o.bitk,w=o.write,y=w<o.read?o.read-w-1:o.end-w,x=m[t],k=m[e];do{for(;v<20;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if(d=_&x,c=i,u=n,S=3*(u+d),0!=(h=c[S]))for(;;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15,C=c[S+2]+(_&m[h]),_>>=h,v-=h;v<15;)b--,_|=(255&l.next_in[g++])<<v,v+=8;for(d=_&k,c=a,u=r,S=3*(u+d),h=c[S];;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15;v<h;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if($=c[S+2]+(_&m[h]),_>>=h,v-=h,y-=C,w>=$)T=w-$,o.window[w++]=o.window[T++],o.window[w++]=o.window[T++],C-=2;else{T=w-$;do{T+=o.end}while(T<0);if(h=o.end-T,C>h){if(C-=h,w-T>0&&h>w-T)do{o.window[w++]=o.window[T++]}while(0!=--h);else s(o.window,T,o.window,w,h),w+=h,T+=h,h=0;T=0}}do{o.window[w++]=o.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3;d+=c[S+2],d+=_&m[h],S=3*(u+d),h=c[S]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3);if(d+=c[S+2],d+=_&m[h],S=3*(u+d),0==(h=c[S])){_>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--;break}}else _>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,o,l,d,c,h){var p,m,v,g,b,w,y,x,k,C,$,T,S,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return o[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(v=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,S=2;0!=--b;)this.x[S]=w+=this.c[C],S++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[v],this.x[0]=b=0,C=0,g=-1,T=-x,this.u[0]=0,$=0,O=0;y<=v;y++)for(p=this.c[y];0!=p--;){for(;y>T+x;){if(g++,T+=x,O=v-T,O=O>x?x:O,(m=1<<(w=y-T))>p+1&&(m-=p+1,S=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++S]);)m-=this.c[S];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[g]=$=this.hn[0],this.hn[0]+=O,0!=g?(this.x[g]=b,this.r[0]=w,this.r[1]=x,w=b>>>T-x,this.r[2]=$-this.u[g-1]-w,s(this.r,0,d,3*(this.u[g-1]+w),3)):o[0]=$}for(this.r[1]=y-T,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-T,w=b>>>T;w<O;w+=m)s(this.r,0,d,3*($+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<T)-1;(b&k)!=this.x[g];)g--,T-=x,k=(1<<T)-1}return 0!=M&&1!=v?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,s,o,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,o,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,$,s,a,o,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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diff --git a/static/scripts/bundled/viz.bundled.js b/static/scripts/bundled/viz.bundled.js
index e41f2eba007..b624c19bf5e 100644
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No jobs found.")},_templateError:function(t,e){return i("<div/>").addClass("errormessagelarge").append(i("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. 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m=e.categorical_filters[a][v],y="",b="";for(var w in m)y=w,b=m[w];g&&(o+=" | "),g=!0;var d=i[a];d&&m[a]&&d==b?o+='<span class="categorical-filter '+a+'-filter current-filter">'+v+"</span>":o+='<span class="categorical-filter '+a+'-filter"><a href="javascript:void(0);" filter_key="'+y+'" filter_val="'+b+'">'+v+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=a.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(146),l=r(s),u=n(13),c=r(u),h=n(41),d=r(h),f=n(61),p=r(f),_=n(26),g=r(_),v=n(3),m=r(v);n(170),n(169),n(171),n(157),n(174),n(159),n(172),n(173),n(25);var y=null,b=null,w=function(){this.initialize&&this.initialize.apply(this,arguments)};w.extend=t.Model.extend;var x=w.extend({initialize:function(t){m.default.cssLoadFile("static/style/jquery.rating.css"),m.default.cssLoadFile("static/style/autocomplete_tagging.css"),m.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),m.default.cssLoadFile("static/style/library.css"),m.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];i(".bookmark").each(function(){t.push({position:i(this).children(".position").text(),annotation:i(this).children(".annotation").text()})});var e=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,n={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:e},bookmarks:t};return i.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(t){Galaxy.modal.hide(),b.vis_id=t.vis_id,b.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=d.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(t){o.each(t,function(t){b.add_drawable(l.default.object_from_template(t,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==i("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,n){var r=i("#right .unified-panel-body"),a=i("<div/>").addClass("bookmark").appendTo(r),o=i("<div/>").addClass("position").appendTo(a),s=(i("<a href=''/>").text(t).appendTo(o).click(function(){return b.go_to(t),!1}),i("<div/>").text(e).appendTo(a));if(n){var l=i("<div/>").addClass("delete-icon-container").prependTo(a).click(function(){return a.slideUp("fast"),a.remove(),b.has_changes=!0,!1});i("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,a},create_visualization:function(t,e,n,r,a){var s=this,u=new l.default.TracksterView(o.extend(t,{header:!1}));return u.editor=!0,i.when(u.load_chroms_deferred).then(function(t){if(e){var i=e.chrom,o=e.start,c=e.end,h=e.overview;i&&void 0!==o&&c?u.change_chrom(i,o,c):u.change_chrom(t[0].chrom)}else u.change_chrom(t[0].chrom);if(n)for(var 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visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){i(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){i.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){y=new x(Galaxy.root),y.createButtonMenu(),y.buttonMenu.$el.attr("style","float: right"),i("#center .unified-panel-header-inner").append(y.buttonMenu.$el),i("#right .unified-panel-title").append("Bookmarks"),i("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),i("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),n={},i={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(n["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(i)},"View in new 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id="new-dbkey">',n=0;n<t.length;n++)e+='<option value="'+t[n][1]+'">'+t[n][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){i(document).trigger("convert_to_values"),b=y.create_visualization({container:i("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){i("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&i.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){b.add_drawable(l.default.object_from_template(t,b,b))}}),i("#add-bookmark-button").click(function(){var t=b.chrom+":"+b.low+"-"+b.high;return y.add_bookmark(t,"Bookmark description",!0)}),y.init_keyboard_nav(b),i(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t,e){e||(e=0);var n=Math.pow(10,e);return Math.round(t*n)/n}function o(e){var n=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,i){n.resolve(206===i.status)}}),n}Object.defineProperty(e,"__esModule",{value:!0});var s=n(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(s),u=n(13),c=r(u),h=n(147),d=r(h),f=n(14),p=r(f),_=n(148),g=r(_),v=n(149),m=r(v),y=n(150),b=r(y),w=n(15),x=r(w),k=n(140),C=r(k),M=n(21),S=r(M),T=n(151),$=r(T);n(25);var A=l.extend,E={},O=function(t,e){E[t.attr("id")]=e},z=function(e,n,i,r){i=".group",E[e.attr("id")]=r,e.bind("drag",{handle:"."+n,relative:!0},function(e,n){var r,a,o,s,l,u=(t(this),t(this).parent()),c=u.children(".track,.group"),h=E[t(this).attr("id")];if(a=t(this).parents(i),0!==a.length){o=a.position().top,s=o+a.outerHeight();var d=E[a.attr("id")];if(n.offsetY<o)return t(this).insertBefore(a),d.remove_drawable(h),void d.container.add_drawable_before(h,d);if(n.offsetY>s)return t(this).insertAfter(a),d.remove_drawable(h),void d.container.add_drawable(h)}for(a=null,l=0;l<c.length;l++)if(r=t(c.get(l)),o=r.position().top,s=o+r.outerHeight(),r.is(i)&&this!==r.get(0)&&n.offsetY>=o&&n.offsetY<=s)return n.offsetY-o<s-n.offsetY?r.find(".content-div").prepend(this):r.find(".content-div").append(this),h.container&&h.container.remove_drawable(h),void E[r.attr("id")].add_drawable(h);for(l=0;l<c.length&&(r=t(c.get(l)),!(n.offsetY<r.position().top)||r.hasClass("reference-track")||r.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(u.append(this),E[u.attr("id")].move_drawable(h,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),E[u.attr("id")].move_drawable(h,n.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",N=["Histogram","Line","Filled","Intensity"],P=function t(e,n,i){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=n,this.drag_handle_class=i.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,i.prefs),this.config.get_value("name")||this.config.set_value("name",i.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==i.header){var r=new d.default.TrackHeaderView({model:this,id:this.id});this.header_div=r.$el,this.container_div.append(this.header_div);var a=r.icons_div;this.action_icons=r.action_icons,this.container_div.hover(function(){a.show()},function(){a.hide()})}};P.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new S.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],A(P.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,n){P.call(this,t,e,n),this.obj_type=n.obj_type,this.drawables=[]};A(q.prototype,P.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,n=0;n<t.length;n++)e=it(t[n],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables.splice(n,0,t),!0)},replace_drawable:function(t,e,n){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables[i]=e,n&&t.container_div.replaceWith(e.container_div),this.changed()),i},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables.splice(n,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,n=this.drawables.slice(0),i=[];0!==n.length;)e=n.shift(),e instanceof t?i.push(e):e.drawables&&(n=n.concat(e.drawables));return i}});var j=function(e,n,i){if(A(i,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,n,i),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in i&&this.unpack_drawables(i.drawables),"filters"in i){var r=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,i.filters),r.parent_div.replaceWith(this.filters_manager.parent_div),i.filters.visible&&this.setup_multitrack_filtering()}};A(j.prototype,P.prototype,q.prototype,{action_icons_def:[P.prototype.action_icons_def[0],P.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},P.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof W),this.action_icons.filters_icon.hide();else{var n,i,r,a=this.drawables[0].get_type(),o=0;for(n=0;n<e;n++){if(r=this.drawables[n],r.get_type()!==a){can_composite=!1;break}r instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(r=this.drawables[0],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],l[s.name]=[s];for(n=1;n<this.drawables.length;n++)for(r=this.drawables[n],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var u,c;for(var h in l)u=l[h],u.length===o&&(c=new b.default.NumberFilter({name:u[0].name,index:u[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new W(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=A(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var D=i.View.extend({initialize:function(t){A(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,n=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,n),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:n.dbkey},function(t){l.each(t,function(t){n.add_drawable(it(t,n,n))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var i=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&n.go_to(t(this).val()),t(this).hide(),t(this).val(""),n.location_span.show(),n.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",i).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){n.location_span.hide(),n.chrom_select.hide(),n.nav_input.val(n.chrom+":"+n.low+"-"+n.high),n.nav_input.css("display","inline-block"),n.nav_input.select(),n.nav_input.focus(),n.nav_input.autocomplete({source:function(e,i){var r=[],a=t.map(n.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){r=r.concat(t)})});t.when.apply(t,a).done(function(){i(t.map(r,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){n.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){n.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){n.change_chrom(n.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){n.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var i=e.offsetX-this.current_x;this.current_x=e.offsetX;var r=Math.round(i/n.viewport_container.width()*(n.max_high-n.max_low));n.move_delta(-r)}),this.overview_close.click(function(){n.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>n.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=n.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,i){var r=t(this),a=i.offsetX-i.current_x,o=r.scrollTop()-(e.clientY-i.current_height);r.scrollTop(o),i.current_height=e.clientY,i.current_x=i.offsetX;var s=Math.round(a/n.viewport_container.width()*(n.high-n.low));n.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,i){return t("<div/>").addClass("zoom-area").css("height",n.browser_content_div.height()+n.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,i){t(i.proxy).css({left:Math.min(e.pageX,i.startX)-n.container.offset().left,width:Math.abs(e.pageX-i.startX)});var r=Math.min(e.pageX,i.startX)-n.container.offset().left,a=Math.max(e.pageX,i.startX)-n.container.offset().left,o=n.high-n.low,s=n.viewport_container.width();n.update_location(Math.round(r/s*o)+n.low,Math.round(a/s*o)+n.low)}).bind("dragend",function(e,i){var r=Math.min(e.pageX,i.startX),a=Math.max(e.pageX,i.startX),o=n.high-n.low,s=n.viewport_container.width(),l=n.low;n.low=Math.round(r/s*o)+l,n.high=Math.round(a/s*o)+l,t(i.proxy).remove(),n.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){n.resize_window()},500)}),t(document).bind("redraw",function(){n.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});A(D.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,n,i){if(this.timer&&clearTimeout(this.timer),i){var r=this;this.timer=setTimeout(function(){r.trigger("navigate",t+":"+e+"-"+n)},500)}else view.trigger("navigate",t+":"+e+"-"+n)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var n=this.chrom_select.val();""!==n&&this.trigger_navigate(n,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var n=this,i=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var r=new J(n);n.add_label_track(r),n.reference_track=r}n.chrom_data=e.chrom_info,n.chrom_select.html(""),n.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var a=0,o=n.chrom_data.length;a<o;a++){var s=n.chrom_data[a].chrom,l=t("<option>");l.text(s),l.val(s),n.chrom_select.append(l)}e.prev_chroms&&n.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&n.chrom_select.append(t('<option value="next">Next 100</option>')),n.chrom_start_index=e.start_index,i.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+n.dbkey)}}),i},change_chrom:function(e,n,i){var r=this;if(!r.chrom_data)return void r.load_chroms_deferred.then(function(){r.change_chrom(e,n,i)});if(e&&"None"!==e){if("previous"===e)return void r.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void r.load_chroms({low:this.chrom_start_index+100});var a=t.grep(r.chrom_data,function(t,n){return t.chrom===e})[0];if(void 0===a)return void r.load_chroms({chrom:e},function(){r.change_chrom(e,n,i)});if(e!==r.chrom){r.chrom=e,r.chrom_select.val(r.chrom),r.max_high=a.len-1,r.reset();for(var o=0,s=r.drawables.length;o<s;o++){var l=r.drawables[o];l.init&&l.init()}r.reference_track&&r.reference_track.init()}void 0===n&&void 0===i?(r.low=0,r.high=r.max_high):(r.low=void 0!==n?Math.max(n,0):0,void 0===i?(r.low=Math.max(r.low-15,0),r.high=r.low+30):r.high=Math.min(i,r.max_high)),r.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),n=e[0],i=e[1]?parseInt(e[1],10):void 0,r=e[2]?parseInt(e[2],10):void 0;this.change_chrom(n,i,r)},move_fraction:function(t){var e=this,n=e.high-e.low;this.move_delta(t*n)},move_delta:function(t){var e=this,n=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+n):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-n):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var i=e.chrom_select.val();this.trigger_navigate(i,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,n){if(q.prototype.remove_drawable.call(this,e),n){var i=this;e.container_div.hide(0,function(){t(this).remove(),i.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var n=this,i=e?[e]:n.drawables;l.each(i,function(e){var i=l.find(n.tracks_to_be_redrawn,function(t){return t[0]===e});i?i[1]=t:n.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){n._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var n=this.high-this.low;0!==this.high&&n<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var i=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,r=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:i,width:Math.max(13,r)}).show(),r<13&&this.overview_box.css("left",i-(13-r)/2),this.overview_highlight&&this.overview_highlight.css({left:i,width:r}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],n=t[1];e&&e._draw(n)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var n=this.high-this.low,i=n/2+this.low,r=n/this.zoom_factor/2;t&&(i=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(i-r),this.high=Math.round(i+r),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,n=t*this.zoom_factor/2;this.low=Math.round(e-n),this.high=Math.round(e+n),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),n=this;e.header_div.hide(),e.is_overview=!0,n.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){n.overview_highlight.show().height(n.overview_drawable.content_div.height()),n.overview_viewport.height(n.overview_drawable.content_div.height()+n.overview_box.outerHeight()),n.overview_close.show(),n.resize_window()},n.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=i.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),n=this.model;t("<div>").addClass("param-label").text(n.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(n.get("html")).appendTo(e).find(":input").val(n.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=i.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,n=this.model,i=this.$el.addClass("dynamic-tool").hide();i.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(i).text(n.get("name"));n.get("inputs").each(function(t){var e=new I({model:t});e.render(),i.append(e.$el)}),i.find("input").click(function(){t(this).select()});var r=t("<div>").addClass("param-row").appendTo(i),a=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(r);t("<input type='submit'>").attr("value","Run on visible region").appendTo(r).click(function(){e.run_on_region()}),a.click(function(){e.run_on_dataset()}),n.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),n=this.model,i=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),r={target_dataset_id:e.dataset.id,action:"rerun",tool_id:n.id,regions:[i.toJSON()]},a=e,o=n.get("name")+a.tool_region_and_parameters_str(i);if(a.container===view){var s=new j(view,view,{name:e.config.get_value("name")}),l=a.container.replace_drawable(a,s,!1);s.container_div.insertBefore(a.view.content_div.children()[l]),s.add_drawable(a),a.container_div.appendTo(s.content_div),t=s}else t=a.container;var u=new a.constructor(view,t,{name:o,hda_ldda:"hda"});u.init_for_tool_data(),u.change_mode(a.mode),u.set_filters_manager(a.filters_manager.copy(u)),u.update_icons(),t.add_drawable(u),u.tiles_div.text("Starting job."),this.run(r,u,function(t){u.set_dataset(new x.default.Dataset(t)),u.tiles_div.text("Running job."),u.init()})},run:function(e,n,i){e.inputs=this.model.get_inputs_dict();var r=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(r.go()).then(function(t){"no converter"===t?(n.container_div.addClass("error"),n.content_div.text(R)):t.error?(n.container_div.addClass("error"),n.content_div.text("Tool cannot be rerun: "+t.message)):i(t)})}}),V=function(t,e){m.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var U=function(e,n,i,r,a){this.track=e,this.region=n,this.low=n.get("start"),this.high=n.get("end"),this.w_scale=i,this.canvas=r,this.html_elt=t("<div class='track-tile'/>").append(r),this.data=a,this.stale=!1};U.prototype.predisplay_actions=function(){};var F=function(t,e,n,i,r){U.call(this,t,e,n,i,r)};F.prototype.predisplay_actions=function(){};var G=function(t,e,n,i,r,a,o,s,l,u,c){U.call(this,t,e,n,i,r),this.mode=a,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=u,this.other_tiles_features_drawn={},this.seq_data=c};A(G.prototype,U.prototype),G.prototype.predisplay_actions=function(){};var H=function(e,n,r){A(r,{drag_handle_class:"draghandle"}),P.call(this,e,n,r),this.dataset=null,r.dataset&&(this.dataset=r.dataset instanceof i.Model?r.dataset:new x.default.Dataset(r.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in r?r.data_query_wait:5e3,this.data_manager="data_manager"in r?r.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in r&&!r.resize||this.add_resize_handle())};A(H.prototype,P.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},P.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},P.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var n="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',r=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},a=function(){var n,r=t('select[name="regions"] option:selected').val(),a=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});n="cur"===r?[a]:"bookmarks"===r?o:[a].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new i.Collection(n).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:n,buttons:{No:r,Yes:a}})}},P.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&P.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,n=!1,i=!1,r=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(n=!0,r.show())},function(){n=!1,i||r.hide()}),r.hide().bind("dragstart",function(n,r){i=!0,r.original_height=t(e.content_div).height()}).bind("drag",function(n,i){var r=Math.min(Math.max(i.original_height+i.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",r),e.visible_height_px=e.max_height_px===r?0:r,e.on_resize()}).bind("dragend",function(t,a){e.tile_cache.clear(),i=!1,n||r.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof J?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof W?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var n=this;if(n.enabled=!1,n.tile_cache.clear(),n.data_manager.clear(),n.content_div.children().remove(),n.container_div.removeClass("nodata error pending"),n.tiles_div=t("<div/>").addClass("tiles").appendTo(n.content_div),n.dataset.id){var i=t.Deferred(),r={hda_ldda:n.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:n.view.chrom,retry:e};return t.getJSON(this.dataset.url(),r,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(n.container_div.addClass("error"),n.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(n.container_div.addClass("nodata"),n.show_message("No data for this chrom/contig.")):"pending"===e?(n.container_div.addClass("pending"),n.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){n.init()},n.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(n.valid_chroms=e.valid_chroms,n.update_icons()),n.tiles_div.text("Ready for display"),n.view.chrom?(n.tiles_div.text(""),n.tiles_div.css("height",n.visible_height_px+"px"),n.enabled=!0,t.when.apply(t,n.predraw_init()).done(function(){i.resolve(),n.container_div.removeClass("nodata error pending"),n.request_draw()})):i.resolve());else{n.container_div.addClass("error");var r=n.show_message("Cannot display dataset due to an error. ");e.message&&(r.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),r.append(t("<span/>").text(" ")),r.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){n.init(!0)})))}}),this.update_icons(),i}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(n&&void 0!==n.min&&void 0!==n.max){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_default_value("min_value",i),e.config.set_default_value("max_value",r),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},get_drawables:function(){return this}});var Y=function(e,n,i){H.call(this,e,n,i);var r=this;if(z(r.container_div,r.drag_handle_class,".group",r),this.filters_manager=new b.default.FiltersManager(this,"filters"in i?i.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=i.tool?new L(l.extend(i.tool,{track:this,tool_state:i.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var a=new B({model:this.tool});a.render(),this.dynamic_tool_div=a.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),i.mode&&this.change_mode(i.mode)};A(Y.prototype,P.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();A(e,{data_manager:this.data_manager});var n=new this.constructor(this.view,t,e);return n.change_mode(this.mode),n.enabled=this.enabled,n},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var n=e&&e.clear_after,i=this.view.low,r=this.view.high,a=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(i=this.view.max_low,r=this.view.max_high,o=a/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var u,h,d=Math.floor(400*s),f=Math.floor(i/d),p=[],_=[];f*d<r;)u=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*d,end:Math.min((f+1)*d,this.view.max_high)}),h=this.draw_helper(u,o,e),p.push(h),t.when(h).then(function(t){_.push(t)}),f+=1;n||this.tiles_div.children(".remove").removeClass("remove").remove();var g=this;t.when.apply(t,p).then(function(){g.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&g.postdraw_actions(_,a,o,n)})}},_add_yaxis_label:function(e,n){var i=this,r="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+r),u=a(i.config.get_value(s),1);n=n||function(){i.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(u):(l=t("<div/>").text(u).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),i.config.set_value(s,a(e,1)),n()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+r).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,n,i){if(l.filter(t,function(t){return t instanceof F}).length>0){this.max_height_px=0;var r=this;l.each(t,function(t){t instanceof F||(t.html_elt.remove(),r.draw_helper(t.region,n,{force:!0,mode:"Coverage"}))}),r._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,n,i){i||(i={});var r=i.force,a=i.mode||this.mode,o=1/n,s=this,u=this._get_drawables(),c=this._gen_tile_cache_key(n,e),h=r?void 0:s.tile_cache.get_elt(c);if(h)return function(t){return t&&"track"in t}(h)&&s.show_tile(h,n),h;if(!1===i.data_fetch)return null;var d=function(){var t=l.find(N,function(t){return t===a})?"Coverage":a,n=l.map(u,function(n){return n.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&n.push(view.reference_track.data_manager.get_data(e,a,o,view.reference_track.data_url_extra_params)),n},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,d()).then(function(){var r,a=d(),o=a;if(l.find(a,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,n,i)).then(function(t){f.resolve(t)});view.reference_track&&(r=view.reference_track.data_manager.subset_entry(a.pop(),e));var h=[],_=[];l.each(u,function(t,e){var i=t.mode,r=o[e];"Auto"===i&&(i=t.get_mode(r),t.update_auto_mode(i)),h.push(i),_.push(t.get_canvas_height(r,i,n,b))});var g,v=s.view.canvas_manager.new_canvas(),m=e.get("start"),y=e.get("end"),b=Math.ceil((y-m)*n)+s.left_offset,w=l.max(_);v.width=b,v.height=i.height||w;var x=v.getContext("2d");x.translate(s.left_offset,0),u.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(u,function(t,i){g=t.draw_tile(o[i],x,h[i],e,n,r)}),void 0!==g&&(s.tile_cache.set_elt(c,g),s.show_tile(g,n)),f.resolve(g)}),f},get_canvas_height:function(t,e,n,i){return this.visible_height_px},_draw_line_track_tile:function(t,e,n,i,r){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var a=e.canvas;return new m.default.LinePainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new F(this,i,r,a,t.data)},draw_tile:function(t,e,n,i,r,a){},show_tile:function(t,e){var n=t.html_elt;t.predisplay_actions();var i=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(i-=this.left_offset),n.css("left",i),n.hasClass("remove")?n.removeClass("remove"):this.tiles_div.append(n),n.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,n.height()-2),n.parent().children().css("height",this.max_height_px+"px");var r=this.max_height_px;0!==this.visible_height_px&&(r=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",r+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};A(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var n=this.view,i=n.high-n.low,r=Math.floor(Math.pow(10,Math.floor(Math.log(i)/Math.log(10)))),a=Math.floor(n.low/r)*r,o=this.view.container.width(),s=t("<div/>").addClass("label-container");a<n.high;){var l=Math.floor((a-n.low)/i*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(a)).css({left:l})),a+=r}this.content_div.children(":first").remove(),this.content_div.append(s)}});var W=function(t,e,n){if(Y.call(this,t,e,n),this.drawables=[],"drawables"in n){for(var i,r=0;r<n.drawables.length;r++)i=n.drawables[r],this.drawables[r]=it(i,t,null),i.left_offset>this.left_offset&&(this.left_offset=i.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};A(W.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],n=0;n<this.drawables.length;n++)e.push(this.drawables[n].init());var i=this;t.when.apply(t,e).then(function(){i.enabled=!0,i.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:P.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new j(this.view,this.container,{name:this.config.get_value("name")}),n=0;n<this.drawables.length;n++)t=this.drawables[n],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,n,i){var r,a=-1;for(r=0;r<t.length;r++){var o=t[r].html_elt.find("canvas").height();o>a&&(a=o)}for(r=0;r<t.length;r++){var s=t[r];s.html_elt.find("canvas").height()!==a&&(this.draw_helper(s.region,n,{force:!0,height:a}),s.html_elt.remove())}var l=this,u=function(){l.update_all_min_max()};this._add_yaxis_label("min",u),this._add_yaxis_label("max",u)}});var J=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};A(J.prototype,P.prototype,Y.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:P.prototype.can_draw,draw_helper:function(t,e,n){var i,r=this.tiles_div.is(":visible"),a=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),i=!0,a=Y.prototype.draw_helper.call(this,t,e,n)):(i=!1,this.tiles_div.hide()),r!==i&&this.view.resize_viewport(),a},can_subset:function(t){return!0},draw_tile:function(t,e,n,i,r){var a=this.data_manager.subset_entry(t,i),o=a.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,u=o.length;l<u;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*r),10);return new U(this,i,r,s,a)}});var K=function(e,n,i){this.mode="Histogram",Y.call(this,e,n,i),this.left_offset=30;var r=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(r.data_manager=new $.default.BBIDataManager({dataset:r.dataset}))})};A(K.prototype,P.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,n,i,r){return this._draw_line_track_tile(t,e,n,i,r)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,n,i){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,n){this.mode="Heatmap",Y.call(this,t,e,n)};A(Z.prototype,P.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,n,i,r){var a=e.canvas;return new m.default.DiagonalHeatmapPainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new U(this,i,r,a,t.data)}});var Q=function(t,e,n){Y.call(this,t,e,n),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};A(Q.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=m.default.ArcLinkedFeaturePainter:this.painter=m.default.LinkedFeaturePainter},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a,o=this;if(0===l.filter(e,function(t){return t instanceof F}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var u=this;l.each(e,function(e){var n=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(n=l.omit(n,l.keys(e.other_tiles_features_drawn)),0!==l.size(n)){var i={data:l.values(n)},r=u.view.canvas_manager.new_canvas(),a=r.getContext("2d");r.height=Math.max(e.canvas.height,u.get_canvas_height(i,e.mode,e.w_scale,100)),r.width=e.canvas.width,a.drawImage(e.canvas,0,0),a.translate(o.left_offset,0);var c=u.draw_tile(i,a,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=r,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,h=o.filters_manager.filters;for(c=0;c<h.length;c++)h[c].update_ui_elt();var d,f,p=!1;for(a=0;a<e.length;a++)if(e[a].data.length)for(d=e[a].data[0],c=0;c<h.length;c++)if(f=h[c],f.applies_to(d)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof G){var _=!0;for(a=0;a<e.length;a++)if(!e[a].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,n){var i=this.view.canvas_manager.dummy_context,r=this.slotters[t];return r&&r.mode===n||(r=new g.default.FeatureSlotter(t,n,100,function(t){return i.measureText(t)}),this.slotters[t]=r),r.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,n,i){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.incremental_slots(n,t.data,e),a=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,a.get_required_height(r,i))},draw_tile:function(t,e,n,i,r,a,o){var s=this,l=e.canvas,u=i.get("start"),c=i.get("end"),h=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,n,i,r);var d=[],f=this.slotters[r].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,g=0,v=t.data.length;g<v;g++){for(var m,y=t.data[g],b=!1,w=0,x=_.length;w<x;w++)if(m=_[w],m.update_attrs(y),!m.keep(y)){b=!0;break}b||(d.push(y),y[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,M=new this.painter(d,u,c,this.config.to_key_value_dict(),n,k,C,a,function(t){return s.view.get_base_color(t)}),S=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=M.draw(e,l.width,l.height,r,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-h}return o?void 0:new G(s,i,r,l,t.data,n,t.message,p,S,incomplete_features,a)}});var tt=function(t,e,n){Y.call(this,t,e,n),this.painter=m.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};A(tt.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,n,i,r){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",i,r);var a=this.view;return new this.painter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n,function(t){return a.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,r),new U(this,i,r,e.canvas,t.data)},get_canvas_height:function(t,e,n,i){if("bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===r&&0!==t.data.length&&(r=t.data[0][7].match(/,/g),r=null===r?1:r.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(r)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a=l.filter(e,function(t){return t instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===a.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var u=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(u).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,n){Q.call(this,t,e,n),this.painter=m.default.ReadPainter,this.update_icons()};A(et.prototype,P.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var nt={CompositeTrack:W,DrawableGroup:j,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},it=function(t,e,n){if("copy"in t)return t.copy(n);var i=t.obj_type;return i||(i=t.track_type),new nt[i](e,n,t)};e.default={TracksterView:D,DrawableGroup:j,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:W,object_from_template:it}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(r),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(i("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(i("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(i("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=i("<div/>").addClass("track-icons").hide().appendTo(this.$el),a.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,n,r,a,o){var s=this;this.action_icons[t]=i("<a/>").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(function(){r(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var n=this.model,i={},r=0,a=n.display_modes.length;r<a;r++){var o=n.display_modes[r];i[o]=function(t){return function(){n.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,i)}}});e.default={TrackHeaderView:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,n,i){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=n,this.measureText=i};a(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),n=Math.ceil(t[2]*this.w_scale),i=t[3];if(void 0!==i&&this.include_label){var r=this.measureText(i).width+7;e-r>=0?(e-=r,"left"):(n+=r,"right")}return[e,n]},_find_slot:function(t){for(var e=t[0],n=t[1],i=0;i<=this.max_rows;i++){var r=!1,a=this.start_end_dct[i];if(void 0!==a)for(var o=0,s=a.length;o<s;o++){var l=a[o];if(n>l[0]&&e<l[1]){r=!0;break}}if(!r)return i}return-1},slot_features:function(t){for(var e,n,i=this.start_end_dct,r=[],a=0,s=0,l=t.length;s<l;s++){e=t[s],n=e[0];var u=this.slots[n];if(u){if(e[1]<u.feature[1]||u.feature[2]<e[2])for(var c=this._get_draw_coords(u.feature),h=this._get_draw_coords(e),d=this.start_end_dct[u.slot],f=0;f<d.length;f++){var p=d[f];p[0]===c[0]&&p[1]===c[1]&&(d[f]=h)}a=Math.max(a,this.slots[n].slot)}else r.push(s)}for(var s=0,l=r.length;s<l;s++){e=t[r[s]],n=e[0];var _=this._get_draw_coords(e),g=this._find_slot(_);g>=0&&(void 0===i[g]&&(i[g]=[]),i[g].push(_),this.slots[n]=new o(g,e),a=Math.max(a,g))}return a+1}}),e.default={FeatureSlotter:s}},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=function(t,e){var n=t[0],i=t[1],r=e[0],a=e[1];return n<r?i<=r?1001:i<=a?1003:1002:n>a?1006:i<=a?1005:1004},o=function(t,e){var n=a(t,e);return 1001!==n&&1006!==n},s=function(t,e,n,i,r,a){void 0===a&&(a=4);var o,s=i-e,l=r-n,u=Math.floor(Math.sqrt(s*s+l*l)/a),c=s/u,h=l/u;for(o=0;o<u;o++,e+=c,n+=h)o%2==0&&t.fillRect(e,n,a,1)},l=function(t,e,n,i){var r=e-i/2,a=e+i/2,o=n-Math.sqrt(3*i/2);t.beginPath(),t.moveTo(r,o),t.lineTo(a,o),t.lineTo(e,n),t.lineTo(r,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},u=function(t){this.default_val=t||1};u.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},h=function(t,e,n,i,a){this.data=t,this.view_start=e,this.view_end=n,this.prefs=r.extend({},this.default_prefs,i),this.mode=a};h.prototype.default_prefs={},h.prototype.draw=function(t,e,n,i){},h.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},h.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},h.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},h.prototype._chrom_pos_to_draw_pos=function(t,e,n){return Math.floor(e*(Math.max(0,t-this.view_start)+n))};var d=function(t,e,n,i,r){h.call(this,t,e,n,i,r)};d.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},d.prototype.draw=function(t,e,n,i){var a=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,u=n,c=this.view_start,h=this.mode,d=this.data;t.save();var f=Math.round(n+o/l*n);"Intensity"!==h&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,g;g=d.length>1?r.map(d.slice(0,-1),function(t,e){return Math.ceil((d[e+1][0]-d[e][0])*i)}):[10];for(var v,m=this.prefs.block_color||this.prefs.color,y=parseInt(m.slice(1),16),b=(16711680&y)>>16,w=(65280&y)>>8,x=255&y,k=!1,C=!1,M=0,S=d.length;M<S;M++)if(t.fillStyle=t.strokeStyle=m,k=C=!1,v=g[M],p=Math.floor((d[M][0]-c-.5)*i),null!==(_=d[M][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===h)_=Math.round(_/l*u),t.fillRect(p,f,v,-_);else if("Intensity"===h){var T=(_-o)/l,$=Math.round(b+(255-b)*(1-T)),A=Math.round(w+(255-w)*(1-T)),E=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+$+","+A+","+E+")",t.fillRect(p,0,v,u)}else _=Math.round(u-(_-o)/l*u),a?t.lineTo(p,_):(a=!0,"Filled"===h?(t.moveTo(p,u),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===h||"Intensity"===h?O=v:(p-=2,O=4),k&&t.fillRect(p,0,O,3),C&&t.fillRect(p,u-3,O,3)}t.fillStyle=m}else a&&"Filled"===h&&t.lineTo(p,u),a=!1;"Filled"===h?(a&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,n,i){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:n,x_end:i})},f.prototype.get_feature_data=function(t,e){var n,i=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[i])return null;t+=this.translation;for(var r=0;r<this.feature_positions[i].length;r++)if(n=this.feature_positions[i][r],t>=n.x_start&&t<=n.x_end)return n.data};var p=function(t,e,n,i,r,a,o){h.call(this,t,e,n,i,r),this.alpha_scaler=a||new u,this.height_scaler=o||new u,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},r.extend(p.prototype,{get_required_height:function(t,e){var n=this.get_row_height(),i=n,r=this.mode;return"no_detail"!==r&&"Squish"!==r&&"Pack"!==r||(n=t*i),n+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,n,i,r){var a=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,u=this.get_row_height(),h=new f(u),d=[],p=0,_=a.length;p<_;p++){var g=a[p],v=g[0],m=g[1],y=g[2],b=r&&void 0!==r[v]?r[v].slot:null;("Dense"===this.mode||null!==b)&&m<s&&y>o&&(l=this.draw_element(t,this.mode,g,b,o,s,i,u,e),h.map_feature_data(g,b,l[0],l[1]),(m<o||y>s)&&d.push(g))}return t.restore(),h.y_translation=this.get_top_padding(e),new c({incomplete_features:d,feature_mapper:h})},draw_element:function(t,e,n,i,r,a,o,s,l){return[0,0]}});var _=function(t,e,n,i,r,a,o){p.call(this,t,e,n,i,r,a,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};r.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,n,i,r,a,o,s,l){var u,c=(n[0],n[1]),h=n[2],d=n[3],f=n[4],p=Math.floor(Math.max(0,(c-r-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(h-r-.5)*o))),g=p,v=_,u=("Dense"===e?0:0+i)*s+this.get_top_padding(l),m=null,y=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,w=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(n),"Dense"===e&&(i=1),"no_detail"===e)t.fillStyle=b,t.fillRect(p,u+5,_-p,1);else{var x=n[5],k=n[6],C=n[7],M=!0;x&&k&&(m=Math.floor(Math.max(0,(x-r)*o)),y=Math.ceil(Math.min(l,Math.max(0,(k-r)*o))));var S,T;if("Squish"===e?(S=1,T=3,M=!1):(S=5,T=9),C){var $,A;"Squish"===e||"Dense"===e?($=u+Math.floor(1.5)+1,A=1):f?($=u,A=T):($+=2.5,A=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,$,_-p,A));for(var E=0,O=C.length;E<O;E++){var z,R,N=C[E],P=Math.floor(Math.max(0,(N[0]-r-.5)*o)),q=Math.ceil(Math.min(l,Math.max((N[1]-r-.5)*o)));if(!(P>q)){if(t.fillStyle=b,t.fillRect(P,u+(T-S)/2+1,q-P,S),void 0!==m&&k>x&&!(P>y||q<m)){var j=Math.max(P,m),D=Math.min(q,y);t.fillRect(j,u+1,D-j,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),j+14<D&&(j+=2,D-=2),t.fillRect(j,u+1,D-j,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,P,q,u),z=P,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(n),I=Math.ceil(T*L),B=Math.round((T-I)/2);1!==L&&(t.fillRect(p,$+1,_-p,B),t.fillRect(p,$+T-B+1,_-p,B))}}else t.fillStyle=b,t.fillRect(p,u+1,_-p,T),f&&M&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,u+1,_-p,T));t.globalAlpha=1,d&&"Pack"===e&&c>r&&(t.fillStyle=w,0===r&&p-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,_+2,u+8,this.max_label_length),v+=t.measureText(d).width+2):(t.textAlign="right",t.fillText(d,p-2,u+8,this.max_label_length),g-=t.measureText(d).width+2))}return t.globalAlpha=1,[g,v]}});var g=function(t,e,n,i,r,a,o,s,l){p.call(this,t,e,n,i,r,a,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};r.extend(g.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",n=[[0,0]],i=n[0],a=0,o=r.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var r=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==i[1]&&(i=[a+r,a+r],n.push(i)):-1==="ISHP".indexOf(o)&&(i[1]+=r,a+=r),[e.indexOf(o),r]});return{blocks:n,cigar:o}},draw_read:function(t,e,n,i,r,s,u,c,h,d){var f=function(t){return Math.floor(Math.max(0,(t-r-.5)*n))};t.textAlign="center";var p,_,g=[r,s],v=0,m=0,y=Math.round(n/2),b=t.canvas.manager.char_width_px,w="+"===h?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,M=i+1,S=new x(t,C,n,e),T=[],$=[],A=this._parse_cigar(c);c=A.cigar,T=A.blocks;for(var E=0;E<T.length;E++){var O=T[E];o([u+O[0],u+O[1]],g)&&(p=f(u+O[0]),_=f(u+O[1]),p===_&&(_+=1),t.fillStyle=w,t.fillRect(p,M,_-p,C))}for(var z=0,R=c.length;z<R;z++){var N=c[z],P="MIDNSHP=X"[N[0]],q=N[1],j=u+v;if(p=f(j),_=f(j+q),o([j,j+q],g))switch(p===_&&(_+=1),P){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var D="";"X"===P?D=d.slice(m,m+q):this.ref_seq&&(D=this.ref_seq.slice(Math.max(0,j-r),Math.min(j-r+q,s-r)));for(var L=Math.max(j,r),I=0;I<D.length;I++)if(D&&!this.prefs.show_differences||"X"===P){var B=Math.floor(Math.max(0,(L+I-r)*n));t.fillStyle=this.base_color_fn(D[I]),k&&n>b?t.fillText(D[I],B,i+9):n>.05&&t.fillRect(B-y,M,Math.max(1,Math.round(n)),C)}"X"===P&&(m+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,M+(C-1)/2,_-p,1),v+=q;break;case"D":S.draw_deletion(p,M,q),v+=q;break;case"I":var V=p-y;if(o([j,j+q],g)){var U=d.slice(m,m+q);if(this.prefs.show_insertions){var F=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b){switch(t.fillStyle="yellow",t.fillRect(F-y,i-9,_-p,9),$[$.length]={type:"triangle",data:[V,i+4,5]},t.fillStyle="#ccc",a([j,j+q],g)){case 1003:U=U.slice(r-j);break;case 1004:U=U.slice(0,j-s);break;case 1005:break;case 1002:U=U.slice(r-j,j-s)}for(var I=0,G=U.length;I<G;I++){var B=Math.floor(Math.max(0,(j+I-r)*n));t.fillText(U[I],B-(_-p)/2,i)}}else t.fillStyle="yellow",t.fillRect(F,i+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b&&$.push({type:"text",data:[U.length,V,i+9]})}m+=q}else v=function(t,e,n){return-1!=="M=NXD".indexOf(e)&&(t+=n),t}(v,P,q),m=function(t,e,n){return-1!=="IX".indexOf(e)&&(t+=n),t}(m,P,q)}t.fillStyle="yellow";for(var H,Y,X,E=0;E<$.length;E++)H=$[E],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,n,i,r,a,o,l,u){var c=(n[0],n[1]),h=n[2],d=n[3],f=Math.floor(Math.max(-.5*o,(c-r-.5)*o)),p=Math.ceil(Math.min(u,Math.max(0,(h-r-.5)*o))),_=("Dense"===e?0:0+i)*l,g="Pack"===e?9:3;this.prefs.label_color;if(n[5]instanceof Array){var v=!0;n[4][1]>=r&&n[4][0]<=a&&n[4][2]?this.draw_read(t,e,o,_,r,a,n[4][0],n[4][2],n[4][3],n[4][4]):v=!1,n[5][1]>=r&&n[5][0]<=a&&n[5][2]?this.draw_read(t,e,o,_,r,a,n[5][0],n[5][2],n[5][3],n[5][4]):v=!1;var m=Math.ceil(Math.min(u,Math.max(-.5*o,(n[4][1]-r-.5)*o))),y=Math.floor(Math.max(-.5*o,(n[5][0]-r-.5)*o));if(v&&y>m){t.fillStyle="#ccc";var b=_+1+(g-1)/2;s(t,m,b,y,b)}}else this.draw_read(t,e,o,_,r,a,c,n[4],n[5],n[6]);return"Pack"===e&&c>=r&&"."!==d&&(t.fillStyle=this.prefs.label_color,0===r&&f-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(d,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,n,i,r,a,o){_.call(this,t,e,n,i,r,a,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};r.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,n=this.data.length;e<n;e++){var i=this.data[e],r=i[1],a=i[2];t=Math.max(t,a-r)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,n=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*n))},draw_connector:function(t,e,n,i,r,a){var o=(n+i)/2,s=i-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,a,i-o,Math.PI,0),t.stroke())}});var m=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};m.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,n=this.rgb[0]/255,i=this.rgb[1]/255,r=this.rgb[2]/255,a=this.alpha,o=Math.max(n,i,r),s=Math.min(n,i,r),l=(o+s)/2,u=o-s;if(o===s)t=e=0;else{switch(e=l>.5?u/(2-o-s):u/(o+s),o){case n:t=(i-r)/u+(i<r?6:0);break;case i:t=(r-n)/u+2;break;case r:t=(n-i)/u+4}t/=6}return{h:360*t,s:e,l:l,a:a}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var n=this,i=e,r=2*i-1,a=n.toHSL().a-t.toHSL().a,o=((r*a==-1?r:(r+a)/(1+r*a))+1)/2,s=1-o,l=[n.rgb[0]*o+t.rgb[0]*s,n.rgb[1]*o+t.rgb[1]*s,n.rgb[2]*o+t.rgb[2]*s],u=n.alpha*i+t.alpha*(1-i);return new m(l,u)}};var y=function(t,e,n,i){this.start_color=new m(t),this.end_color=new m(e),this.start_value=n,this.end_value=i,this.value_range=i-n};y.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var b=function(t,e,n,i,r){this.positive_ramp=new y(e,n,0,r),this.negative_ramp=new y(e,t,0,-i),this.start_value=i,this.end_value=r};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var w=function(t,e,n,i,r){h.call(this,t,e,n,i,r);var a,o;if(void 0===this.prefs.min_value){var s=1/0;for(a=0,o=this.data.length;a<o;a++)s=Math.min(s,this.data[a][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(a=0,o=this.data.length;a<o;a++)l=Math.max(l,this.data[a][6]);this.prefs.max_value=l}};w.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},w.prototype.draw=function(t,e,n,i){var r,a,o,s,l,u,c=this.prefs.min_value,h=this.prefs.max_value,d=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,h),g=function(t){return(t-d)*i};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,m=f.length;v<m;v++)r=f[v],a=g(r[1]),o=g(r[2]),s=g(r[4]),l=g(r[5]),u=r[6],t.fillStyle=_.map_value(u),t.fillRect(a,s,o-a,l-s);t.restore()};var x=function(t,e,n,i){this.ctx=t,this.row_height=e,this.px_per_base=n,this.draw_details=("Pack"===i||"Auto"===i)&&n>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};r.extend(x.prototype,{draw_deletion:function(t,e,n){this.ctx.fillStyle="black";var i=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-i),this.ctx.fillRect(t,e,n*this.px_per_base,i)}});var k=function(t,e,n,i,r,a){h.call(this,t,e,n,i,r),this.base_color_fn=a,this.divider_height=1};r.extend(k.prototype,h.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,n,i){t.save();var a,o,s,l,u,c,h,d,f,p,_,g=function(t,e){var n=t.length,i=e.length,r=0,a=1,o=null;return"-"===e?(o="deletion",a=t.length):0===t.indexOf(e)&&n>i?(o="deletion",a=n-i,r=i):0===e.indexOf(t)&&n<i&&(o="insertion",a=i-n,r=i),null!==o?{type:o,start:r,len:a}:{}},v=Math.max(1,Math.floor(i)),m=this.data.length?this.data[0][7].split(",").length:0,y="Squish"===this.mode?5:10,b=i<.1?y:"Squish"===this.mode?3:9,w=!0,k=new x(t,y,i,this.mode);1===m&&(y=b=i<t.canvas.manager.char_width_px?this.prefs.summary_height:y,k.row_height=y,w=!1),this.prefs.show_sample_data&&w&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(a=this.data[C],o=a[1],s=a[3],l=[a[4].split(",")],u=a[7].split(","),c=a.slice(8),l=r.map(r.flatten(l),function(t){var e={type:"snp",value:t,start:0},n=g(s,t);return r.extend(e,n)}),!(o<this.view_start||o>this.view_end)){if(w)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(d=this.get_start_draw_pos(o+l[_].start,i),t.fillRect(d,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var M=c/u.length,S=Math.ceil(this.prefs.summary_height*M);t.fillRect(d,f-S,v,S),f-=S}if(this.prefs.show_sample_data)for(f=w?this.prefs.summary_height+this.divider_height:0,_=0;_<u.length;_++,f+=y)if(p=u[_]?u[_].split(/\/|\|/):["0","0"],h=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(h=l[parseInt(p[0],10)-1],t.globalAlpha=1):(h="0"!==p[0]?p[0]:p[1],h=l[parseInt(h,10)-1],t.globalAlpha=.5),h)if(d=this.get_start_draw_pos(o+h.start,i),"snp"===h.type){var T=h.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,i),f+y):t.fillRect(d,f+1,v,b)}else"deletion"===h.type&&k.draw_deletion(d,f+1,h.len)}t.restore()}}),e.default={Scaler:u,LinePainter:d,LinkedFeaturePainter:_,ReadPainter:g,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:w,VariantPainter:k}},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};a(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,n,i){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(i)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var n=this;n.parent_div=t("<div/>").addClass("filter-row slider-row");var i=t("<div/>").addClass("elt-label").appendTo(n.parent_div),r=(t("<span/>").addClass("slider-name").text(n.name+"  ").appendTo(i),t("<span/>").text(this.low+"-"+this.high)),a=t("<span/>").addClass("slider-value").appendTo(i).append("[").append(r).append("]");n.values_span=r;var l=t("<div/>").addClass("slider").appendTo(n.parent_div);n.control_element=t("<div/>").attr("id",n.name+"-filter-control").appendTo(l),n.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){n.slide(t,e)},change:function(t,e){n.control_element.slider("option","slide").call(n.control_element,t,e)}}),n.slider=n.control_element,n.slider_label=r,function(e,n,i){e.click(function(){var e=n.text(),r=parseFloat(i.slider("option","max")),a=r<=1?4:r<=1e6?r.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),i.slider("option","values")&&(a=2*a+1,o=!0),n.text(""),t("<input type='text'/>").attr("size",a).attr("maxlength",a).attr("value",e).appendTo(n).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),n.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var n=i.slider("option","min"),r=i.slider("option","max"),a=function(t){return isNaN(t)||t>r||t<n},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],a(l[0])||a(l[1]))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this)}else if(l=parseFloat(l),a(l))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this);i.slider(o?"values":"value",l),s.removeClass("input")}})})}(a,r,n.control_element);var u=t("<div/>").addClass("display-controls").appendTo(n.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){n.manager.alpha_filter!==n?(n.manager.alpha_filter=n,n.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),n.transparency_icon.addClass("active").show()):(n.manager.alpha_filter=null,n.transparency_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){n.manager.height_filter!==n?(n.manager.height_filter=n,n.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),n.height_icon.addClass("active").show()):(n.manager.height_filter=null,n.height_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),n.parent_div.hover(function(){n.transparency_icon.show(),n.height_icon.show()},function(){n.manager.alpha_filter!==n&&n.transparency_icon.hide(),n.manager.height_filter!==n&&n.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(n.parent_div)};a(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return a(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var n=e.values;this.values_span.text(n[0]+"-"+n[1]),this.low=n[0],this.high=n[1];var i=this;setTimeout(function(){n[0]===i.low&&n[1]===i.high&&i.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var n=!0,i=0;i<e.length;i++)if(!this._keep_val(e[i])){n=!1;break}return n}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var n=t[this.index];n instanceof Array||(n=[n]);for(var i=0;i<n.length;i++){var r=n[i];r<this.min&&(this.min=Math.floor(r),e=!0),r>this.max&&(this.max=Math.ceil(r),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var u=function(e,n){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),n&&"filters"in n){for(var i,r=("alpha_filter"in n?n.alpha_filter:null),a=("height_filter"in n?n.height_filter:null),o=n.filters,s=0;s<o.length;s++)"number"===o[s].type?(i=new l(o[s]),this.add_filter(i),i.name===r&&(this.alpha_filter=i,i.transparency_icon.addClass("active").show()),i.name===a&&(this.height_filter=i,i.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in n&&n.visible&&this.parent_div.show()}if(0!==this.filters.length){var u=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(u).click(function(){c.run_on_dataset()})}};a(u.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},n=[],i=0;i<this.filters.length;i++)t=this.filters[i],n.push(t.to_dict());return e.filters=n,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new u(t),n=0;n<this.filters.length;n++)e.add_filter(this.filters[n].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,n,i=(function(t,e,n){return e in t||(t[e]=n),t[e]}),r={},a=0;a<this.filters.length;a++)e=this.filters[a],e.tool_id&&(e.min!==e.low&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in r)o[o.length]=[s,r[s]];!function e(n,i){var r=i[0],a=r[0],o=r[1],s="("+o.join(") and (")+")",l={cond:s,input:n,target_dataset_id:n,tool_id:a};i=i.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+a,buttons:{Close:Galaxy.modal.hide()}}):0===i.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,i)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:u,NumberFilter:l}}).call(e,n(0))},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(13),r=function(t){return t&&t.__esModule?t:{default:t}}(i),a=n(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=r.default.GenomeDataManager.extend({load_data:function(e,n,i,r){var a=t.Deferred();this.set_data(e,a);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(n,i){t.when(n.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var n=[],i={max:Number.MIN_VALUE};t.forEach(function(t){i.max!==t.min-1&&(n.push([i.max+1,0]),n.push([t.min-2,0])),n.push([t.min-1,t.score]),n.push([t.max,t.score]),i=t});var r={data:n,region:e,dataset_type:"bigwig"};l.set_data(e,r),a.resolve(r)})}),a}});e.default={BBIDataManager:s}}).call(e,n(0))},function(t,e,n){(function(i){var r,a;r=[n(153),n(154),n(155)],void 0!==(a=function(t,e){"use strict";function n(){}function r(t){t&&(this.id=t)}function a(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,n){Math.pow(10,6);return i.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(n-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*w+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function u(t,e,n,i){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=n,this.isSummary=i}function c(t){var e=i.Deferred(),n=new l;return n.url=t,i.when(o(n.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var r=t,a=new Uint8Array(r),o=new Int16Array(r),l=new Int32Array(r),u=a[0]+w*a[1]+x*a[2]+k*a[3];if(u==v)n.type="bigwig";else{if(u!=y)return u==m||u==b?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+u.toString(16));n.type="bigbed"}n.version=o[2],n.numZoomLevels=o[3],n.chromTreeOffset=s(a,8),n.unzoomedDataOffset=s(a,16),n.unzoomedIndexOffset=s(a,24),n.fieldCount=o[16],n.definedFieldCount=o[17],n.asOffset=s(a,36),n.totalSummaryOffset=s(a,44),n.uncompressBufSize=l[13],n.extHeaderOffset=s(a,56),n.zoomLevels=[];for(var c=0;c<n.numZoomLevels;++c){var h=l[6*c+16],d=s(a,24*c+72),f=s(a,24*c+80);n.zoomLevels.push({reduction:h,dataOffset:d,indexOffset:f})}i.when(n.readChromTree()).then(function(){n.getAutoSQL(function(t){return n.schema=t,e.resolve(n)})})}),e}function h(t,e,n,i,r){this.bbi=t,this.type=e,this.fieldCount=n,this.offset=i,this.field=r}var d=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,g=e.arrayCopy,v=2291137574,m=654086024,y=2273964779,b=3958540679,w=256,x=65536,k=16777216,C=4294967296,M=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),i.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var n=new Uint8Array(e),i=new Int16Array(e),r=new Int32Array(e),a=(r[0],r[1],r[2]),o=(r[3],s(n,16),function(e){var r=n[e],l=i[e/2+1];e+=4;for(var u=0;u<l;++u)if(0===r){e+=a;var c=s(n,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var h="",d=0;d<a;++d){var f=n[e++];0!==f&&(h+=String.fromCharCode(f))}var p=n[e+3]<<24|n[e+2]<<16|n[e+1]<<8|n[e+0];n[e+7],n[e+6],n[e+5],n[e+4],e+=8,t.chromsToIDs[h]=p,0===h.indexOf("chr")&&(t.chromsToIDs[h.substr(3)]=p),t.idsToChroms[p]=h,t.maxID=Math.max(t.maxID,p)}});o(32)})},u.prototype.readWigData=function(t,e,n){var i=this.bwg.chromsToIDs[t];return void 0===i?[]:this.readWigDataById(i,e,n)},u.prototype.readWigDataById=function(t,e,n){var r=this,a=i.Deferred();if(!this.cirHeader)return i.when(o(r.bwg.url,this.cirTreeOffset,48)).then(function(o){r.cirHeader=o;var s=new Int32Array(r.cirHeader);r.cirBlockSize=s[1],i.when(r.readWigDataById(t,e,n)).then(function(t){a.resolve(t)})}),a;var l=[],u=0,c=(Date.now(),function(i,r,a,o){return(t<0||i==t)&&r<=n&&a>=e}),h=function(t,e){if(r.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),u+=t.length,1==t.length&&t[0]-r.cirTreeOffset==48&&r.cachedCirRoot)return _(r.cachedCirRoot,0,e),void(0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}));for(var n,o=4+32*r.cirBlockSize,s=0;s<t.length;++s){var h=new d(t[s],t[s]+o);n=n?f(n,h):h}for(var g=n.ranges(),v=0;v<g.length;++v){var m=g[v];p(t,m,e)}},p=function(t,e,n,s){e.max(),e.min();i.when(o(r.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),n),t[s]-r.cirTreeOffset==48&&t[s]-e.min()==0&&(r.cachedCirRoot=o),0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}))})},_=function(i,r,a){var o=new Uint8Array(i),u=new Int16Array(i),c=new Int32Array(i),d=o[r],f=u[r/2+1];if(r+=4,0!==d)for(var p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16),w=s(o,r+24);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&l.push({offset:b,size:w}),r+=32}else{for(var x=[],p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&x.push(b),r+=24}x.length>0&&h(x,a+1)}};return h([r.cirTreeOffset+48],1),a},u.prototype.fetchFeatures=function(t,e){var r=this,a=i.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,i,a){a||(a={});var o=new n;o._chromId=t,o.segment=r.bwg.idsToChroms[t],o.min=e,o.max=i,o.type=r.bwg.type;for(var l in a)o[l]=a[l];s.push(o)},u=function(){if(0===e.length){Date.now();return a.resolve(s)}var n=e[0];if(n.data)r.parseFeatures(n.data,l,t),e.splice(0,1),u();else{for(var c=n.offset,h=n.size,d=1;d<e.length&&e[d].offset==c+h;)h+=e[d].size,++d;i.when(o(r.bwg.url,c,h)).then(function(t){for(var n=0,i=0;n<h;){var a,o=e[i];if(r.bwg.uncompressBufSize>0)a=_(t,n+2,o.size-2);else{var s=new Uint8Array(o.size);g(new Uint8Array(t,n,o.size),0,s,0,o.size),a=s.buffer}o.data=a,n+=o.size,++i}u()})}};return u(),a},u.prototype.parseFeatures=function(t,e,n){var a=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=t.byteLength/32,c=0;c<u;++c){var h=s[8*c],_=s[8*c+1],g=s[8*c+2],v=s[8*c+3],m=(l[8*c+4],l[8*c+5]),y=l[8*c+6];l[8*c+7];if(n(h,_+1,g)){var b={type:"bigwig",score:y/v,maxScore:m};"bigbed"==this.bwg.type&&(b.type="density"),e(h,_+1,g,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),h=s[0],w=s[1],x=(s[2],s[3]),k=s[4],C=a[20],u=o[11];if(3==C)for(var c=0;c<u;++c){var S=l[c+6],T=w+c*x+1,$=w+c*x+k;n(h,T,$)&&e(h,T,$,{score:S})}else if(2==C)for(var c=0;c<u;++c){var _=s[2*c+6]+1,g=_+k-1,S=l[2*c+7];n(h,_,g)&&e(h,_,g,{score:S})}else if(1==C)for(var c=0;c<u;++c){var _=s[3*c+6]+1,g=s[3*c+7],S=l[3*c+8];_>g&&(_=g),n(h,_,g)&&e(h,_,g,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var A=0,E=this.bwg.definedFieldCount,O=this.bwg.schema;A<a.length;){var h=a[A+3]<<24|a[A+2]<<16|a[A+1]<<8|a[A+0],_=a[A+7]<<24|a[A+6]<<16|a[A+5]<<8|a[A+4],g=a[A+11]<<24|a[A+10]<<16|a[A+9]<<8|a[A+8];A+=12;for(var z="";;){var R=a[A++];if(0==R)break;z+=String.fromCharCode(R)}var N,P={};if(N=z.length>0?z.split("\t"):[],N.length>0&&E>3&&(P.label=N[0]),N.length>1&&E>4){var S=parseInt(N[1]);isNaN(S)||(P.score=S)}if(N.length>2&&E>5&&(P.orientation=N[2]),N.length>5&&E>8){var q=N[5];M.test(q)&&(P.itemRgb="rgb("+q+")")}if(N.length>E-3&&O)for(var j=E-3;j<N.length;++j)P[O.fields[j+3].name]=N[j];if(n(h,_+1,g,N))if(E<12)e(h,_+1,g,P);else{var D=0|N[3],L=0|N[4],I=0|N[6],B=N[7].split(","),V=N[8].split(",");if(P.exonFrames){var U=P.exonFrames.split(",");P.exonFrames=void 0}P.type="transcript";var F=new r;for(var G in P)F[G]=P[G];if(F.id=N[0],F.segment=this.bwg.idsToChroms[h],F.min=_+1,F.max=g,F.notes=[],P.groups=[F],N.length>9){var H=P.geneName||N[9],Y=H;N.length>10&&(Y=N[10]),P.geneName2&&(Y=P.geneName2);var X=i.extend({},F);X.id=H,X.label=Y,X.type="gene",P.groups.push(X)}for(var W=[],J=0;J<I;++J){var K=(0|V[J])+_,Z=K+(0|B[J]),Q=new d(K,Z);W.push(Q)}for(var tt=f(W),et=tt.ranges(),nt=0;nt<et.length;++nt){var it=et[nt];e(h,it.min()+1,it.max(),P)}if(L>D){var rt="+"==P.orientation?new d(D,L+3):new d(D-3,L),at=p(tt,rt);if(at){P.type="translation";for(var ot=at.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var nt=0;nt<ot.length;++nt){var ut=nt;"-"==P.orientation&&(ut=ot.length-nt-1);var it=ot[ut];if(P.readframe=st,U){var ct=parseInt(U[ut+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(P.readframe=ct,P.readframeExplicit=!0)}var ht=it.max()-it.min();st=(st+ht)%3,e(h,it.min()+1,it.max(),P)}}}}}}},u.prototype.getFirstAdjacent=function(t,e,n,i){var r=this.bwg.chromsToIDs[t];if(void 0===r)return i([]);this.getFirstAdjacentById(r,e,n,i)},u.prototype.getFirstAdjacentById=function(t,e,n,i){var r=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(a){r.cirHeader=a;var o=new Int32Array(r.cirHeader);r.cirBlockSize=o[1],r.getFirstAdjacentById(t,e,n,i)});var a=null,o=-1,l=-1,u=0,c=(Date.now(),function(t,e){u+=t.length;for(var n,i=4+32*r.cirBlockSize,a=0;a<t.length;++a){var o=new d(t[a],t[a]+i);n=n?f(n,o):o}for(var s=n.ranges(),l=0;l<s.length;++l){var c=s[l];h(t,c,e)}}),h=function(o,s,l,c){s.max(),s.min();r.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var h=0;h<o.length;++h)if(s.contains(o[h])&&(p(c,o[h]-s.min(),l),0==--u)){if(!a)return n>0&&(0!=t||e>0)?r.getFirstAdjacentById(0,0,n,i):n<0&&(t!=r.bwg.maxID||e<1e9)?r.getFirstAdjacentById(r.bwg.maxID,1e9,n,i):i([]);r.fetchFeatures(function(i,r,a,o){return n<0&&(i<t||a<e)||n>0&&(i>t||r>e)},[a],function(t){for(var e=null,r=-1,a=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,u=s.min,c=s.max;(null==e||n<0&&(l>r||c>a)||n>0&&(l<r||u<a))&&(e=s,a=n<0?c:u,r=l)}return i(null!=e?[e]:[])})}})},p=function(i,u,h){var d=new Uint8Array(i),f=new Int16Array(i),p=new Int32Array(i),_=d[u],g=f[u/2+1];if(u+=4,0!=_)for(var v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=s(d,u+16),C=s(d,u+24);(n<0&&(y<t||y==t&&b<=e)||n>0&&(w>t||w==t&&x>=e))&&(/_random/.exec(r.bwg.idsToChroms[y])||(null==a||n<0&&(w>o||w==o&&x>l)||n>0&&(y<o||y==o&&b<l))&&(a={offset:k,size:C},l=n<0?x:b,o=n<0?w:y)),u+=32}else{for(var M=-1,S=-1,v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=p[m+4]<<32|p[m+5];(n<0&&(y<t||y==t&&b<=e)&&w>=t||n>0&&(w>t||w==t&&x>=e)&&y<=t)&&(M<0||x>S)&&(M=k,S=n<0?x:b,n<0?w:y),u+=24}M>=0&&c([M],h+1)}};c([r.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,n){var i,r=n-e;if(r<=25e3||0===this.zoomLevels.length)i=this.getUnzoomedView();else for(var a=0;a<this.zoomLevels.length;a++)if(r/this.zoomLevels[a].reduction<25e3){i=this.getZoomedView(a);break}return i.readWigData(t,e,n)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new u(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new u(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,n,i,r){var a=this;if(!(t>=this.zoomLevels.length-1)){var o;return 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c=15,h=1440,d=0,f=0,p=1,_=-5,g=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],v=0,m=9,y=5,b=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],w=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],M=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,n){return t||(t=c),n&&(n=!1),this.istate=new e,this.istate.inflateInit(this,n?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new n(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var n,i;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,n=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,i=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+i)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&i)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?n:(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(n=t.istate.blocks.proc(t,n))){t.istate.mode=13,t.istate.marker=0;break}if(n==f&&(n=e),n!=p)return n;if(n=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,n){var i=0,r=n;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,n)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),r>=1<<t.istate.wbits&&(r=(1<<t.istate.wbits)-1,i=n-r),t.istate.blocks.set_dictionary(e,i,r),t.istate.mode=7,f)};var S=[0,0,255,255];e.prototype.inflateSync=function(t){var e,n,i,r,a;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(n=t.next_in_index,i=t.istate.marker;0!=e&&i<4;)t.next_in[n]==S[i]?i++:i=0!=t.next_in[n]?0:4-i,n++,e--;return t.total_in+=n-t.next_in_index,t.next_in_index=n,t.avail_in=e,t.istate.marker=i,4!=i?-3:(r=t.total_in,a=t.total_out,this.inflateReset(t),t.total_in=r,t.total_out=a,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];n.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},n.prototype.proc=function(t,e){var n,i,r,s,l,u,c;for(s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u;;)switch(this.mode){case v:for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}switch(n=7&i,this.last=1&n,n>>>1){case 0:i>>>=3,r-=3,n=7&r,i>>>=n,r-=n,this.mode=1;break;case 1:var h=new Int32Array(1),d=new Int32Array(1),_=[],m=[];a(h,d,_,m,t),this.codes.init(h[0],d[0],_[0],0,m[0],0,t),i>>>=3,r-=3,this.mode=6;break;case 2:i>>>=3,r-=3,this.mode=3;break;case 3:return i>>>=3,r-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}break;case 1:for(;r<32;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if((~i>>>16&65535)!=(65535&i))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.left=65535&i,i=r=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);if(0==c&&(u==end&&0!=read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c&&(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,u==this.end&&0!=this.read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c)))return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(e=f,n=this.left,n>l&&(n=l),n>c&&(n=c),o(t.next_in,s,this.window,u,n),s+=n,l-=n,u+=n,c-=n,0!=(this.left-=n))break;this.mode=0!=this.last?7:v;break;case 3:for(;r<14;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(this.table=n=16383&i,(31&n)>29||(n>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(n=258+(31&n)+(n>>5&31),null==this.blens||this.blens.length<n)this.blens=new Int32Array(n);else for(var y=0;y<n;y++)this.blens[y]=0;i>>>=14,r-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}this.blens[T[this.index++]]=7&i,i>>>=3,r-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(n=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=n,-3==e&&(this.blens=null,this.mode=9),this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(n=this.table,!(this.index<258+(31&n)+(n>>5&31)))break;var y,b,w;for(n=this.bb[0];r<n;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(n=this.hufts[3*(this.tb[0]+(i&g[n]))+1],(w=this.hufts[3*(this.tb[0]+(i&g[n]))+2])<16)i>>>=n,r-=n,this.blens[this.index++]=w;else{for(y=18==w?7:w-14,b=18==w?11:3;r<n+y;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(i>>>=n,r-=n,b+=i&g[y],i>>>=y,r-=y,y=this.index,n=this.table,y+b>258+(31&n)+(n>>5&31)||16==w&&y<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);w=16==w?this.blens[y-1]:0;do{this.blens[y++]=w}while(0!=--b);this.index=y}}this.tb[0]=-1;var h=new Int32Array(1),d=new Int32Array(1),_=new Int32Array(1),m=new Int32Array(1);if(h[0]=9,d[0]=6,n=this.table,(n=this.inftree.inflate_trees_dynamic(257+(31&n),1+(n>>5&31),this.blens,h,d,_,m,this.hufts,t))!=f)return-3==n&&(this.blens=null,this.mode=13),e=n,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.codes.init(h[0],d[0],this.hufts,_[0],this.hufts,m[0],t),this.mode=6;case 6:if(this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,this.read!=this.write)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);default:return e=-2,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}},n.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},n.prototype.set_dictionary=function(t,e,n){o(t,e,window,0,n),this.read=this.write=n},n.prototype.sync_point=function(){return 1==this.mode},n.prototype.inflate_flush=function(t,e){var n,i,r;return i=t.next_out_index,r=this.read,n=(r<=this.write?this.write:this.end)-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n,r==this.end&&(r=0,this.write==this.end&&(this.write=0),n=this.write-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n),t.next_out_index=i,this.read=r,e};i.prototype.init=function(t,e,n,i,r,a,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=n,this.ltree_index=i,this.dtree=r,this.dtree_index=a,this.tree=null},i.prototype.proc=function(t,e,n){var i,r,a,o,s,l,u,c=0,h=0,d=0;for(d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,n=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,n!=f)){this.mode=n==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>>=this.tree[r+1],h-=this.tree[r+1],0==(a=this.tree[r])){this.lit=this.tree[r+2],this.mode=6;break}if(0!=(16&a)){this.get=15&a,this.len=this.tree[r+2],this.mode=2;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}if(0!=(32&a)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 2:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.len+=c&g[i],c>>=i,h-=i,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>=this.tree[r+1],h-=this.tree[r+1],0!=(16&(a=this.tree[r]))){this.get=15&a,this.dist=this.tree[r+2],this.mode=4;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}return this.mode=9,e.msg="invalid distance code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 4:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.dist+=c&g[i],c>>=i,h-=i,this.mode=5;case 5:for(u=s-this.dist;u<0;)u+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);t.window[s++]=t.window[u++],l--,u==t.end&&(u=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(h>7&&(h-=8,o++,d--),t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);this.mode=8;case 8:return n=p,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 9:return n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);default:return n=-2,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n)}},i.prototype.free=function(t){},i.prototype.inflate_fast=function(t,e,n,i,r,a,s,l){var u,c,h,d,_,v,m,y,b,w,x,k,C,M,S,T;m=l.next_in_index,y=l.avail_in,_=s.bitb,v=s.bitk,b=s.write,w=b<s.read?s.read-b-1:s.end-b,x=g[t],k=g[e];do{for(;v<20;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(u=_&x,c=n,h=i,T=3*(h+u),0!=(d=c[T]))for(;;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15,C=c[T+2]+(_&g[d]),_>>=d,v-=d;v<15;)y--,_|=(255&l.next_in[m++])<<v,v+=8;for(u=_&k,c=r,h=a,T=3*(h+u),d=c[T];;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15;v<d;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(M=c[T+2]+(_&g[d]),_>>=d,v-=d,w-=C,b>=M)S=b-M,s.window[b++]=s.window[S++],s.window[b++]=s.window[S++],C-=2;else{S=b-M;do{S+=s.end}while(S<0);if(d=s.end-S,C>d){if(C-=d,b-S>0&&d>b-S)do{s.window[b++]=s.window[S++]}while(0!=--d);else o(s.window,S,s.window,b,d),b+=d,S+=d,d=0;S=0}}do{s.window[b++]=s.window[S++]}while(0!=--C);break}if(0!=(64&d))return l.msg="invalid distance code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3;u+=c[T+2],u+=_&g[d],T=3*(h+u),d=c[T]}break}if(0!=(64&d))return 0!=(32&d)?(C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3);if(u+=c[T+2],u+=_&g[d],T=3*(h+u),0==(d=c[T])){_>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--;break}}else _>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--}while(w>=258&&y>=10);return C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,f},r.prototype.huft_build=function(t,e,n,i,r,a,s,l,u,c,d){var p,g,v,m,y,b,w,x,k,C,M,S,T,$,A;C=0,y=n;do{this.c[t[e+C]]++,C++,y--}while(0!=y);if(this.c[0]==n)return s[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(w=b,x<b&&(x=b),y=15;0!=y&&0==this.c[y];y--);for(v=y,x>y&&(x=y),l[0]=x,$=1<<b;b<y;b++,$<<=1)if(($-=this.c[b])<0)return-3;if(($-=this.c[y])<0)return-3;for(this.c[y]+=$,this.x[1]=b=0,C=1,T=2;0!=--y;)this.x[T]=b+=this.c[C],T++,C++;y=0,C=0;do{0!=(b=t[e+C])&&(this.v[this.x[b]++]=y),C++}while(++y<n);for(n=this.x[v],this.x[0]=y=0,C=0,m=-1,S=-x,this.u[0]=0,M=0,A=0;w<=v;w++)for(p=this.c[w];0!=p--;){for(;w>S+x;){if(m++,S+=x,A=v-S,A=A>x?x:A,(g=1<<(b=w-S))>p+1&&(g-=p+1,T=w,b<A))for(;++b<A&&!((g<<=1)<=this.c[++T]);)g-=this.c[T];if(A=1<<b,this.hn[0]+A>h)return-3;this.u[m]=M=this.hn[0],this.hn[0]+=A,0!=m?(this.x[m]=y,this.r[0]=b,this.r[1]=x,b=y>>>S-x,this.r[2]=M-this.u[m-1]-b,o(this.r,0,u,3*(this.u[m-1]+b),3)):s[0]=M}for(this.r[1]=w-S,C>=n?this.r[0]=192:d[C]<i?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=a[this.v[C]-i]+16+64,this.r[2]=r[this.v[C++]-i]),g=1<<w-S,b=y>>>S;b<A;b+=g)o(this.r,0,u,3*(M+b),3);for(b=1<<w-1;0!=(y&b);b>>>=1)y^=b;for(y^=b,k=(1<<S)-1;(y&k)!=this.x[m];)m--,S-=x,k=(1<<S)-1}return 0!=$&&1!=v?_:f},r.prototype.inflate_trees_bits=function(t,e,n,i,r){var a;return this.initWorkArea(19),this.hn[0]=0,a=this.huft_build(t,0,19,19,null,null,n,e,i,this.hn,this.v),-3==a?r.msg="oversubscribed dynamic bit lengths tree":a!=_&&0!=e[0]||(r.msg="incomplete dynamic bit lengths tree",a=-3),a},r.prototype.inflate_trees_dynamic=function(t,e,n,i,r,a,o,s,l){var u;return this.initWorkArea(288),this.hn[0]=0,(u=this.huft_build(n,0,t,257,x,k,a,i,s,this.hn,this.v))!=f||0==i[0]?(-3==u?l.msg="oversubscribed literal/length tree":-4!=u&&(l.msg="incomplete literal/length tree",u=-3),u):(this.initWorkArea(288),u=this.huft_build(n,t,e,0,C,M,o,r,s,this.hn,this.v),u!=f||0==r[0]&&t>257?(-3==u?l.msg="oversubscribed distance tree":u==_?(l.msg="incomplete distance tree",u=-3):-4!=u&&(l.msg="empty distance tree with lengths",u=-3),u):f)},r.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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u.default.Button({icon:"fa-check",tooltip:"Execute: "+n.name+" ("+n.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){i.wait(),t.portlet.disable(),e.submit(n,function(){i.unwait(),t.portlet.enable()})}});n.buttons={execute:i},n.job_id&&n.job_remap&&n.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",n.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var n=this,a={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!n.validate(a))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=i("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return r.each(a.inputs,function(t,e){o.append(i("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",a),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:a,success:function(t){if(e&&e(),n.$el.children().hide(),n.$el.append(n._templateSuccess(t)),t.jobs&&t.jobs.length>0){n.$el.append(i("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:a.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var i=!1;if(t&&t.err_data){var r=n.form.data.matchResponse(t.err_data);for(var o in r){n.form.highlight(o,r[o]),i=!0;break}}i||n.modal.show({title:"Job submission failed",body:n._templateError(a,t&&t.err_msg),buttons:{Close:function(){n.modal.hide()}}})}})},validate:function(t){var e=t.inputs,n=-1,i=null;for(var r in e){var a=e[r],o=this.form.data.match(r),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==a)return this.form.highlight(o),!1;if(a&&a.batch){var u=a.values.length,c=u>0&&a.values[0]&&a.values[0].src;if(c)if(null===i)i=c;else if(i!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=u;else if(n!==u)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+u+"</b> selection(s) while a previous field contains <b>"+n+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,n=1==e?"1 job has":e+" jobs have",a=i("<div/>").addClass("donemessagelarge").append(i("<p/>").text(n+" been successfully added to the queue - resulting in the following datasets:"));return r.each(t.outputs,function(t){a.append(i("<p/>").addClass("messagerow").append(i("<b/>").text(t.hid+": "+t.name)))}),a.append(i("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),a}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return i("<div/>").addClass("errormessagelarge").append(i("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(i("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:g}}).call(e,n(1),n(0),n(2))},,function(t,e,n){"use strict";(function(t,n,i){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==n.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,n){if(n){var i,r=this.attributes.filters[t];if(null===r||void 0===r)i=e;else if("string"==typeof r)if("All"==r||r==e)i=e;else{var a=[];a[0]=r,a[1]=e,i=a}else i=r,-1===i.indexOf(e)&&i.push(e);this.attributes.filters[t]=i}else this.attributes.filters[t]=e},remove_filter:function(t,e){var i=this.attributes.filters[t];if(null===i||void 0===i)return!1;if("string"==typeof i)this.attributes.filters[t]="";else{var r=n.indexOf(i,e);-1!==r&&(i[r]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return n.each(n.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+i.param(this.get_url_data())+"&"+i.param(t)}})}).call(e,n(1),n(2),n(0))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=function(t){return t&&t.__esModule?t:{default:t}}(r);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" 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t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var n in t.columns){var i=t.columns[n];i.visible&&(e+='<th id="'+i.key+'-header">',i.href?e+='<a href="'+i.href+'" class="sort-link" sort_key="'+i.key+'">'+i.label+"</a>":e+=i.label,e+='<span class="sort-arrow">'+i.extra+"</span></th>")}return e+="</tr>"},body:function(e){var n="",i=0;0==e.items.length&&(n+='<tr><td colspan="100"><em>No Items</em></td></tr>',i=1);for(var r in e.items){var a=e.items[r],o=a.encode_id;n+="<tr ",e.current_item_id==a.id&&(n+='class="current"'),n+=">",e.show_item_checkboxes&&(n+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var 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f=t.operations[d];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(d in t.operations)if(t.operations[d].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(d in t.operations){var f=t.operations[d];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+i.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,n=t.filters,i="none";t.advanced_search&&(i="block");var r=!1;for(var a in t.columns){var o=t.columns[a];if("advanced"==o.filterable){var s=o.key,l=n[s],u=e[s];l&&u&&l!=u&&(i="block"),r=!0}}var c="block";"block"==i&&(c="none");var h='<div 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m=e.categorical_filters[a][v],y="",b="";for(var w in m)y=w,b=m[w];g&&(o+=" | "),g=!0;var d=i[a];d&&m[a]&&d==b?o+='<span class="categorical-filter '+a+'-filter current-filter">'+v+"</span>":o+='<span class="categorical-filter '+a+'-filter"><a href="javascript:void(0);" filter_key="'+y+'" filter_val="'+b+'">'+v+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=a.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(146),l=r(s),u=n(13),c=r(u),h=n(41),d=r(h),f=n(61),p=r(f),_=n(26),g=r(_),v=n(3),m=r(v);n(170),n(169),n(171),n(157),n(174),n(159),n(172),n(173),n(25);var y=null,b=null,w=function(){this.initialize&&this.initialize.apply(this,arguments)};w.extend=t.Model.extend;var x=w.extend({initialize:function(t){m.default.cssLoadFile("static/style/jquery.rating.css"),m.default.cssLoadFile("static/style/autocomplete_tagging.css"),m.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),m.default.cssLoadFile("static/style/library.css"),m.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];i(".bookmark").each(function(){t.push({position:i(this).children(".position").text(),annotation:i(this).children(".annotation").text()})});var e=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,n={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:e},bookmarks:t};return i.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(t){Galaxy.modal.hide(),b.vis_id=t.vis_id,b.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=d.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(t){o.each(t,function(t){b.add_drawable(l.default.object_from_template(t,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==i("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,n){var r=i("#right .unified-panel-body"),a=i("<div/>").addClass("bookmark").appendTo(r),o=i("<div/>").addClass("position").appendTo(a),s=(i("<a href=''/>").text(t).appendTo(o).click(function(){return b.go_to(t),!1}),i("<div/>").text(e).appendTo(a));if(n){var l=i("<div/>").addClass("delete-icon-container").prependTo(a).click(function(){return a.slideUp("fast"),a.remove(),b.has_changes=!0,!1});i("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,a},create_visualization:function(t,e,n,r,a){var s=this,u=new l.default.TracksterView(o.extend(t,{header:!1}));return u.editor=!0,i.when(u.load_chroms_deferred).then(function(t){if(e){var i=e.chrom,o=e.start,c=e.end,h=e.overview;i&&void 0!==o&&c?u.change_chrom(i,o,c):u.change_chrom(t[0].chrom)}else u.change_chrom(t[0].chrom);if(n)for(var d=0;d<n.length;d++)u.add_drawable(l.default.object_from_template(n[d],u,u));for(var d=0;d<u.drawables.length;d++)if(u.drawables[d].config.get_value("name")===h){u.set_overview(u.drawables[d]);break}if(r)for(var f,d=0;d<r.length;d++)f=r[d],s.add_bookmark(f.position,f.annotation,a);u.has_changes=!1}),this.set_up_router({view:u}),u},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){i(document).keyup(function(e){if(!i(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){i(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){i.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){y=new x(Galaxy.root),y.createButtonMenu(),y.buttonMenu.$el.attr("style","float: right"),i("#center .unified-panel-header-inner").append(y.buttonMenu.$el),i("#right .unified-panel-title").append("Bookmarks"),i("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),i("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),n={},i={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(n["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(i)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new g.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){i(parent.document).find("input[name=id]:checked").each(function(){t.id=i(this).val(),window.location=Galaxy.root+"visualization/trackster?"+i.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;b=y.create_visualization({container:i("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;i.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(i("#new-title").val(),i("#new-dbkey").val()),Galaxy.modal.hide()}}});var n=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(n,galaxy_config.app.default_dbkey)&&i("#new-dbkey").val(galaxy_config.app.default_dbkey),i("#new-title").focus(),i("select[name='dbkey']").select2(),i("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',n=0;n<t.length;n++)e+='<option value="'+t[n][1]+'">'+t[n][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>'},create_browser:function(t,e){i(document).trigger("convert_to_values"),b=y.create_visualization({container:i("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){i("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&i.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){b.add_drawable(l.default.object_from_template(t,b,b))}}),i("#add-bookmark-button").click(function(){var t=b.chrom+":"+b.low+"-"+b.high;return y.add_bookmark(t,"Bookmark description",!0)}),y.init_keyboard_nav(b),i(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t,e){e||(e=0);var n=Math.pow(10,e);return Math.round(t*n)/n}function o(e){var n=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,i){n.resolve(206===i.status)}}),n}Object.defineProperty(e,"__esModule",{value:!0});var s=n(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(s),u=n(13),c=r(u),h=n(147),d=r(h),f=n(14),p=r(f),_=n(148),g=r(_),v=n(149),m=r(v),y=n(150),b=r(y),w=n(15),x=r(w),k=n(140),C=r(k),M=n(21),S=r(M),T=n(151),$=r(T);n(25);var A=l.extend,E={},O=function(t,e){E[t.attr("id")]=e},z=function(e,n,i,r){i=".group",E[e.attr("id")]=r,e.bind("drag",{handle:"."+n,relative:!0},function(e,n){var r,a,o,s,l,u=(t(this),t(this).parent()),c=u.children(".track,.group"),h=E[t(this).attr("id")];if(a=t(this).parents(i),0!==a.length){o=a.position().top,s=o+a.outerHeight();var d=E[a.attr("id")];if(n.offsetY<o)return t(this).insertBefore(a),d.remove_drawable(h),void d.container.add_drawable_before(h,d);if(n.offsetY>s)return t(this).insertAfter(a),d.remove_drawable(h),void d.container.add_drawable(h)}for(a=null,l=0;l<c.length;l++)if(r=t(c.get(l)),o=r.position().top,s=o+r.outerHeight(),r.is(i)&&this!==r.get(0)&&n.offsetY>=o&&n.offsetY<=s)return n.offsetY-o<s-n.offsetY?r.find(".content-div").prepend(this):r.find(".content-div").append(this),h.container&&h.container.remove_drawable(h),void E[r.attr("id")].add_drawable(h);for(l=0;l<c.length&&(r=t(c.get(l)),!(n.offsetY<r.position().top)||r.hasClass("reference-track")||r.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(u.append(this),E[u.attr("id")].move_drawable(h,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),E[u.attr("id")].move_drawable(h,n.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",N=["Histogram","Line","Filled","Intensity"],P=function t(e,n,i){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=n,this.drag_handle_class=i.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,i.prefs),this.config.get_value("name")||this.config.set_value("name",i.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==i.header){var r=new d.default.TrackHeaderView({model:this,id:this.id});this.header_div=r.$el,this.container_div.append(this.header_div);var a=r.icons_div;this.action_icons=r.action_icons,this.container_div.hover(function(){a.show()},function(){a.hide()})}};P.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new S.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],A(P.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,n){P.call(this,t,e,n),this.obj_type=n.obj_type,this.drawables=[]};A(q.prototype,P.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,n=0;n<t.length;n++)e=it(t[n],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables.splice(n,0,t),!0)},replace_drawable:function(t,e,n){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables[i]=e,n&&t.container_div.replaceWith(e.container_div),this.changed()),i},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables.splice(n,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,n=this.drawables.slice(0),i=[];0!==n.length;)e=n.shift(),e instanceof t?i.push(e):e.drawables&&(n=n.concat(e.drawables));return i}});var j=function(e,n,i){if(A(i,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,n,i),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in i&&this.unpack_drawables(i.drawables),"filters"in i){var r=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,i.filters),r.parent_div.replaceWith(this.filters_manager.parent_div),i.filters.visible&&this.setup_multitrack_filtering()}};A(j.prototype,P.prototype,q.prototype,{action_icons_def:[P.prototype.action_icons_def[0],P.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},P.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof W),this.action_icons.filters_icon.hide();else{var n,i,r,a=this.drawables[0].get_type(),o=0;for(n=0;n<e;n++){if(r=this.drawables[n],r.get_type()!==a){can_composite=!1;break}r instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(r=this.drawables[0],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],l[s.name]=[s];for(n=1;n<this.drawables.length;n++)for(r=this.drawables[n],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var u,c;for(var h in l)u=l[h],u.length===o&&(c=new b.default.NumberFilter({name:u[0].name,index:u[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new W(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=A(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var D=i.View.extend({initialize:function(t){A(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,n=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,n),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:n.dbkey},function(t){l.each(t,function(t){n.add_drawable(it(t,n,n))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var i=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&n.go_to(t(this).val()),t(this).hide(),t(this).val(""),n.location_span.show(),n.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",i).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){n.location_span.hide(),n.chrom_select.hide(),n.nav_input.val(n.chrom+":"+n.low+"-"+n.high),n.nav_input.css("display","inline-block"),n.nav_input.select(),n.nav_input.focus(),n.nav_input.autocomplete({source:function(e,i){var r=[],a=t.map(n.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){r=r.concat(t)})});t.when.apply(t,a).done(function(){i(t.map(r,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){n.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){n.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){n.change_chrom(n.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){n.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var i=e.offsetX-this.current_x;this.current_x=e.offsetX;var r=Math.round(i/n.viewport_container.width()*(n.max_high-n.max_low));n.move_delta(-r)}),this.overview_close.click(function(){n.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>n.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=n.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,i){var r=t(this),a=i.offsetX-i.current_x,o=r.scrollTop()-(e.clientY-i.current_height);r.scrollTop(o),i.current_height=e.clientY,i.current_x=i.offsetX;var s=Math.round(a/n.viewport_container.width()*(n.high-n.low));n.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,i){return t("<div/>").addClass("zoom-area").css("height",n.browser_content_div.height()+n.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,i){t(i.proxy).css({left:Math.min(e.pageX,i.startX)-n.container.offset().left,width:Math.abs(e.pageX-i.startX)});var r=Math.min(e.pageX,i.startX)-n.container.offset().left,a=Math.max(e.pageX,i.startX)-n.container.offset().left,o=n.high-n.low,s=n.viewport_container.width();n.update_location(Math.round(r/s*o)+n.low,Math.round(a/s*o)+n.low)}).bind("dragend",function(e,i){var r=Math.min(e.pageX,i.startX),a=Math.max(e.pageX,i.startX),o=n.high-n.low,s=n.viewport_container.width(),l=n.low;n.low=Math.round(r/s*o)+l,n.high=Math.round(a/s*o)+l,t(i.proxy).remove(),n.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){n.resize_window()},500)}),t(document).bind("redraw",function(){n.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});A(D.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,n,i){if(this.timer&&clearTimeout(this.timer),i){var r=this;this.timer=setTimeout(function(){r.trigger("navigate",t+":"+e+"-"+n)},500)}else view.trigger("navigate",t+":"+e+"-"+n)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var n=this.chrom_select.val();""!==n&&this.trigger_navigate(n,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var n=this,i=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var r=new J(n);n.add_label_track(r),n.reference_track=r}n.chrom_data=e.chrom_info,n.chrom_select.html(""),n.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var a=0,o=n.chrom_data.length;a<o;a++){var s=n.chrom_data[a].chrom,l=t("<option>");l.text(s),l.val(s),n.chrom_select.append(l)}e.prev_chroms&&n.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&n.chrom_select.append(t('<option value="next">Next 100</option>')),n.chrom_start_index=e.start_index,i.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+n.dbkey)}}),i},change_chrom:function(e,n,i){var r=this;if(!r.chrom_data)return void r.load_chroms_deferred.then(function(){r.change_chrom(e,n,i)});if(e&&"None"!==e){if("previous"===e)return void r.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void r.load_chroms({low:this.chrom_start_index+100});var a=t.grep(r.chrom_data,function(t,n){return t.chrom===e})[0];if(void 0===a)return void r.load_chroms({chrom:e},function(){r.change_chrom(e,n,i)});if(e!==r.chrom){r.chrom=e,r.chrom_select.val(r.chrom),r.max_high=a.len-1,r.reset();for(var o=0,s=r.drawables.length;o<s;o++){var l=r.drawables[o];l.init&&l.init()}r.reference_track&&r.reference_track.init()}void 0===n&&void 0===i?(r.low=0,r.high=r.max_high):(r.low=void 0!==n?Math.max(n,0):0,void 0===i?(r.low=Math.max(r.low-15,0),r.high=r.low+30):r.high=Math.min(i,r.max_high)),r.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),n=e[0],i=e[1]?parseInt(e[1],10):void 0,r=e[2]?parseInt(e[2],10):void 0;this.change_chrom(n,i,r)},move_fraction:function(t){var e=this,n=e.high-e.low;this.move_delta(t*n)},move_delta:function(t){var e=this,n=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+n):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-n):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var i=e.chrom_select.val();this.trigger_navigate(i,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,n){if(q.prototype.remove_drawable.call(this,e),n){var i=this;e.container_div.hide(0,function(){t(this).remove(),i.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var n=this,i=e?[e]:n.drawables;l.each(i,function(e){var i=l.find(n.tracks_to_be_redrawn,function(t){return t[0]===e});i?i[1]=t:n.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){n._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var n=this.high-this.low;0!==this.high&&n<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var i=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,r=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:i,width:Math.max(13,r)}).show(),r<13&&this.overview_box.css("left",i-(13-r)/2),this.overview_highlight&&this.overview_highlight.css({left:i,width:r}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],n=t[1];e&&e._draw(n)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var n=this.high-this.low,i=n/2+this.low,r=n/this.zoom_factor/2;t&&(i=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(i-r),this.high=Math.round(i+r),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,n=t*this.zoom_factor/2;this.low=Math.round(e-n),this.high=Math.round(e+n),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),n=this;e.header_div.hide(),e.is_overview=!0,n.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){n.overview_highlight.show().height(n.overview_drawable.content_div.height()),n.overview_viewport.height(n.overview_drawable.content_div.height()+n.overview_box.outerHeight()),n.overview_close.show(),n.resize_window()},n.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=i.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),n=this.model;t("<div>").addClass("param-label").text(n.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(n.get("html")).appendTo(e).find(":input").val(n.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=i.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,n=this.model,i=this.$el.addClass("dynamic-tool").hide();i.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(i).text(n.get("name"));n.get("inputs").each(function(t){var e=new I({model:t});e.render(),i.append(e.$el)}),i.find("input").click(function(){t(this).select()});var r=t("<div>").addClass("param-row").appendTo(i),a=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(r);t("<input type='submit'>").attr("value","Run on visible region").appendTo(r).click(function(){e.run_on_region()}),a.click(function(){e.run_on_dataset()}),n.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),n=this.model,i=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),r={target_dataset_id:e.dataset.id,action:"rerun",tool_id:n.id,regions:[i.toJSON()]},a=e,o=n.get("name")+a.tool_region_and_parameters_str(i);if(a.container===view){var s=new j(view,view,{name:e.config.get_value("name")}),l=a.container.replace_drawable(a,s,!1);s.container_div.insertBefore(a.view.content_div.children()[l]),s.add_drawable(a),a.container_div.appendTo(s.content_div),t=s}else t=a.container;var u=new a.constructor(view,t,{name:o,hda_ldda:"hda"});u.init_for_tool_data(),u.change_mode(a.mode),u.set_filters_manager(a.filters_manager.copy(u)),u.update_icons(),t.add_drawable(u),u.tiles_div.text("Starting job."),this.run(r,u,function(t){u.set_dataset(new x.default.Dataset(t)),u.tiles_div.text("Running job."),u.init()})},run:function(e,n,i){e.inputs=this.model.get_inputs_dict();var r=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(r.go()).then(function(t){"no converter"===t?(n.container_div.addClass("error"),n.content_div.text(R)):t.error?(n.container_div.addClass("error"),n.content_div.text("Tool cannot be rerun: "+t.message)):i(t)})}}),V=function(t,e){m.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var U=function(e,n,i,r,a){this.track=e,this.region=n,this.low=n.get("start"),this.high=n.get("end"),this.w_scale=i,this.canvas=r,this.html_elt=t("<div class='track-tile'/>").append(r),this.data=a,this.stale=!1};U.prototype.predisplay_actions=function(){};var F=function(t,e,n,i,r){U.call(this,t,e,n,i,r)};F.prototype.predisplay_actions=function(){};var G=function(t,e,n,i,r,a,o,s,l,u,c){U.call(this,t,e,n,i,r),this.mode=a,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=u,this.other_tiles_features_drawn={},this.seq_data=c};A(G.prototype,U.prototype),G.prototype.predisplay_actions=function(){};var H=function(e,n,r){A(r,{drag_handle_class:"draghandle"}),P.call(this,e,n,r),this.dataset=null,r.dataset&&(this.dataset=r.dataset instanceof i.Model?r.dataset:new x.default.Dataset(r.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in r?r.data_query_wait:5e3,this.data_manager="data_manager"in r?r.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in r&&!r.resize||this.add_resize_handle())};A(H.prototype,P.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},P.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},P.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var n="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',r=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},a=function(){var n,r=t('select[name="regions"] option:selected').val(),a=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});n="cur"===r?[a]:"bookmarks"===r?o:[a].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new i.Collection(n).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:n,buttons:{No:r,Yes:a}})}},P.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&P.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,n=!1,i=!1,r=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(n=!0,r.show())},function(){n=!1,i||r.hide()}),r.hide().bind("dragstart",function(n,r){i=!0,r.original_height=t(e.content_div).height()}).bind("drag",function(n,i){var r=Math.min(Math.max(i.original_height+i.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",r),e.visible_height_px=e.max_height_px===r?0:r,e.on_resize()}).bind("dragend",function(t,a){e.tile_cache.clear(),i=!1,n||r.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof J?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof W?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var n=this;if(n.enabled=!1,n.tile_cache.clear(),n.data_manager.clear(),n.content_div.children().remove(),n.container_div.removeClass("nodata error pending"),n.tiles_div=t("<div/>").addClass("tiles").appendTo(n.content_div),n.dataset.id){var i=t.Deferred(),r={hda_ldda:n.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:n.view.chrom,retry:e};return t.getJSON(this.dataset.url(),r,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(n.container_div.addClass("error"),n.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(n.container_div.addClass("nodata"),n.show_message("No data for this chrom/contig.")):"pending"===e?(n.container_div.addClass("pending"),n.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){n.init()},n.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(n.valid_chroms=e.valid_chroms,n.update_icons()),n.tiles_div.text("Ready for display"),n.view.chrom?(n.tiles_div.text(""),n.tiles_div.css("height",n.visible_height_px+"px"),n.enabled=!0,t.when.apply(t,n.predraw_init()).done(function(){i.resolve(),n.container_div.removeClass("nodata error pending"),n.request_draw()})):i.resolve());else{n.container_div.addClass("error");var r=n.show_message("Cannot display dataset due to an error. ");e.message&&(r.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),r.append(t("<span/>").text(" ")),r.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){n.init(!0)})))}}),this.update_icons(),i}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(n&&void 0!==n.min&&void 0!==n.max){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_default_value("min_value",i),e.config.set_default_value("max_value",r),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},get_drawables:function(){return this}});var Y=function(e,n,i){H.call(this,e,n,i);var r=this;if(z(r.container_div,r.drag_handle_class,".group",r),this.filters_manager=new b.default.FiltersManager(this,"filters"in i?i.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=i.tool?new L(l.extend(i.tool,{track:this,tool_state:i.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var a=new B({model:this.tool});a.render(),this.dynamic_tool_div=a.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),i.mode&&this.change_mode(i.mode)};A(Y.prototype,P.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();A(e,{data_manager:this.data_manager});var n=new this.constructor(this.view,t,e);return n.change_mode(this.mode),n.enabled=this.enabled,n},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var n=e&&e.clear_after,i=this.view.low,r=this.view.high,a=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(i=this.view.max_low,r=this.view.max_high,o=a/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var u,h,d=Math.floor(400*s),f=Math.floor(i/d),p=[],_=[];f*d<r;)u=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*d,end:Math.min((f+1)*d,this.view.max_high)}),h=this.draw_helper(u,o,e),p.push(h),t.when(h).then(function(t){_.push(t)}),f+=1;n||this.tiles_div.children(".remove").removeClass("remove").remove();var g=this;t.when.apply(t,p).then(function(){g.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&g.postdraw_actions(_,a,o,n)})}},_add_yaxis_label:function(e,n){var i=this,r="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+r),u=a(i.config.get_value(s),1);n=n||function(){i.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(u):(l=t("<div/>").text(u).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),i.config.set_value(s,a(e,1)),n()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+r).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,n,i){if(l.filter(t,function(t){return t instanceof F}).length>0){this.max_height_px=0;var r=this;l.each(t,function(t){t instanceof F||(t.html_elt.remove(),r.draw_helper(t.region,n,{force:!0,mode:"Coverage"}))}),r._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,n,i){i||(i={});var r=i.force,a=i.mode||this.mode,o=1/n,s=this,u=this._get_drawables(),c=this._gen_tile_cache_key(n,e),h=r?void 0:s.tile_cache.get_elt(c);if(h)return function(t){return t&&"track"in t}(h)&&s.show_tile(h,n),h;if(!1===i.data_fetch)return null;var d=function(){var t=l.find(N,function(t){return t===a})?"Coverage":a,n=l.map(u,function(n){return n.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&n.push(view.reference_track.data_manager.get_data(e,a,o,view.reference_track.data_url_extra_params)),n},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,d()).then(function(){var r,a=d(),o=a;if(l.find(a,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,n,i)).then(function(t){f.resolve(t)});view.reference_track&&(r=view.reference_track.data_manager.subset_entry(a.pop(),e));var h=[],_=[];l.each(u,function(t,e){var i=t.mode,r=o[e];"Auto"===i&&(i=t.get_mode(r),t.update_auto_mode(i)),h.push(i),_.push(t.get_canvas_height(r,i,n,b))});var g,v=s.view.canvas_manager.new_canvas(),m=e.get("start"),y=e.get("end"),b=Math.ceil((y-m)*n)+s.left_offset,w=l.max(_);v.width=b,v.height=i.height||w;var x=v.getContext("2d");x.translate(s.left_offset,0),u.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(u,function(t,i){g=t.draw_tile(o[i],x,h[i],e,n,r)}),void 0!==g&&(s.tile_cache.set_elt(c,g),s.show_tile(g,n)),f.resolve(g)}),f},get_canvas_height:function(t,e,n,i){return this.visible_height_px},_draw_line_track_tile:function(t,e,n,i,r){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var a=e.canvas;return new m.default.LinePainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new F(this,i,r,a,t.data)},draw_tile:function(t,e,n,i,r,a){},show_tile:function(t,e){var n=t.html_elt;t.predisplay_actions();var i=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(i-=this.left_offset),n.css("left",i),n.hasClass("remove")?n.removeClass("remove"):this.tiles_div.append(n),n.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,n.height()-2),n.parent().children().css("height",this.max_height_px+"px");var r=this.max_height_px;0!==this.visible_height_px&&(r=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",r+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};A(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var n=this.view,i=n.high-n.low,r=Math.floor(Math.pow(10,Math.floor(Math.log(i)/Math.log(10)))),a=Math.floor(n.low/r)*r,o=this.view.container.width(),s=t("<div/>").addClass("label-container");a<n.high;){var l=Math.floor((a-n.low)/i*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(a)).css({left:l})),a+=r}this.content_div.children(":first").remove(),this.content_div.append(s)}});var W=function(t,e,n){if(Y.call(this,t,e,n),this.drawables=[],"drawables"in n){for(var i,r=0;r<n.drawables.length;r++)i=n.drawables[r],this.drawables[r]=it(i,t,null),i.left_offset>this.left_offset&&(this.left_offset=i.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};A(W.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],n=0;n<this.drawables.length;n++)e.push(this.drawables[n].init());var i=this;t.when.apply(t,e).then(function(){i.enabled=!0,i.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:P.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new j(this.view,this.container,{name:this.config.get_value("name")}),n=0;n<this.drawables.length;n++)t=this.drawables[n],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,n,i){var r,a=-1;for(r=0;r<t.length;r++){var o=t[r].html_elt.find("canvas").height();o>a&&(a=o)}for(r=0;r<t.length;r++){var s=t[r];s.html_elt.find("canvas").height()!==a&&(this.draw_helper(s.region,n,{force:!0,height:a}),s.html_elt.remove())}var l=this,u=function(){l.update_all_min_max()};this._add_yaxis_label("min",u),this._add_yaxis_label("max",u)}});var J=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};A(J.prototype,P.prototype,Y.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:P.prototype.can_draw,draw_helper:function(t,e,n){var i,r=this.tiles_div.is(":visible"),a=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),i=!0,a=Y.prototype.draw_helper.call(this,t,e,n)):(i=!1,this.tiles_div.hide()),r!==i&&this.view.resize_viewport(),a},can_subset:function(t){return!0},draw_tile:function(t,e,n,i,r){var a=this.data_manager.subset_entry(t,i),o=a.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,u=o.length;l<u;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*r),10);return new U(this,i,r,s,a)}});var K=function(e,n,i){this.mode="Histogram",Y.call(this,e,n,i),this.left_offset=30;var r=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(r.data_manager=new $.default.BBIDataManager({dataset:r.dataset}))})};A(K.prototype,P.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,n,i,r){return this._draw_line_track_tile(t,e,n,i,r)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,n,i){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,n){this.mode="Heatmap",Y.call(this,t,e,n)};A(Z.prototype,P.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,n,i,r){var a=e.canvas;return new m.default.DiagonalHeatmapPainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new U(this,i,r,a,t.data)}});var Q=function(t,e,n){Y.call(this,t,e,n),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};A(Q.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=m.default.ArcLinkedFeaturePainter:this.painter=m.default.LinkedFeaturePainter},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a,o=this;if(0===l.filter(e,function(t){return t instanceof F}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var u=this;l.each(e,function(e){var n=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(n=l.omit(n,l.keys(e.other_tiles_features_drawn)),0!==l.size(n)){var i={data:l.values(n)},r=u.view.canvas_manager.new_canvas(),a=r.getContext("2d");r.height=Math.max(e.canvas.height,u.get_canvas_height(i,e.mode,e.w_scale,100)),r.width=e.canvas.width,a.drawImage(e.canvas,0,0),a.translate(o.left_offset,0);var c=u.draw_tile(i,a,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=r,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,h=o.filters_manager.filters;for(c=0;c<h.length;c++)h[c].update_ui_elt();var d,f,p=!1;for(a=0;a<e.length;a++)if(e[a].data.length)for(d=e[a].data[0],c=0;c<h.length;c++)if(f=h[c],f.applies_to(d)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof G){var _=!0;for(a=0;a<e.length;a++)if(!e[a].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,n){var i=this.view.canvas_manager.dummy_context,r=this.slotters[t];return r&&r.mode===n||(r=new g.default.FeatureSlotter(t,n,100,function(t){return i.measureText(t)}),this.slotters[t]=r),r.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,n,i){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.incremental_slots(n,t.data,e),a=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,a.get_required_height(r,i))},draw_tile:function(t,e,n,i,r,a,o){var s=this,l=e.canvas,u=i.get("start"),c=i.get("end"),h=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,n,i,r);var d=[],f=this.slotters[r].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,g=0,v=t.data.length;g<v;g++){for(var m,y=t.data[g],b=!1,w=0,x=_.length;w<x;w++)if(m=_[w],m.update_attrs(y),!m.keep(y)){b=!0;break}b||(d.push(y),y[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,M=new this.painter(d,u,c,this.config.to_key_value_dict(),n,k,C,a,function(t){return s.view.get_base_color(t)}),S=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=M.draw(e,l.width,l.height,r,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-h}return o?void 0:new G(s,i,r,l,t.data,n,t.message,p,S,incomplete_features,a)}});var tt=function(t,e,n){Y.call(this,t,e,n),this.painter=m.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};A(tt.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,n,i,r){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",i,r);var a=this.view;return new this.painter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n,function(t){return a.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,r),new U(this,i,r,e.canvas,t.data)},get_canvas_height:function(t,e,n,i){if("bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===r&&0!==t.data.length&&(r=t.data[0][7].match(/,/g),r=null===r?1:r.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(r)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a=l.filter(e,function(t){return t instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===a.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var u=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(u).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,n){Q.call(this,t,e,n),this.painter=m.default.ReadPainter,this.update_icons()};A(et.prototype,P.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var nt={CompositeTrack:W,DrawableGroup:j,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},it=function(t,e,n){if("copy"in t)return t.copy(n);var i=t.obj_type;return i||(i=t.track_type),new nt[i](e,n,t)};e.default={TracksterView:D,DrawableGroup:j,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:W,object_from_template:it}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(r),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(i("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(i("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(i("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=i("<div/>").addClass("track-icons").hide().appendTo(this.$el),a.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,n,r,a,o){var s=this;this.action_icons[t]=i("<a/>").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(function(){r(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var n=this.model,i={},r=0,a=n.display_modes.length;r<a;r++){var o=n.display_modes[r];i[o]=function(t){return function(){n.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,i)}}});e.default={TrackHeaderView:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,n,i){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=n,this.measureText=i};a(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),n=Math.ceil(t[2]*this.w_scale),i=t[3];if(void 0!==i&&this.include_label){var r=this.measureText(i).width+7;e-r>=0?(e-=r,"left"):(n+=r,"right")}return[e,n]},_find_slot:function(t){for(var e=t[0],n=t[1],i=0;i<=this.max_rows;i++){var r=!1,a=this.start_end_dct[i];if(void 0!==a)for(var o=0,s=a.length;o<s;o++){var l=a[o];if(n>l[0]&&e<l[1]){r=!0;break}}if(!r)return i}return-1},slot_features:function(t){for(var e,n,i=this.start_end_dct,r=[],a=0,s=0,l=t.length;s<l;s++){e=t[s],n=e[0];var u=this.slots[n];if(u){if(e[1]<u.feature[1]||u.feature[2]<e[2])for(var c=this._get_draw_coords(u.feature),h=this._get_draw_coords(e),d=this.start_end_dct[u.slot],f=0;f<d.length;f++){var p=d[f];p[0]===c[0]&&p[1]===c[1]&&(d[f]=h)}a=Math.max(a,this.slots[n].slot)}else r.push(s)}for(var s=0,l=r.length;s<l;s++){e=t[r[s]],n=e[0];var _=this._get_draw_coords(e),g=this._find_slot(_);g>=0&&(void 0===i[g]&&(i[g]=[]),i[g].push(_),this.slots[n]=new o(g,e),a=Math.max(a,g))}return a+1}}),e.default={FeatureSlotter:s}},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=function(t,e){var n=t[0],i=t[1],r=e[0],a=e[1];return n<r?i<=r?1001:i<=a?1003:1002:n>a?1006:i<=a?1005:1004},o=function(t,e){var n=a(t,e);return 1001!==n&&1006!==n},s=function(t,e,n,i,r,a){void 0===a&&(a=4);var o,s=i-e,l=r-n,u=Math.floor(Math.sqrt(s*s+l*l)/a),c=s/u,h=l/u;for(o=0;o<u;o++,e+=c,n+=h)o%2==0&&t.fillRect(e,n,a,1)},l=function(t,e,n,i){var r=e-i/2,a=e+i/2,o=n-Math.sqrt(3*i/2);t.beginPath(),t.moveTo(r,o),t.lineTo(a,o),t.lineTo(e,n),t.lineTo(r,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},u=function(t){this.default_val=t||1};u.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},h=function(t,e,n,i,a){this.data=t,this.view_start=e,this.view_end=n,this.prefs=r.extend({},this.default_prefs,i),this.mode=a};h.prototype.default_prefs={},h.prototype.draw=function(t,e,n,i){},h.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},h.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},h.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},h.prototype._chrom_pos_to_draw_pos=function(t,e,n){return Math.floor(e*(Math.max(0,t-this.view_start)+n))};var d=function(t,e,n,i,r){h.call(this,t,e,n,i,r)};d.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},d.prototype.draw=function(t,e,n,i){var a=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,u=n,c=this.view_start,h=this.mode,d=this.data;t.save();var f=Math.round(n+o/l*n);"Intensity"!==h&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,g;g=d.length>1?r.map(d.slice(0,-1),function(t,e){return Math.ceil((d[e+1][0]-d[e][0])*i)}):[10];for(var v,m=this.prefs.block_color||this.prefs.color,y=parseInt(m.slice(1),16),b=(16711680&y)>>16,w=(65280&y)>>8,x=255&y,k=!1,C=!1,M=0,S=d.length;M<S;M++)if(t.fillStyle=t.strokeStyle=m,k=C=!1,v=g[M],p=Math.floor((d[M][0]-c-.5)*i),null!==(_=d[M][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===h)_=Math.round(_/l*u),t.fillRect(p,f,v,-_);else if("Intensity"===h){var T=(_-o)/l,$=Math.round(b+(255-b)*(1-T)),A=Math.round(w+(255-w)*(1-T)),E=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+$+","+A+","+E+")",t.fillRect(p,0,v,u)}else _=Math.round(u-(_-o)/l*u),a?t.lineTo(p,_):(a=!0,"Filled"===h?(t.moveTo(p,u),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===h||"Intensity"===h?O=v:(p-=2,O=4),k&&t.fillRect(p,0,O,3),C&&t.fillRect(p,u-3,O,3)}t.fillStyle=m}else a&&"Filled"===h&&t.lineTo(p,u),a=!1;"Filled"===h?(a&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,n,i){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:n,x_end:i})},f.prototype.get_feature_data=function(t,e){var n,i=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[i])return null;t+=this.translation;for(var r=0;r<this.feature_positions[i].length;r++)if(n=this.feature_positions[i][r],t>=n.x_start&&t<=n.x_end)return n.data};var p=function(t,e,n,i,r,a,o){h.call(this,t,e,n,i,r),this.alpha_scaler=a||new u,this.height_scaler=o||new u,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},r.extend(p.prototype,{get_required_height:function(t,e){var n=this.get_row_height(),i=n,r=this.mode;return"no_detail"!==r&&"Squish"!==r&&"Pack"!==r||(n=t*i),n+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,n,i,r){var a=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,u=this.get_row_height(),h=new f(u),d=[],p=0,_=a.length;p<_;p++){var g=a[p],v=g[0],m=g[1],y=g[2],b=r&&void 0!==r[v]?r[v].slot:null;("Dense"===this.mode||null!==b)&&m<s&&y>o&&(l=this.draw_element(t,this.mode,g,b,o,s,i,u,e),h.map_feature_data(g,b,l[0],l[1]),(m<o||y>s)&&d.push(g))}return t.restore(),h.y_translation=this.get_top_padding(e),new c({incomplete_features:d,feature_mapper:h})},draw_element:function(t,e,n,i,r,a,o,s,l){return[0,0]}});var _=function(t,e,n,i,r,a,o){p.call(this,t,e,n,i,r,a,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};r.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,n,i,r,a,o,s,l){var u,c=(n[0],n[1]),h=n[2],d=n[3],f=n[4],p=Math.floor(Math.max(0,(c-r-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(h-r-.5)*o))),g=p,v=_,u=("Dense"===e?0:0+i)*s+this.get_top_padding(l),m=null,y=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,w=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(n),"Dense"===e&&(i=1),"no_detail"===e)t.fillStyle=b,t.fillRect(p,u+5,_-p,1);else{var x=n[5],k=n[6],C=n[7],M=!0;x&&k&&(m=Math.floor(Math.max(0,(x-r)*o)),y=Math.ceil(Math.min(l,Math.max(0,(k-r)*o))));var S,T;if("Squish"===e?(S=1,T=3,M=!1):(S=5,T=9),C){var $,A;"Squish"===e||"Dense"===e?($=u+Math.floor(1.5)+1,A=1):f?($=u,A=T):($+=2.5,A=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,$,_-p,A));for(var E=0,O=C.length;E<O;E++){var z,R,N=C[E],P=Math.floor(Math.max(0,(N[0]-r-.5)*o)),q=Math.ceil(Math.min(l,Math.max((N[1]-r-.5)*o)));if(!(P>q)){if(t.fillStyle=b,t.fillRect(P,u+(T-S)/2+1,q-P,S),void 0!==m&&k>x&&!(P>y||q<m)){var j=Math.max(P,m),D=Math.min(q,y);t.fillRect(j,u+1,D-j,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),j+14<D&&(j+=2,D-=2),t.fillRect(j,u+1,D-j,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,P,q,u),z=P,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(n),I=Math.ceil(T*L),B=Math.round((T-I)/2);1!==L&&(t.fillRect(p,$+1,_-p,B),t.fillRect(p,$+T-B+1,_-p,B))}}else t.fillStyle=b,t.fillRect(p,u+1,_-p,T),f&&M&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,u+1,_-p,T));t.globalAlpha=1,d&&"Pack"===e&&c>r&&(t.fillStyle=w,0===r&&p-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,_+2,u+8,this.max_label_length),v+=t.measureText(d).width+2):(t.textAlign="right",t.fillText(d,p-2,u+8,this.max_label_length),g-=t.measureText(d).width+2))}return t.globalAlpha=1,[g,v]}});var g=function(t,e,n,i,r,a,o,s,l){p.call(this,t,e,n,i,r,a,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};r.extend(g.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",n=[[0,0]],i=n[0],a=0,o=r.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var r=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==i[1]&&(i=[a+r,a+r],n.push(i)):-1==="ISHP".indexOf(o)&&(i[1]+=r,a+=r),[e.indexOf(o),r]});return{blocks:n,cigar:o}},draw_read:function(t,e,n,i,r,s,u,c,h,d){var f=function(t){return Math.floor(Math.max(0,(t-r-.5)*n))};t.textAlign="center";var p,_,g=[r,s],v=0,m=0,y=Math.round(n/2),b=t.canvas.manager.char_width_px,w="+"===h?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,M=i+1,S=new x(t,C,n,e),T=[],$=[],A=this._parse_cigar(c);c=A.cigar,T=A.blocks;for(var E=0;E<T.length;E++){var O=T[E];o([u+O[0],u+O[1]],g)&&(p=f(u+O[0]),_=f(u+O[1]),p===_&&(_+=1),t.fillStyle=w,t.fillRect(p,M,_-p,C))}for(var z=0,R=c.length;z<R;z++){var N=c[z],P="MIDNSHP=X"[N[0]],q=N[1],j=u+v;if(p=f(j),_=f(j+q),o([j,j+q],g))switch(p===_&&(_+=1),P){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var D="";"X"===P?D=d.slice(m,m+q):this.ref_seq&&(D=this.ref_seq.slice(Math.max(0,j-r),Math.min(j-r+q,s-r)));for(var L=Math.max(j,r),I=0;I<D.length;I++)if(D&&!this.prefs.show_differences||"X"===P){var B=Math.floor(Math.max(0,(L+I-r)*n));t.fillStyle=this.base_color_fn(D[I]),k&&n>b?t.fillText(D[I],B,i+9):n>.05&&t.fillRect(B-y,M,Math.max(1,Math.round(n)),C)}"X"===P&&(m+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,M+(C-1)/2,_-p,1),v+=q;break;case"D":S.draw_deletion(p,M,q),v+=q;break;case"I":var V=p-y;if(o([j,j+q],g)){var U=d.slice(m,m+q);if(this.prefs.show_insertions){var F=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b){switch(t.fillStyle="yellow",t.fillRect(F-y,i-9,_-p,9),$[$.length]={type:"triangle",data:[V,i+4,5]},t.fillStyle="#ccc",a([j,j+q],g)){case 1003:U=U.slice(r-j);break;case 1004:U=U.slice(0,j-s);break;case 1005:break;case 1002:U=U.slice(r-j,j-s)}for(var I=0,G=U.length;I<G;I++){var B=Math.floor(Math.max(0,(j+I-r)*n));t.fillText(U[I],B-(_-p)/2,i)}}else t.fillStyle="yellow",t.fillRect(F,i+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b&&$.push({type:"text",data:[U.length,V,i+9]})}m+=q}else v=function(t,e,n){return-1!=="M=NXD".indexOf(e)&&(t+=n),t}(v,P,q),m=function(t,e,n){return-1!=="IX".indexOf(e)&&(t+=n),t}(m,P,q)}t.fillStyle="yellow";for(var H,Y,X,E=0;E<$.length;E++)H=$[E],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,n,i,r,a,o,l,u){var c=(n[0],n[1]),h=n[2],d=n[3],f=Math.floor(Math.max(-.5*o,(c-r-.5)*o)),p=Math.ceil(Math.min(u,Math.max(0,(h-r-.5)*o))),_=("Dense"===e?0:0+i)*l,g="Pack"===e?9:3;this.prefs.label_color;if(n[5]instanceof Array){var v=!0;n[4][1]>=r&&n[4][0]<=a&&n[4][2]?this.draw_read(t,e,o,_,r,a,n[4][0],n[4][2],n[4][3],n[4][4]):v=!1,n[5][1]>=r&&n[5][0]<=a&&n[5][2]?this.draw_read(t,e,o,_,r,a,n[5][0],n[5][2],n[5][3],n[5][4]):v=!1;var m=Math.ceil(Math.min(u,Math.max(-.5*o,(n[4][1]-r-.5)*o))),y=Math.floor(Math.max(-.5*o,(n[5][0]-r-.5)*o));if(v&&y>m){t.fillStyle="#ccc";var b=_+1+(g-1)/2;s(t,m,b,y,b)}}else this.draw_read(t,e,o,_,r,a,c,n[4],n[5],n[6]);return"Pack"===e&&c>=r&&"."!==d&&(t.fillStyle=this.prefs.label_color,0===r&&f-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(d,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,n,i,r,a,o){_.call(this,t,e,n,i,r,a,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};r.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,n=this.data.length;e<n;e++){var i=this.data[e],r=i[1],a=i[2];t=Math.max(t,a-r)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,n=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*n))},draw_connector:function(t,e,n,i,r,a){var o=(n+i)/2,s=i-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,a,i-o,Math.PI,0),t.stroke())}});var m=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};m.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,n=this.rgb[0]/255,i=this.rgb[1]/255,r=this.rgb[2]/255,a=this.alpha,o=Math.max(n,i,r),s=Math.min(n,i,r),l=(o+s)/2,u=o-s;if(o===s)t=e=0;else{switch(e=l>.5?u/(2-o-s):u/(o+s),o){case n:t=(i-r)/u+(i<r?6:0);break;case i:t=(r-n)/u+2;break;case r:t=(n-i)/u+4}t/=6}return{h:360*t,s:e,l:l,a:a}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var n=this,i=e,r=2*i-1,a=n.toHSL().a-t.toHSL().a,o=((r*a==-1?r:(r+a)/(1+r*a))+1)/2,s=1-o,l=[n.rgb[0]*o+t.rgb[0]*s,n.rgb[1]*o+t.rgb[1]*s,n.rgb[2]*o+t.rgb[2]*s],u=n.alpha*i+t.alpha*(1-i);return new m(l,u)}};var y=function(t,e,n,i){this.start_color=new m(t),this.end_color=new m(e),this.start_value=n,this.end_value=i,this.value_range=i-n};y.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var b=function(t,e,n,i,r){this.positive_ramp=new y(e,n,0,r),this.negative_ramp=new y(e,t,0,-i),this.start_value=i,this.end_value=r};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var w=function(t,e,n,i,r){h.call(this,t,e,n,i,r);var a,o;if(void 0===this.prefs.min_value){var s=1/0;for(a=0,o=this.data.length;a<o;a++)s=Math.min(s,this.data[a][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(a=0,o=this.data.length;a<o;a++)l=Math.max(l,this.data[a][6]);this.prefs.max_value=l}};w.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},w.prototype.draw=function(t,e,n,i){var r,a,o,s,l,u,c=this.prefs.min_value,h=this.prefs.max_value,d=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,h),g=function(t){return(t-d)*i};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,m=f.length;v<m;v++)r=f[v],a=g(r[1]),o=g(r[2]),s=g(r[4]),l=g(r[5]),u=r[6],t.fillStyle=_.map_value(u),t.fillRect(a,s,o-a,l-s);t.restore()};var x=function(t,e,n,i){this.ctx=t,this.row_height=e,this.px_per_base=n,this.draw_details=("Pack"===i||"Auto"===i)&&n>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};r.extend(x.prototype,{draw_deletion:function(t,e,n){this.ctx.fillStyle="black";var i=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-i),this.ctx.fillRect(t,e,n*this.px_per_base,i)}});var k=function(t,e,n,i,r,a){h.call(this,t,e,n,i,r),this.base_color_fn=a,this.divider_height=1};r.extend(k.prototype,h.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,n,i){t.save();var a,o,s,l,u,c,h,d,f,p,_,g=function(t,e){var n=t.length,i=e.length,r=0,a=1,o=null;return"-"===e?(o="deletion",a=t.length):0===t.indexOf(e)&&n>i?(o="deletion",a=n-i,r=i):0===e.indexOf(t)&&n<i&&(o="insertion",a=i-n,r=i),null!==o?{type:o,start:r,len:a}:{}},v=Math.max(1,Math.floor(i)),m=this.data.length?this.data[0][7].split(",").length:0,y="Squish"===this.mode?5:10,b=i<.1?y:"Squish"===this.mode?3:9,w=!0,k=new x(t,y,i,this.mode);1===m&&(y=b=i<t.canvas.manager.char_width_px?this.prefs.summary_height:y,k.row_height=y,w=!1),this.prefs.show_sample_data&&w&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(a=this.data[C],o=a[1],s=a[3],l=[a[4].split(",")],u=a[7].split(","),c=a.slice(8),l=r.map(r.flatten(l),function(t){var e={type:"snp",value:t,start:0},n=g(s,t);return r.extend(e,n)}),!(o<this.view_start||o>this.view_end)){if(w)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(d=this.get_start_draw_pos(o+l[_].start,i),t.fillRect(d,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var M=c/u.length,S=Math.ceil(this.prefs.summary_height*M);t.fillRect(d,f-S,v,S),f-=S}if(this.prefs.show_sample_data)for(f=w?this.prefs.summary_height+this.divider_height:0,_=0;_<u.length;_++,f+=y)if(p=u[_]?u[_].split(/\/|\|/):["0","0"],h=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(h=l[parseInt(p[0],10)-1],t.globalAlpha=1):(h="0"!==p[0]?p[0]:p[1],h=l[parseInt(h,10)-1],t.globalAlpha=.5),h)if(d=this.get_start_draw_pos(o+h.start,i),"snp"===h.type){var T=h.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,i),f+y):t.fillRect(d,f+1,v,b)}else"deletion"===h.type&&k.draw_deletion(d,f+1,h.len)}t.restore()}}),e.default={Scaler:u,LinePainter:d,LinkedFeaturePainter:_,ReadPainter:g,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:w,VariantPainter:k}},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};a(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,n,i){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(i)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var n=this;n.parent_div=t("<div/>").addClass("filter-row slider-row");var i=t("<div/>").addClass("elt-label").appendTo(n.parent_div),r=(t("<span/>").addClass("slider-name").text(n.name+"  ").appendTo(i),t("<span/>").text(this.low+"-"+this.high)),a=t("<span/>").addClass("slider-value").appendTo(i).append("[").append(r).append("]");n.values_span=r;var l=t("<div/>").addClass("slider").appendTo(n.parent_div);n.control_element=t("<div/>").attr("id",n.name+"-filter-control").appendTo(l),n.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){n.slide(t,e)},change:function(t,e){n.control_element.slider("option","slide").call(n.control_element,t,e)}}),n.slider=n.control_element,n.slider_label=r,function(e,n,i){e.click(function(){var e=n.text(),r=parseFloat(i.slider("option","max")),a=r<=1?4:r<=1e6?r.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),i.slider("option","values")&&(a=2*a+1,o=!0),n.text(""),t("<input type='text'/>").attr("size",a).attr("maxlength",a).attr("value",e).appendTo(n).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),n.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var n=i.slider("option","min"),r=i.slider("option","max"),a=function(t){return isNaN(t)||t>r||t<n},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],a(l[0])||a(l[1]))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this)}else if(l=parseFloat(l),a(l))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this);i.slider(o?"values":"value",l),s.removeClass("input")}})})}(a,r,n.control_element);var u=t("<div/>").addClass("display-controls").appendTo(n.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){n.manager.alpha_filter!==n?(n.manager.alpha_filter=n,n.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),n.transparency_icon.addClass("active").show()):(n.manager.alpha_filter=null,n.transparency_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){n.manager.height_filter!==n?(n.manager.height_filter=n,n.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),n.height_icon.addClass("active").show()):(n.manager.height_filter=null,n.height_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),n.parent_div.hover(function(){n.transparency_icon.show(),n.height_icon.show()},function(){n.manager.alpha_filter!==n&&n.transparency_icon.hide(),n.manager.height_filter!==n&&n.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(n.parent_div)};a(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return a(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var n=e.values;this.values_span.text(n[0]+"-"+n[1]),this.low=n[0],this.high=n[1];var i=this;setTimeout(function(){n[0]===i.low&&n[1]===i.high&&i.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var n=!0,i=0;i<e.length;i++)if(!this._keep_val(e[i])){n=!1;break}return n}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var n=t[this.index];n instanceof Array||(n=[n]);for(var i=0;i<n.length;i++){var r=n[i];r<this.min&&(this.min=Math.floor(r),e=!0),r>this.max&&(this.max=Math.ceil(r),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var u=function(e,n){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),n&&"filters"in n){for(var i,r=("alpha_filter"in n?n.alpha_filter:null),a=("height_filter"in n?n.height_filter:null),o=n.filters,s=0;s<o.length;s++)"number"===o[s].type?(i=new l(o[s]),this.add_filter(i),i.name===r&&(this.alpha_filter=i,i.transparency_icon.addClass("active").show()),i.name===a&&(this.height_filter=i,i.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in n&&n.visible&&this.parent_div.show()}if(0!==this.filters.length){var u=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(u).click(function(){c.run_on_dataset()})}};a(u.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},n=[],i=0;i<this.filters.length;i++)t=this.filters[i],n.push(t.to_dict());return e.filters=n,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new u(t),n=0;n<this.filters.length;n++)e.add_filter(this.filters[n].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,n,i=(function(t,e,n){return e in t||(t[e]=n),t[e]}),r={},a=0;a<this.filters.length;a++)e=this.filters[a],e.tool_id&&(e.min!==e.low&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in r)o[o.length]=[s,r[s]];!function e(n,i){var r=i[0],a=r[0],o=r[1],s="("+o.join(") and (")+")",l={cond:s,input:n,target_dataset_id:n,tool_id:a};i=i.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+a,buttons:{Close:Galaxy.modal.hide()}}):0===i.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,i)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:u,NumberFilter:l}}).call(e,n(0))},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(13),r=function(t){return t&&t.__esModule?t:{default:t}}(i),a=n(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=r.default.GenomeDataManager.extend({load_data:function(e,n,i,r){var a=t.Deferred();this.set_data(e,a);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(n,i){t.when(n.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var n=[],i={max:Number.MIN_VALUE};t.forEach(function(t){i.max!==t.min-1&&(n.push([i.max+1,0]),n.push([t.min-2,0])),n.push([t.min-1,t.score]),n.push([t.max,t.score]),i=t});var r={data:n,region:e,dataset_type:"bigwig"};l.set_data(e,r),a.resolve(r)})}),a}});e.default={BBIDataManager:s}}).call(e,n(0))},function(t,e,n){(function(i){var r,a;r=[n(153),n(154),n(155)],void 0!==(a=function(t,e){"use strict";function n(){}function r(t){t&&(this.id=t)}function a(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,n){Math.pow(10,6);return i.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(n-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*w+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function u(t,e,n,i){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=n,this.isSummary=i}function c(t){var e=i.Deferred(),n=new l;return n.url=t,i.when(o(n.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var r=t,a=new Uint8Array(r),o=new Int16Array(r),l=new Int32Array(r),u=a[0]+w*a[1]+x*a[2]+k*a[3];if(u==v)n.type="bigwig";else{if(u!=y)return u==m||u==b?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+u.toString(16));n.type="bigbed"}n.version=o[2],n.numZoomLevels=o[3],n.chromTreeOffset=s(a,8),n.unzoomedDataOffset=s(a,16),n.unzoomedIndexOffset=s(a,24),n.fieldCount=o[16],n.definedFieldCount=o[17],n.asOffset=s(a,36),n.totalSummaryOffset=s(a,44),n.uncompressBufSize=l[13],n.extHeaderOffset=s(a,56),n.zoomLevels=[];for(var c=0;c<n.numZoomLevels;++c){var h=l[6*c+16],d=s(a,24*c+72),f=s(a,24*c+80);n.zoomLevels.push({reduction:h,dataOffset:d,indexOffset:f})}i.when(n.readChromTree()).then(function(){n.getAutoSQL(function(t){return n.schema=t,e.resolve(n)})})}),e}function h(t,e,n,i,r){this.bbi=t,this.type=e,this.fieldCount=n,this.offset=i,this.field=r}var d=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,g=e.arrayCopy,v=2291137574,m=654086024,y=2273964779,b=3958540679,w=256,x=65536,k=16777216,C=4294967296,M=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),i.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var n=new Uint8Array(e),i=new Int16Array(e),r=new Int32Array(e),a=(r[0],r[1],r[2]),o=(r[3],s(n,16),function(e){var r=n[e],l=i[e/2+1];e+=4;for(var u=0;u<l;++u)if(0===r){e+=a;var c=s(n,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var h="",d=0;d<a;++d){var f=n[e++];0!==f&&(h+=String.fromCharCode(f))}var p=n[e+3]<<24|n[e+2]<<16|n[e+1]<<8|n[e+0];n[e+7],n[e+6],n[e+5],n[e+4],e+=8,t.chromsToIDs[h]=p,0===h.indexOf("chr")&&(t.chromsToIDs[h.substr(3)]=p),t.idsToChroms[p]=h,t.maxID=Math.max(t.maxID,p)}});o(32)})},u.prototype.readWigData=function(t,e,n){var i=this.bwg.chromsToIDs[t];return void 0===i?[]:this.readWigDataById(i,e,n)},u.prototype.readWigDataById=function(t,e,n){var r=this,a=i.Deferred();if(!this.cirHeader)return i.when(o(r.bwg.url,this.cirTreeOffset,48)).then(function(o){r.cirHeader=o;var s=new Int32Array(r.cirHeader);r.cirBlockSize=s[1],i.when(r.readWigDataById(t,e,n)).then(function(t){a.resolve(t)})}),a;var l=[],u=0,c=(Date.now(),function(i,r,a,o){return(t<0||i==t)&&r<=n&&a>=e}),h=function(t,e){if(r.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),u+=t.length,1==t.length&&t[0]-r.cirTreeOffset==48&&r.cachedCirRoot)return _(r.cachedCirRoot,0,e),void(0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}));for(var n,o=4+32*r.cirBlockSize,s=0;s<t.length;++s){var h=new d(t[s],t[s]+o);n=n?f(n,h):h}for(var g=n.ranges(),v=0;v<g.length;++v){var m=g[v];p(t,m,e)}},p=function(t,e,n,s){e.max(),e.min();i.when(o(r.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),n),t[s]-r.cirTreeOffset==48&&t[s]-e.min()==0&&(r.cachedCirRoot=o),0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}))})},_=function(i,r,a){var o=new Uint8Array(i),u=new Int16Array(i),c=new Int32Array(i),d=o[r],f=u[r/2+1];if(r+=4,0!==d)for(var p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16),w=s(o,r+24);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&l.push({offset:b,size:w}),r+=32}else{for(var x=[],p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&x.push(b),r+=24}x.length>0&&h(x,a+1)}};return h([r.cirTreeOffset+48],1),a},u.prototype.fetchFeatures=function(t,e){var r=this,a=i.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,i,a){a||(a={});var o=new n;o._chromId=t,o.segment=r.bwg.idsToChroms[t],o.min=e,o.max=i,o.type=r.bwg.type;for(var l in a)o[l]=a[l];s.push(o)},u=function(){if(0===e.length){Date.now();return a.resolve(s)}var n=e[0];if(n.data)r.parseFeatures(n.data,l,t),e.splice(0,1),u();else{for(var c=n.offset,h=n.size,d=1;d<e.length&&e[d].offset==c+h;)h+=e[d].size,++d;i.when(o(r.bwg.url,c,h)).then(function(t){for(var n=0,i=0;n<h;){var a,o=e[i];if(r.bwg.uncompressBufSize>0)a=_(t,n+2,o.size-2);else{var s=new Uint8Array(o.size);g(new Uint8Array(t,n,o.size),0,s,0,o.size),a=s.buffer}o.data=a,n+=o.size,++i}u()})}};return u(),a},u.prototype.parseFeatures=function(t,e,n){var a=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=t.byteLength/32,c=0;c<u;++c){var h=s[8*c],_=s[8*c+1],g=s[8*c+2],v=s[8*c+3],m=(l[8*c+4],l[8*c+5]),y=l[8*c+6];l[8*c+7];if(n(h,_+1,g)){var b={type:"bigwig",score:y/v,maxScore:m};"bigbed"==this.bwg.type&&(b.type="density"),e(h,_+1,g,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),h=s[0],w=s[1],x=(s[2],s[3]),k=s[4],C=a[20],u=o[11];if(3==C)for(var c=0;c<u;++c){var S=l[c+6],T=w+c*x+1,$=w+c*x+k;n(h,T,$)&&e(h,T,$,{score:S})}else if(2==C)for(var c=0;c<u;++c){var _=s[2*c+6]+1,g=_+k-1,S=l[2*c+7];n(h,_,g)&&e(h,_,g,{score:S})}else if(1==C)for(var c=0;c<u;++c){var _=s[3*c+6]+1,g=s[3*c+7],S=l[3*c+8];_>g&&(_=g),n(h,_,g)&&e(h,_,g,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var A=0,E=this.bwg.definedFieldCount,O=this.bwg.schema;A<a.length;){var h=a[A+3]<<24|a[A+2]<<16|a[A+1]<<8|a[A+0],_=a[A+7]<<24|a[A+6]<<16|a[A+5]<<8|a[A+4],g=a[A+11]<<24|a[A+10]<<16|a[A+9]<<8|a[A+8];A+=12;for(var z="";;){var R=a[A++];if(0==R)break;z+=String.fromCharCode(R)}var N,P={};if(N=z.length>0?z.split("\t"):[],N.length>0&&E>3&&(P.label=N[0]),N.length>1&&E>4){var S=parseInt(N[1]);isNaN(S)||(P.score=S)}if(N.length>2&&E>5&&(P.orientation=N[2]),N.length>5&&E>8){var q=N[5];M.test(q)&&(P.itemRgb="rgb("+q+")")}if(N.length>E-3&&O)for(var j=E-3;j<N.length;++j)P[O.fields[j+3].name]=N[j];if(n(h,_+1,g,N))if(E<12)e(h,_+1,g,P);else{var D=0|N[3],L=0|N[4],I=0|N[6],B=N[7].split(","),V=N[8].split(",");if(P.exonFrames){var U=P.exonFrames.split(",");P.exonFrames=void 0}P.type="transcript";var F=new r;for(var G in P)F[G]=P[G];if(F.id=N[0],F.segment=this.bwg.idsToChroms[h],F.min=_+1,F.max=g,F.notes=[],P.groups=[F],N.length>9){var H=P.geneName||N[9],Y=H;N.length>10&&(Y=N[10]),P.geneName2&&(Y=P.geneName2);var X=i.extend({},F);X.id=H,X.label=Y,X.type="gene",P.groups.push(X)}for(var W=[],J=0;J<I;++J){var K=(0|V[J])+_,Z=K+(0|B[J]),Q=new d(K,Z);W.push(Q)}for(var tt=f(W),et=tt.ranges(),nt=0;nt<et.length;++nt){var it=et[nt];e(h,it.min()+1,it.max(),P)}if(L>D){var rt="+"==P.orientation?new d(D,L+3):new d(D-3,L),at=p(tt,rt);if(at){P.type="translation";for(var ot=at.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var nt=0;nt<ot.length;++nt){var ut=nt;"-"==P.orientation&&(ut=ot.length-nt-1);var it=ot[ut];if(P.readframe=st,U){var ct=parseInt(U[ut+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(P.readframe=ct,P.readframeExplicit=!0)}var ht=it.max()-it.min();st=(st+ht)%3,e(h,it.min()+1,it.max(),P)}}}}}}},u.prototype.getFirstAdjacent=function(t,e,n,i){var r=this.bwg.chromsToIDs[t];if(void 0===r)return i([]);this.getFirstAdjacentById(r,e,n,i)},u.prototype.getFirstAdjacentById=function(t,e,n,i){var r=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(a){r.cirHeader=a;var o=new Int32Array(r.cirHeader);r.cirBlockSize=o[1],r.getFirstAdjacentById(t,e,n,i)});var a=null,o=-1,l=-1,u=0,c=(Date.now(),function(t,e){u+=t.length;for(var n,i=4+32*r.cirBlockSize,a=0;a<t.length;++a){var o=new d(t[a],t[a]+i);n=n?f(n,o):o}for(var s=n.ranges(),l=0;l<s.length;++l){var c=s[l];h(t,c,e)}}),h=function(o,s,l,c){s.max(),s.min();r.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var h=0;h<o.length;++h)if(s.contains(o[h])&&(p(c,o[h]-s.min(),l),0==--u)){if(!a)return n>0&&(0!=t||e>0)?r.getFirstAdjacentById(0,0,n,i):n<0&&(t!=r.bwg.maxID||e<1e9)?r.getFirstAdjacentById(r.bwg.maxID,1e9,n,i):i([]);r.fetchFeatures(function(i,r,a,o){return n<0&&(i<t||a<e)||n>0&&(i>t||r>e)},[a],function(t){for(var e=null,r=-1,a=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,u=s.min,c=s.max;(null==e||n<0&&(l>r||c>a)||n>0&&(l<r||u<a))&&(e=s,a=n<0?c:u,r=l)}return i(null!=e?[e]:[])})}})},p=function(i,u,h){var d=new Uint8Array(i),f=new Int16Array(i),p=new Int32Array(i),_=d[u],g=f[u/2+1];if(u+=4,0!=_)for(var v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=s(d,u+16),C=s(d,u+24);(n<0&&(y<t||y==t&&b<=e)||n>0&&(w>t||w==t&&x>=e))&&(/_random/.exec(r.bwg.idsToChroms[y])||(null==a||n<0&&(w>o||w==o&&x>l)||n>0&&(y<o||y==o&&b<l))&&(a={offset:k,size:C},l=n<0?x:b,o=n<0?w:y)),u+=32}else{for(var M=-1,S=-1,v=0;v<g;++v){var 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t||(t=c),n&&(n=!1),this.istate=new e,this.istate.inflateInit(this,n?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new n(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var n,i;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,n=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,i=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+i)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&i)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?n:(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(n=t.istate.blocks.proc(t,n))){t.istate.mode=13,t.istate.marker=0;break}if(n==f&&(n=e),n!=p)return n;if(n=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,n){var i=0,r=n;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,n)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),r>=1<<t.istate.wbits&&(r=(1<<t.istate.wbits)-1,i=n-r),t.istate.blocks.set_dictionary(e,i,r),t.istate.mode=7,f)};var S=[0,0,255,255];e.prototype.inflateSync=function(t){var e,n,i,r,a;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(n=t.next_in_index,i=t.istate.marker;0!=e&&i<4;)t.next_in[n]==S[i]?i++:i=0!=t.next_in[n]?0:4-i,n++,e--;return t.total_in+=n-t.next_in_index,t.next_in_index=n,t.avail_in=e,t.istate.marker=i,4!=i?-3:(r=t.total_in,a=t.total_out,this.inflateReset(t),t.total_in=r,t.total_out=a,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];n.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},n.prototype.proc=function(t,e){var n,i,r,s,l,u,c;for(s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u;;)switch(this.mode){case v:for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}switch(n=7&i,this.last=1&n,n>>>1){case 0:i>>>=3,r-=3,n=7&r,i>>>=n,r-=n,this.mode=1;break;case 1:var h=new Int32Array(1),d=new Int32Array(1),_=[],m=[];a(h,d,_,m,t),this.codes.init(h[0],d[0],_[0],0,m[0],0,t),i>>>=3,r-=3,this.mode=6;break;case 2:i>>>=3,r-=3,this.mode=3;break;case 3:return i>>>=3,r-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}break;case 1:for(;r<32;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if((~i>>>16&65535)!=(65535&i))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.left=65535&i,i=r=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);if(0==c&&(u==end&&0!=read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c&&(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,u==this.end&&0!=this.read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c)))return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(e=f,n=this.left,n>l&&(n=l),n>c&&(n=c),o(t.next_in,s,this.window,u,n),s+=n,l-=n,u+=n,c-=n,0!=(this.left-=n))break;this.mode=0!=this.last?7:v;break;case 3:for(;r<14;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(this.table=n=16383&i,(31&n)>29||(n>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(n=258+(31&n)+(n>>5&31),null==this.blens||this.blens.length<n)this.blens=new Int32Array(n);else for(var y=0;y<n;y++)this.blens[y]=0;i>>>=14,r-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}this.blens[T[this.index++]]=7&i,i>>>=3,r-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(n=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=n,-3==e&&(this.blens=null,this.mode=9),this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(n=this.table,!(this.index<258+(31&n)+(n>>5&31)))break;var y,b,w;for(n=this.bb[0];r<n;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(n=this.hufts[3*(this.tb[0]+(i&g[n]))+1],(w=this.hufts[3*(this.tb[0]+(i&g[n]))+2])<16)i>>>=n,r-=n,this.blens[this.index++]=w;else{for(y=18==w?7:w-14,b=18==w?11:3;r<n+y;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(i>>>=n,r-=n,b+=i&g[y],i>>>=y,r-=y,y=this.index,n=this.table,y+b>258+(31&n)+(n>>5&31)||16==w&&y<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);w=16==w?this.blens[y-1]:0;do{this.blens[y++]=w}while(0!=--b);this.index=y}}this.tb[0]=-1;var h=new Int32Array(1),d=new Int32Array(1),_=new Int32Array(1),m=new Int32Array(1);if(h[0]=9,d[0]=6,n=this.table,(n=this.inftree.inflate_trees_dynamic(257+(31&n),1+(n>>5&31),this.blens,h,d,_,m,this.hufts,t))!=f)return-3==n&&(this.blens=null,this.mode=13),e=n,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.codes.init(h[0],d[0],this.hufts,_[0],this.hufts,m[0],t),this.mode=6;case 6:if(this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,this.read!=this.write)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);default:return e=-2,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}},n.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},n.prototype.set_dictionary=function(t,e,n){o(t,e,window,0,n),this.read=this.write=n},n.prototype.sync_point=function(){return 1==this.mode},n.prototype.inflate_flush=function(t,e){var n,i,r;return i=t.next_out_index,r=this.read,n=(r<=this.write?this.write:this.end)-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n,r==this.end&&(r=0,this.write==this.end&&(this.write=0),n=this.write-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n),t.next_out_index=i,this.read=r,e};i.prototype.init=function(t,e,n,i,r,a,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=n,this.ltree_index=i,this.dtree=r,this.dtree_index=a,this.tree=null},i.prototype.proc=function(t,e,n){var i,r,a,o,s,l,u,c=0,h=0,d=0;for(d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,n=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,n!=f)){this.mode=n==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>>=this.tree[r+1],h-=this.tree[r+1],0==(a=this.tree[r])){this.lit=this.tree[r+2],this.mode=6;break}if(0!=(16&a)){this.get=15&a,this.len=this.tree[r+2],this.mode=2;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}if(0!=(32&a)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 2:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.len+=c&g[i],c>>=i,h-=i,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>=this.tree[r+1],h-=this.tree[r+1],0!=(16&(a=this.tree[r]))){this.get=15&a,this.dist=this.tree[r+2],this.mode=4;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}return this.mode=9,e.msg="invalid distance code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 4:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.dist+=c&g[i],c>>=i,h-=i,this.mode=5;case 5:for(u=s-this.dist;u<0;)u+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);t.window[s++]=t.window[u++],l--,u==t.end&&(u=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(h>7&&(h-=8,o++,d--),t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);this.mode=8;case 8:return n=p,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 9:return n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);default:return n=-2,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n)}},i.prototype.free=function(t){},i.prototype.inflate_fast=function(t,e,n,i,r,a,s,l){var u,c,h,d,_,v,m,y,b,w,x,k,C,M,S,T;m=l.next_in_index,y=l.avail_in,_=s.bitb,v=s.bitk,b=s.write,w=b<s.read?s.read-b-1:s.end-b,x=g[t],k=g[e];do{for(;v<20;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(u=_&x,c=n,h=i,T=3*(h+u),0!=(d=c[T]))for(;;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15,C=c[T+2]+(_&g[d]),_>>=d,v-=d;v<15;)y--,_|=(255&l.next_in[m++])<<v,v+=8;for(u=_&k,c=r,h=a,T=3*(h+u),d=c[T];;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15;v<d;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(M=c[T+2]+(_&g[d]),_>>=d,v-=d,w-=C,b>=M)S=b-M,s.window[b++]=s.window[S++],s.window[b++]=s.window[S++],C-=2;else{S=b-M;do{S+=s.end}while(S<0);if(d=s.end-S,C>d){if(C-=d,b-S>0&&d>b-S)do{s.window[b++]=s.window[S++]}while(0!=--d);else o(s.window,S,s.window,b,d),b+=d,S+=d,d=0;S=0}}do{s.window[b++]=s.window[S++]}while(0!=--C);break}if(0!=(64&d))return l.msg="invalid distance code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3;u+=c[T+2],u+=_&g[d],T=3*(h+u),d=c[T]}break}if(0!=(64&d))return 0!=(32&d)?(C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3);if(u+=c[T+2],u+=_&g[d],T=3*(h+u),0==(d=c[T])){_>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--;break}}else _>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--}while(w>=258&&y>=10);return C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,f},r.prototype.huft_build=function(t,e,n,i,r,a,s,l,u,c,d){var p,g,v,m,y,b,w,x,k,C,M,S,T,$,A;C=0,y=n;do{this.c[t[e+C]]++,C++,y--}while(0!=y);if(this.c[0]==n)return s[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(w=b,x<b&&(x=b),y=15;0!=y&&0==this.c[y];y--);for(v=y,x>y&&(x=y),l[0]=x,$=1<<b;b<y;b++,$<<=1)if(($-=this.c[b])<0)return-3;if(($-=this.c[y])<0)return-3;for(this.c[y]+=$,this.x[1]=b=0,C=1,T=2;0!=--y;)this.x[T]=b+=this.c[C],T++,C++;y=0,C=0;do{0!=(b=t[e+C])&&(this.v[this.x[b]++]=y),C++}while(++y<n);for(n=this.x[v],this.x[0]=y=0,C=0,m=-1,S=-x,this.u[0]=0,M=0,A=0;w<=v;w++)for(p=this.c[w];0!=p--;){for(;w>S+x;){if(m++,S+=x,A=v-S,A=A>x?x:A,(g=1<<(b=w-S))>p+1&&(g-=p+1,T=w,b<A))for(;++b<A&&!((g<<=1)<=this.c[++T]);)g-=this.c[T];if(A=1<<b,this.hn[0]+A>h)return-3;this.u[m]=M=this.hn[0],this.hn[0]+=A,0!=m?(this.x[m]=y,this.r[0]=b,this.r[1]=x,b=y>>>S-x,this.r[2]=M-this.u[m-1]-b,o(this.r,0,u,3*(this.u[m-1]+b),3)):s[0]=M}for(this.r[1]=w-S,C>=n?this.r[0]=192:d[C]<i?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=a[this.v[C]-i]+16+64,this.r[2]=r[this.v[C++]-i]),g=1<<w-S,b=y>>>S;b<A;b+=g)o(this.r,0,u,3*(M+b),3);for(b=1<<w-1;0!=(y&b);b>>>=1)y^=b;for(y^=b,k=(1<<S)-1;(y&k)!=this.x[m];)m--,S-=x,k=(1<<S)-1}return 0!=$&&1!=v?_:f},r.prototype.inflate_trees_bits=function(t,e,n,i,r){var a;return this.initWorkArea(19),this.hn[0]=0,a=this.huft_build(t,0,19,19,null,null,n,e,i,this.hn,this.v),-3==a?r.msg="oversubscribed dynamic bit lengths tree":a!=_&&0!=e[0]||(r.msg="incomplete dynamic bit lengths tree",a=-3),a},r.prototype.inflate_trees_dynamic=function(t,e,n,i,r,a,o,s,l){var u;return this.initWorkArea(288),this.hn[0]=0,(u=this.huft_build(n,0,t,257,x,k,a,i,s,this.hn,this.v))!=f||0==i[0]?(-3==u?l.msg="oversubscribed literal/length tree":-4!=u&&(l.msg="incomplete literal/length tree",u=-3),u):(this.initWorkArea(288),u=this.huft_build(n,t,e,0,C,M,o,r,s,this.hn,this.v),u!=f||0==r[0]&&t>257?(-3==u?l.msg="oversubscribed distance tree":u==_?(l.msg="incomplete distance tree",u=-3):-4!=u&&(l.msg="empty distance tree with lengths",u=-3),u):f)},r.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var $=new Uint8Array(1),A="function"==typeof $.subarray;return{inflateBuffer:u,arrayCopy:o}}.apply(e,i))&&(t.exports=r)},function(t,e,n){(function(i){var r,a,o;!function(i,s){a=[n(0)],r=s,void 0!==(o="function"==typeof r?r.apply(e,a):r)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var n={},r=0,a={0:200,1223:204},o={},s=i.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),n.cors=!!s&&"withCredentials"in s,n.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(n.cors||s&&!t.crossDomain)return{send:function(n,i){var s,l=t.xhr(),u=++r,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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a=this.circular_views.length,o=new M({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();s.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();s.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),s.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),x=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new m;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),l=o.attr("chrom"),c=n.genome.get_chrom_region(l),h=n.track.get("data_manager");h.can_get_more_detailed_data(c)&&(a=n.track.get("data_manager").get_more_detailed_data(c,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=s.find(n.chroms_layout,function(t){return t.data.chrom===l}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=s.reject(s.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds;this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=s.zip(n,i);s.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var l=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",l).style("fill",l),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return s.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),k=x.extend({initialize:function(t){x.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=s.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});s.extend(k.prototype,y);var C=x.extend({initialize:function(t){x.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return i?t.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",e.data.chrom).attr("d",i):null},_get_path_function:function(t,e){if("string"==typeof e||!e.data||0===e.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,e.data.length]).range([t.startAngle,t.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(t){return n(t[1])}).angle(function(t,e){return i(e)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var t=this,e=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),e,!0).classed("min_max",!0);s.each(n,function(e){i(e).click(function(){new _.default.ConfigSettingCollectionView({collection:t.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var t=this,e=s.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>.08}),n=s.filter(e,function(t,e){return e%3==0}),i=s.flatten(s.map(n,function(e){return t._data_bounds_ticks_fn()(e)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"})}},_data_bounds_ticks_fn:function(){var t=this;return visibleChroms=0,function(e){return[{radius:t.radius_bounds[0],angle:e.startAngle,label:t.formatNum(t.data_bounds[0])},{radius:t.radius_bounds[1],angle:e.startAngle,label:t.formatNum(t.data_bounds[1])}]}},get_data_bounds:function(t){}});s.extend(C.prototype,y);var M=C.extend({get_data_bounds:function(t){var e=s.flatten(s.map(t,function(t){return t?s.map(t.data,function(t){return parseInt(t[1],10)||0}):0}));return[s.min(e),this._quantile(e,.98)||s.max(e)]}}),S=x.extend({render:function(){var t=this;i.when(t.track.get("data_manager").data_is_ready()).then(function(){i.when(t.track.get("data_manager").get_genome_wide_data(t.genome)).then(function(e){var n=[],i=t.genome.get_chroms_info();s.each(e,function(e,r){var a=i[r].chrom,o=s.map(e.data,function(e){var n=t._get_region_angle(a,e[1]),i=t._get_region_angle(e[3],e[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),t.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",t.get_fill_color()).attr("d",u.svg.chord().radius(t.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(t){this.radius_bounds=t,this.parent_elt.selectAll("path").transition().attr("d",u.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(t,e){var n=s.find(this.chroms_layout,function(e){return e.data.chrom===t});return 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diff --git a/static/scripts/bundled/workflow.bundled.js b/static/scripts/bundled/workflow.bundled.js
index 5353c9d4269..9390cfaf9e4 100644
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i=t.value.match(e);i&&(r=r.concat(i))}}),o.post_job_actions&&t.each(o.post_job_actions,function(i,n){n.action_arguments&&t.each(n.action_arguments,function(t,i){var n=i.match(e);n&&(r=r.concat(n))})}),r&&t.each(r,function(e,n){-1===t.inArray(n,i)&&i.push(n)})}),i&&0!==i.length?(t.each(i,function(t,e){a+="<div>"+e.substring(2,e.length-1)+"</div>"}),n.html(a),o.show()):(n.html(a),o.hide())},showAttributes:function(){t(".right-content").hide(),t("#edit-attributes").show()},showForm:function(e,i){var n="right-content",o=n+"-"+i.id,a=t("#"+n);if(e&&0==a.find("#"+o).length){var r=t('<div id="'+o+'" class="'+n+'"/>');if(e.node=i,e.workflow=this.workflow,e.datatypes=this.datatypes,e.icon=g.default[i.type],e.cls="ui-portlet-narrow",i){var s="tool"==i.type?"Tool":"Default";r.append(new w.default[s](e).form.$el),a.append(r)}else Galaxy.emit.debug("workflow-view::initialize()","Node not found in workflow.")}t("."+n).hide(),a.find("#"+o).show(),a.show(),a.scrollTop()},isSubType:function(t,e){return t=this.ext_to_type[t],e=this.ext_to_type[e],this.type_to_type[t]&&e in this.type_to_type[t]},prebuildNode:function(e,i,n){var o=this,a=t("<div class='toolForm toolFormInCanvas'/>"),r=t("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+i+"</div></div>");s(r.find(".nodeTitle"),e),a.append(r),a.css("left",t(window).scrollLeft()+20),a.css("top",t(window).scrollTop()+20),a.append(t("<div class='toolFormBody'></div>"));var l=new m.default(this,{element:a});l.type=e,l.content_id=n;var u="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";a.find(".toolFormBody").append(u);var c=t("<div class='buttons' style='float: right;'></div>");c.append(t("<div/>").addClass("fa-icon-button fa fa-times").click(function(t){l.destroy()})),a.appendTo("#canvas-container");var d=t("#canvas-container").position(),h=t("#canvas-container").parent(),f=a.width(),p=a.height();return a.css({left:-d.left+h.width()/2-f/2,top:-d.top+h.height()/2-p/2}),c.prependTo(a.find(".toolFormTitle")),f+=c.width()+10,a.css("width",f),a.bind("dragstart",function(){o.workflow.activate_node(l)}).bind("dragend",function(){o.workflow.node_changed(this),o.workflow.fit_canvas_to_nodes(),o.canvas_manager.draw_overview()}).bind("dragclickonly",function(){o.workflow.activate_node(l)}).bind("drag",function(e,i){var n=t(this).offsetParent().offset(),o=i.offsetX-n.left,a=i.offsetY-n.top;t(this).css({left:o,top:a}),t(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t){function n(t,e){this.app=t,this.canvas_container=e,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(223),a=function(t){return t&&t.__esModule?t:{default:t}}(o),r=i(42),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r);t.extend(n.prototype,{canLabelOutputWith:function(t){return!t||!(t in this.workflowOutputLabels)},registerOutputLabel:function(t){t&&(this.workflowOutputLabels[t]=!0)},unregisterOutputLabel:function(t){t&&delete this.workflowOutputLabels[t]},updateOutputLabel:function(t,e){t&&this.unregisterOutputLabel(t),this.canLabelOutputWith(e)||s.warning("Workflow contains duplicate workflow output labels "+e+". This must be fixed before it can be saved."),e&&this.registerOutputLabel(e)},attemptUpdateOutputLabel:function(t,e,i){return!!this.canLabelOutputWith(i)&&(t.labelWorkflowOutput(e,i),t.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(t,e,i){var n=this.app.prebuildNode(t,e,i);return this.add_node(n),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(n),n},add_node:function(t){t.id=this.id_counter,t.element.attr("id","wf-node-step-"+t.id),this.id_counter++,this.nodes[t.id]=t,this.has_changes=!0,t.workflow=this},remove_node:function(t){this.active_node==t&&this.clear_active_node(),delete this.nodes[t.id],this.has_changes=!0},remove_all:function(){var e=this;t.each(this.nodes,function(t,i){i.destroy(),e.remove_node(i)})},rectify_workflow_outputs:function(){var e=!1,i=!1;if(t.each(this.nodes,function(n,o){o.workflow_outputs&&o.workflow_outputs.length>0&&(e=!0),t.each(o.post_job_actions,function(t,e){"HideDatasetAction"===e.action_type&&(i=!0)})}),!1!==e||!1!==i){var n=this;t.each(this.nodes,function(i,o){if("tool"===o.type){var a=!1;null===o.post_job_actions&&(o.post_job_actions={},a=!0);var r=[];t.each(o.post_job_actions,function(t,e){"HideDatasetAction"==e.action_type&&r.push(t)}),r.length>0&&t.each(r,function(t,e){a=!0,delete o.post_job_actions[e]}),e&&t.each(o.output_terminals,function(t,e){if(!0==!o.isWorkflowOutput(e.name)){a=!0;var i={action_type:"HideDatasetAction",output_name:e.name,action_arguments:{}};o.post_job_actions["HideDatasetAction"+e.name]=null,o.post_job_actions["HideDatasetAction"+e.name]=i}}),n.active_node==o&&!0===a&&n.reload_active_node()}})}},to_simple:function(){var e={};return t.each(this.nodes,function(i,n){var o={};t.each(n.input_terminals,function(e,i){o[i.name]=null;var n=[];t.each(i.connectors,function(t,e){if(e.handle1){var a={id:e.handle1.node.id,output_name:e.handle1.name},r=i.attributes.input.input_subworkflow_step_id;void 0!==r&&(a.input_subworkflow_step_id=r),n[t]=a,o[i.name]=n}})});var a={};n.post_job_actions&&t.each(n.post_job_actions,function(t,e){var i={action_type:e.action_type,output_name:e.output_name,action_arguments:e.action_arguments};a[e.action_type+e.output_name]=null,a[e.action_type+e.output_name]=i}),n.workflow_outputs||(n.workflow_outputs=[]);var r={id:n.id,type:n.type,content_id:n.content_id,tool_version:n.config_form.version,tool_state:n.tool_state,errors:n.errors,input_connections:o,position:t(n.element).position(),annotation:n.annotation,post_job_actions:n.post_job_actions,uuid:n.uuid,label:n.label,workflow_outputs:n.workflow_outputs};e[n.id]=r}),{steps:e}},from_simple:function(e,i){var n=void 0===i||i,o=this,r=0;n?o.name=e.name:r=Object.keys(o.nodes).length;var s=r,l=!1;t.each(e.steps,function(e,i){var a=o.app.prebuildNode(i.type,i.name,i.content_id);n||(i.uuid=null,t.each(i.workflow_outputs,function(t,e){e.uuid=null})),a.init_field_data(i),i.position&&a.element.css({top:i.position.top,left:i.position.left}),a.id=parseInt(i.id)+r,o.nodes[a.id]=a,s=Math.max(s,parseInt(e)+r),l||(a.workflow_outputs.length>0?l=!0:t.each(a.post_job_actions||[],function(t,e){"HideDatasetAction"===e.action_type&&(l=!0)}))}),o.id_counter=s+1,t.each(e.steps,function(e,i){var n=o.nodes[parseInt(e)+r];t.each(i.input_connections,function(e,i){i&&(t.isArray(i)||(i=[i]),t.each(i,function(t,i){var s=o.nodes[parseInt(i.id)+r],l=new a.default;l.connect(s.output_terminals[i.output_name],n.input_terminals[e]),l.redraw()}))}),l&&t.each(n.output_terminals,function(e,i){if(void 0===n.post_job_actions["HideDatasetAction"+i.name]){n.addWorkflowOutput(i.name);t(n.element).find(".callout."+i.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),o.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,t("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var t=this.active_node;this.clear_active_node(),this.activate_node(t)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showAttributes()},activate_node:function(t){this.active_node!=t&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(t.config_form,t),t.make_active(),this.active_node=t)},node_changed:function(t,e){this.has_changes=!0,this.active_node==t&&e&&(this.check_changes_in_active_form(),this.app.showForm(t.config_form,t)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var e={},i={};t.each(this.nodes,function(t,n){void 0===e[t]&&(e[t]=0),void 0===i[t]&&(i[t]=[])}),t.each(this.nodes,function(n,o){t.each(o.input_terminals,function(n,a){t.each(a.connectors,function(t,n){var a=n.handle1.node;e[o.id]+=1,i[a.id].push(o.id)})})});for(var n=[];;){var o=[];for(var a in e)0===e[a]&&o.push(a);if(0===o.length)break;n.push(o);for(var r in o){var s=o[r];delete e[s];for(var l in i[s])e[i[s][l]]-=1}}if(!e.length){var u=this.nodes,c=80;t.each(n,function(e,i){i.sort(function(e,i){return t(u[e].element).position().top-t(u[i].element).position().top});var n=0,o=30;t.each(i,function(e,i){var a=u[i],r=t(a.element);t(r).css({top:o,left:c}),n=Math.max(n,t(r).width()),o+=t(r).height()+30}),c+=n+80}),t.each(u,function(t,e){e.redraw()})}},bounds_for_all_nodes:function(){var e,i=1/0,n=-1/0,o=1/0,a=-1/0;return t.each(this.nodes,function(r,s){var l=t(s.element);e=l.position(),i=Math.min(i,e.left),n=Math.max(n,e.left+l.width()),o=Math.min(o,e.top),a=Math.max(a,e.top+l.width())}),{xmin:i,xmax:n,ymin:o,ymax:a}},fit_canvas_to_nodes:function(){function e(t,e){return Math.ceil(t/e)*e}function i(t,e){if(t<e||t>3*e){return-(t-(Math.ceil(t%e/e)+1)*e)}return 0}var n=this.bounds_for_all_nodes(),o=this.canvas_container.position(),a=this.canvas_container.parent(),r=i(n.xmin,100),s=i(n.ymin,100);r=Math.max(r,o.left),s=Math.max(s,o.top);var l=o.left-r,u=o.top-s,c=e(n.xmax+100,100)+r,d=e(n.ymax+100,100)+s;c=Math.max(c,-l+a.width()),d=Math.max(d,-u+a.height()),this.canvas_container.css({left:l,top:u,width:c,height:d}),this.canvas_container.children().each(function(){var e=t(this).position();t(this).css("left",e.left+r),t(this).css("top",e.top+s)})}}),e.default=n}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t,e,i){this.app=t,this.cv=e,this.cc=this.cv.find("#canvas-container"),this.overview=i,this.oc=i.find("#overview-canvas"),this.ov=i.find("#overview-viewport"),this.init_drag()}function n(t){this.panel=t}Object.defineProperty(e,"__esModule",{value:!0}),t.extend(i.prototype,{init_drag:function(){var e=this,i=function(t,i){t=Math.min(t,e.cv.width()/2),t=Math.max(t,-e.cc.width()+e.cv.width()/2),i=Math.min(i,e.cv.height()/2),i=Math.max(i,-e.cc.height()+e.cv.height()/2),e.cc.css({left:t,top:i}),e.cv.css({"background-position-x":t,"background-position-y":i}),e.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new n(this)});var o,a;this.cv.bind("dragstart",function(){var i=t(this).offset(),n=e.cc.position();a=n.top-i.top,o=n.left-i.left}).bind("drag",function(t,e){i(e.offsetX+o,e.offsetY+a)}).bind("dragend",function(){e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),this.overview.click(function(t){if(e.overview.hasClass("blockaclick"))e.overview.removeClass("blockaclick");else{var n=e.cc.width(),o=e.cc.height(),a=e.oc.width(),r=e.oc.height(),s=t.pageX-e.oc.offset().left-e.ov.width()/2,l=t.pageY-e.oc.offset().top-e.ov.height()/2;i(-s/a*n,-l/r*o),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}}),this.ov.bind("drag",function(t,n){var o=e.cc.width(),a=e.cc.height(),r=e.oc.width(),s=e.oc.height(),l=n.offsetX-e.overview.offset().left,u=n.offsetY-e.overview.offset().top;i(-l/r*o,-u/s*a)}).bind("dragend",function(){e.overview.addClass("blockaclick"),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),t("#overview-border").bind("drag",function(i,n){var o=t(this).offsetParent(),a=o.offset(),r=Math.max(o.width()-(n.offsetX-a.left),o.height()-(n.offsetY-a.top));t(this).css({width:r,height:r}),e.draw_overview()}),t("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,i=this.oc,n=this.ov,o=t.width(),a=t.height(),r=i.width(),s=i.height(),l=t.position();n.css({left:-l.left/o*r,top:-l.top/a*s,width:e.width()/o*r-2,height:e.height()/a*s-2})},draw_overview:function(){var e,i,n,o,a=t("#overview-canvas"),r=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=t("#canvas-container").width(),u=t("#canvas-container").height(),c=this.cv.width(),d=this.cv.height();l<c&&u<d?(n=l/c*r,o=(r-n)/2,e=u/d*r,i=(r-e)/2):l<u?(i=0,e=r,n=Math.ceil(e*l/u),o=(r-n)/2):(n=r,o=0,e=Math.ceil(n*u/l),i=(r-e)/2),a.parent().css({left:o,top:i,width:n,height:e}),a.attr("width",n),a.attr("height",e),t.each(this.app.workflow.nodes,function(i,o){s.fillStyle="#D2C099",s.strokeStyle="#D8B365",s.lineWidth=1;var a=t(o.element),r=a.position(),c=r.left/l*n,d=r.top/u*e,h=a.width()/l*n,f=a.height()/u*e;o.errors?(s.fillStyle="#FFCCCC",s.strokeStyle="#AA6666"):void 0!==o.workflow_outputs&&o.workflow_outputs.length>0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(c,d,h,f),s.strokeRect(c,d,h,f)}),this.update_viewport_overlay()}}),t.extend(n.prototype,{test:function(e,i){clearTimeout(this.timeout);var n=e.pageX,o=e.pageY,a=t(this.panel),r=a.position(),s=a.width(),l=a.height(),u=a.parent(),c=u.width(),d=u.height(),h=u.offset(),f=h.left,p=h.top,m=f+u.width(),v=p+u.height(),g=-(s-c/2),_=-(l-d/2),w=c/2,b=d/2,y=!1;if(n-5<f){if(r.left<w){var x=Math.min(23,w-r.left);a.css("left",r.left+x),y=!0}}else if(n+5>m){if(r.left>g){var x=Math.min(23,r.left-g);a.css("left",r.left-x),y=!0}}else if(o-5<p){if(r.top<b){var x=Math.min(23,b-r.top);a.css("top",r.top+x),y=!0}}else if(o+5>v&&r.top>_){var x=Math.min(23,r.top-g);a.css("top",r.top-x+"px"),y=!0}if(y){i();var a=this;this.timeout=setTimeout(function(){a.test(e,i)},50)}},stop:function(t,e){clearTimeout(this.timeout)}}),e.default=i}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,o){Object.defineProperty(e,"__esModule",{value:!0});var a=i(288),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return n.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var i={output_name:t};return e&&(i.label=e),this.workflow_outputs.push(i),!0}return!1},labelWorkflowOutput:function(t,e){var i=!1,n=null;if(this.isWorkflowOutput(t)){var o=this.getWorkflowOutput(t);n=o.label,o.label=e,i=n!=e}else i=this.addWorkflowOutput(t,e);return i&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),i},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.connectors.length>0&&e.push(i)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var i=t[e];if(i.connectors.length>0&&i.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&i.connectors.length>0&&e.push(i)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&e.push(i)}),e},hasMappedOverInputTerminals:function(){var t=!1;return n.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){o.each(this.input_terminals,function(t,e){e.redraw()}),o.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){o.each(this.input_terminals,function(t,e){e.destroy()}),o.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),o(this.element).remove()},make_active:function(){o(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),o(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,i=new r.default({el:this.element[0],node:e});e.nodeView=i,o.each(t.data_inputs,function(t,e){i.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&i.addRule(),o.each(t.data_outputs,function(t,e){i.addDataOutput(e)}),i.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,i=e.nodeView,a=[];if(o.each(i.outputViews,function(e,i){var o=i.output.name,r=t.data_outputs,s=!1;n.each(r,function(t){t.name==o&&(s=!0)}),!1===s&&a.push(o)}),n.each(a,function(t){n.each(i.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),i.outputViews[t].remove(),delete i.outputViews[t],delete e.output_terminals[t]}),o.each(e.workflow_outputs,function(t,i){i&&!e.output_terminals[i.output_name]&&e.workflow_outputs.splice(t,1)}),o.each(t.data_outputs,function(t,n){i.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):i.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var r=t.post_job_actions;this.post_job_actions=r||{}}e.nodeView.renderToolErrors();var s=i.$("div.inputs"),l=i.newInputsDiv(),u={};n.each(t.data_inputs,function(t){var i=e.nodeView.addDataInput(t,l);u[t.name]=i}),n.each(n.difference(n.values(i.terminalViews),n.values(u)),function(t){t.el.terminal.destroy()}),i.terminalViews=u,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&i.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=o(this.element).find(".toolFormBody");e.find("div").remove();var i="<div style='color: red; text-style: italic;'>"+t+"</div>";this.config_form=i,e.html(i),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=s}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=i(289),l=o(s),u=i(291),c=o(u);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return n("<div/>").addClass("inputs")},updateMaxWidth:function(t){this.output_width=Math.max(this.output_width,t)},addRule:function(){this.tool_body.append(n("<div/>").addClass("rule"))},addDataInput:function(t,e){var i=!0;e||(e=this.$(".inputs"),i=!1);var n=this.terminalViews[t.name],o="dataset_collection"==t.input_type?l.default.InputCollectionTerminalView:l.default.InputTerminalView;if(!n||n instanceof o||(n.el.terminal.destroy(),n=null),n){var a=n.el.terminal;a.update(t),a.destroyInvalidConnections()}else n=new o({node:this.node,input:t});this.terminalViews[t.name]=n;var r=n.el,s=new c.default.DataInputView({terminalElement:r,input:t,nodeView:this,skipResize:i}),u=s.$el;return e.append(u.prepend(n.terminalElements())),n},addDataOutput:function(t){var e=t.collection?l.default.OutputCollectionTerminalView:l.default.OutputTerminalView,i=new e({node:this.node,output:t}),n=new c.default.DataOutputView({output:t,terminalElement:i.el,nodeView:this});this.outputViews[t.name]=n,this.tool_body.append(n.$el.append(i.terminalElements()))},redrawWorkflowOutputs:function(){r.each(this.outputViews,function(t){t.redrawWorkflowOutput()})},updateDataOutput:function(t){this.node.output_terminals[t.name].update(t)}})}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(290),s=a(r),l=i(223),u=a(l);window.workflow_globals=window.workflow_globals||{};var c=t.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(t){this.$el.tooltip({delay:500,title:"Run tool in parallel over 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e=t.node,i=t.input,n=i.name,o=this.terminalForInput(i);o.multiple||this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.input_terminals[n]=o},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(t,e){var i=this.el.terminal;return o(e.drag).hasClass("output-terminal")&&i.canAccept(e.drag.terminal)},onDropStart:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(t,e){var i=this.el.terminal;new u.default(e.drag.terminal,i).redraw()},onHover:function(){var t=this.el,e=t.terminal;if(e.connectors.length>0){var i=o("<div class='callout'></div>").css({display:"none"}).appendTo("body").append(o("<div class='button'></div>").append(o("<div/>").addClass("fa-icon-button fa fa-times").click(function(){o.each(e.connectors,function(t,e){e&&e.destroy()}),i.remove()}))).bind("mouseleave",function(){o(this).remove()});i.css({top:o(t).offset().top-2,left:o(t).offset().left-i.width(),"padding-right":o(t).width()}).show()}}}),p=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForInput:function(t){return new s.default.InputTerminal({element:this.el,input:t})}}),m=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForInput:function(t){return new s.default.InputCollectionTerminal({element:this.el,input:t})}}),v=h.extend({className:"terminal output-terminal",initialize:function(t){var e=t.node,i=t.output,n=i.name,o=this.terminalForOutput(i);this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.output_terminals[n]=o},events:{drag:"onDrag",dragstart:"onDragStart",dragend:"onDragEnd"},onDrag:function(t,e){var i=function(){var t=o(e.proxy).offsetParent().offset(),i=e.offsetX-t.left,n=e.offsetY-t.top;o(e.proxy).css({left:i,top:n}),e.proxy.terminal.redraw(),window.workflow_globals.canvas_manager.update_viewport_overlay()};i(),o("#canvas-container").get(0).scroll_panel.test(t,i)},onDragStart:function(t,e){o(e.available).addClass("input-terminal-active"),window.workflow_globals.workflow.check_changes_in_active_form();var i=o('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new s.default.OutputTerminal({element:i});var n=new u.default;return n.dragging=!0,n.connect(this.el.terminal,i.terminal),i},onDragEnd:function(t,e){var i=e.proxy.terminal.connectors[0];i&&i.destroy(),o(e.proxy).remove(),o(e.available).removeClass("input-terminal-active"),o("#canvas-container").get(0).scroll_panel.stop()}}),g=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.extensions;return new s.default.OutputTerminal({element:this.el,datatypes:e})}}),_=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.collection_type,i=t.collection_type_source;return new s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:i,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:g,InputCollectionTerminalView:m,OutputCollectionTerminalView:_}}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,i,n){function o(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(t){return!1},canMapOver:function(t){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},r={isCollection:!0,canMatch:function(t){return a!==t},canMapOver:function(t){return!1},toString:function(){return"AnyCollectionType[]"},append:function(t){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(t){return t===this}};t.extend(o.prototype,{append:function(t){return t===a?this:t===r?otherCollectionType:new o(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==a&&(t===r||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===a)return!1;if(t===r)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new o(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var s=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||a,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),l=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){n.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),n.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),u=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||n.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),n.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||n.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var t;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:t=!1:t=!0:t=!1,t},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(n.first(n.values(this.node.output_terminals)).mapOver()):n.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var i=this.datatypes[e];if("input"==i)return!0;var n=new Array;if(n=n.concat(t.datatypes),t.node.post_job_actions)for(var o in t.node.post_job_actions){var a=t.node.post_job_actions[o];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=t.name||!a.action_arguments||n.push(a.action_arguments.newtype)}for(var r in n){var s=n[r];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(n[r],i))return!0}}return!1},_otherCollectionType:function(t){var e=a;t.isCollection&&(e=t.collectionType);var i=t.mapOver();return i.isCollection&&(e=i.append(e)),e}}),d=c.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._otherCollectionType(e);i.isCollection&&this.setMapOver(i)}},attachable:function(t){var e=this._otherCollectionType(t),i=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(i.isCollection&&i.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(n.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!i.isCollection&&this._producesAcceptableDatatype(t)}}),h=c.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?n.each(t.collection_types,function(t){e.push(new o(t))}):e.push(r),this.collectionTypes=e},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._effectiveMapOver(e);this.setMapOver(i)}},_effectiveMapOver:function(t){var e=this.collectionTypes,i=this._otherCollectionType(t);if(!n.some(e,function(t){return t.canMatch(i)}))for(var o in e){var r=e[o];if(i.canMapOver(r)){var s=i.effectiveMapOver(r);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var t=this.mapOver();return n.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var i=this._effectiveCollectionTypes(),o=this.mapOver();if(n.some(i,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(o.isCollection)return!1;if(n.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),f=l.extend({initialize:function(t){if(l.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=r}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=r}e.collectionType!=this.collectionType.collectionType&&n.each(this.connectors,function(t){t.destroy()}),this.collectionType=e}});e.default={InputTerminal:d,OutputTerminal:u,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:o,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:r}}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var n=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),o=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,n=e.name,o=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(n=n+" ("+e.extensions.join(", ")+")"),this.$el.html(n),this.calloutView=null,["tool","subworkflow"].indexOf(o.type)>=0){var r=new a({label:n,output:e,node:o});this.calloutView=r,this.$el.append(r.el),this.$el.hover(function(){r.hoverImage()},function(){r.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,n=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(i("<div class='buttons'></div>").append(i("<img/>").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;n.isWorkflowOutput(t)?(n.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(n.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. 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a.css({left:-d.left+h.width()/2-f/2,top:-d.top+h.height()/2-p/2}),c.prependTo(a.find(".toolFormTitle")),f+=c.width()+10,a.css("width",f),a.bind("dragstart",function(){o.workflow.activate_node(l)}).bind("dragend",function(){o.workflow.node_changed(this),o.workflow.fit_canvas_to_nodes(),o.canvas_manager.draw_overview()}).bind("dragclickonly",function(){o.workflow.activate_node(l)}).bind("drag",function(e,i){var n=t(this).offsetParent().offset(),o=i.offsetX-n.left,a=i.offsetY-n.top;t(this).css({left:o,top:a}),t(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t){function n(t,e){this.app=t,this.canvas_container=e,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(224),a=function(t){return t&&t.__esModule?t:{default:t}}(o),r=i(42),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r);t.extend(n.prototype,{canLabelOutputWith:function(t){return!t||!(t in this.workflowOutputLabels)},registerOutputLabel:function(t){t&&(this.workflowOutputLabels[t]=!0)},unregisterOutputLabel:function(t){t&&delete this.workflowOutputLabels[t]},updateOutputLabel:function(t,e){t&&this.unregisterOutputLabel(t),this.canLabelOutputWith(e)||s.warning("Workflow contains duplicate workflow output labels "+e+". This must be fixed before it can be saved."),e&&this.registerOutputLabel(e)},attemptUpdateOutputLabel:function(t,e,i){return!!this.canLabelOutputWith(i)&&(t.labelWorkflowOutput(e,i),t.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(t,e,i){var n=this.app.prebuildNode(t,e,i);return this.add_node(n),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(n),n},add_node:function(t){t.id=this.id_counter,t.element.attr("id","wf-node-step-"+t.id),this.id_counter++,this.nodes[t.id]=t,this.has_changes=!0,t.workflow=this},remove_node:function(t){this.active_node==t&&this.clear_active_node(),delete this.nodes[t.id],this.has_changes=!0},remove_all:function(){var e=this;t.each(this.nodes,function(t,i){i.destroy(),e.remove_node(i)})},rectify_workflow_outputs:function(){var e=!1,i=!1;if(t.each(this.nodes,function(n,o){o.workflow_outputs&&o.workflow_outputs.length>0&&(e=!0),t.each(o.post_job_actions,function(t,e){"HideDatasetAction"===e.action_type&&(i=!0)})}),!1!==e||!1!==i){var n=this;t.each(this.nodes,function(i,o){if("tool"===o.type){var a=!1;null===o.post_job_actions&&(o.post_job_actions={},a=!0);var r=[];t.each(o.post_job_actions,function(t,e){"HideDatasetAction"==e.action_type&&r.push(t)}),r.length>0&&t.each(r,function(t,e){a=!0,delete o.post_job_actions[e]}),e&&t.each(o.output_terminals,function(t,e){if(!0==!o.isWorkflowOutput(e.name)){a=!0;var i={action_type:"HideDatasetAction",output_name:e.name,action_arguments:{}};o.post_job_actions["HideDatasetAction"+e.name]=null,o.post_job_actions["HideDatasetAction"+e.name]=i}}),n.active_node==o&&!0===a&&n.reload_active_node()}})}},to_simple:function(){var e={};return t.each(this.nodes,function(i,n){var o={};t.each(n.input_terminals,function(e,i){o[i.name]=null;var n=[];t.each(i.connectors,function(t,e){if(e.handle1){var a={id:e.handle1.node.id,output_name:e.handle1.name},r=i.attributes.input.input_subworkflow_step_id;void 0!==r&&(a.input_subworkflow_step_id=r),n[t]=a,o[i.name]=n}})});var a={};n.post_job_actions&&t.each(n.post_job_actions,function(t,e){var i={action_type:e.action_type,output_name:e.output_name,action_arguments:e.action_arguments};a[e.action_type+e.output_name]=null,a[e.action_type+e.output_name]=i}),n.workflow_outputs||(n.workflow_outputs=[]);var r={id:n.id,type:n.type,content_id:n.content_id,tool_version:n.config_form.version,tool_state:n.tool_state,errors:n.errors,input_connections:o,position:t(n.element).position(),annotation:n.annotation,post_job_actions:n.post_job_actions,uuid:n.uuid,label:n.label,workflow_outputs:n.workflow_outputs};e[n.id]=r}),{steps:e}},from_simple:function(e,i){var n=void 0===i||i,o=this,r=0;n?o.name=e.name:r=Object.keys(o.nodes).length;var s=r,l=!1;t.each(e.steps,function(e,i){var a=o.app.prebuildNode(i.type,i.name,i.content_id);n||(i.uuid=null,t.each(i.workflow_outputs,function(t,e){e.uuid=null})),a.init_field_data(i),i.position&&a.element.css({top:i.position.top,left:i.position.left}),a.id=parseInt(i.id)+r,o.nodes[a.id]=a,s=Math.max(s,parseInt(e)+r),l||(a.workflow_outputs.length>0?l=!0:t.each(a.post_job_actions||[],function(t,e){"HideDatasetAction"===e.action_type&&(l=!0)}))}),o.id_counter=s+1,t.each(e.steps,function(e,i){var n=o.nodes[parseInt(e)+r];t.each(i.input_connections,function(e,i){i&&(t.isArray(i)||(i=[i]),t.each(i,function(t,i){var s=o.nodes[parseInt(i.id)+r],l=new a.default;l.connect(s.output_terminals[i.output_name],n.input_terminals[e]),l.redraw()}))}),l&&t.each(n.output_terminals,function(e,i){if(void 0===n.post_job_actions["HideDatasetAction"+i.name]){n.addWorkflowOutput(i.name);t(n.element).find(".callout."+i.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),o.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,t("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var t=this.active_node;this.clear_active_node(),this.activate_node(t)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showAttributes()},activate_node:function(t){this.active_node!=t&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(t.config_form,t),t.make_active(),this.active_node=t)},node_changed:function(t,e){this.has_changes=!0,this.active_node==t&&e&&(this.check_changes_in_active_form(),this.app.showForm(t.config_form,t)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var e={},i={};t.each(this.nodes,function(t,n){void 0===e[t]&&(e[t]=0),void 0===i[t]&&(i[t]=[])}),t.each(this.nodes,function(n,o){t.each(o.input_terminals,function(n,a){t.each(a.connectors,function(t,n){var a=n.handle1.node;e[o.id]+=1,i[a.id].push(o.id)})})});for(var n=[];;){var o=[];for(var a in e)0===e[a]&&o.push(a);if(0===o.length)break;n.push(o);for(var r in o){var s=o[r];delete e[s];for(var l in i[s])e[i[s][l]]-=1}}if(!e.length){var u=this.nodes,c=80;t.each(n,function(e,i){i.sort(function(e,i){return t(u[e].element).position().top-t(u[i].element).position().top});var n=0,o=30;t.each(i,function(e,i){var a=u[i],r=t(a.element);t(r).css({top:o,left:c}),n=Math.max(n,t(r).width()),o+=t(r).height()+30}),c+=n+80}),t.each(u,function(t,e){e.redraw()})}},bounds_for_all_nodes:function(){var e,i=1/0,n=-1/0,o=1/0,a=-1/0;return t.each(this.nodes,function(r,s){var l=t(s.element);e=l.position(),i=Math.min(i,e.left),n=Math.max(n,e.left+l.width()),o=Math.min(o,e.top),a=Math.max(a,e.top+l.width())}),{xmin:i,xmax:n,ymin:o,ymax:a}},fit_canvas_to_nodes:function(){function e(t,e){return Math.ceil(t/e)*e}function i(t,e){if(t<e||t>3*e){return-(t-(Math.ceil(t%e/e)+1)*e)}return 0}var n=this.bounds_for_all_nodes(),o=this.canvas_container.position(),a=this.canvas_container.parent(),r=i(n.xmin,100),s=i(n.ymin,100);r=Math.max(r,o.left),s=Math.max(s,o.top);var l=o.left-r,u=o.top-s,c=e(n.xmax+100,100)+r,d=e(n.ymax+100,100)+s;c=Math.max(c,-l+a.width()),d=Math.max(d,-u+a.height()),this.canvas_container.css({left:l,top:u,width:c,height:d}),this.canvas_container.children().each(function(){var e=t(this).position();t(this).css("left",e.left+r),t(this).css("top",e.top+s)})}}),e.default=n}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t,e,i){this.app=t,this.cv=e,this.cc=this.cv.find("#canvas-container"),this.overview=i,this.oc=i.find("#overview-canvas"),this.ov=i.find("#overview-viewport"),this.init_drag()}function n(t){this.panel=t}Object.defineProperty(e,"__esModule",{value:!0}),t.extend(i.prototype,{init_drag:function(){var e=this,i=function(t,i){t=Math.min(t,e.cv.width()/2),t=Math.max(t,-e.cc.width()+e.cv.width()/2),i=Math.min(i,e.cv.height()/2),i=Math.max(i,-e.cc.height()+e.cv.height()/2),e.cc.css({left:t,top:i}),e.cv.css({"background-position-x":t,"background-position-y":i}),e.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new n(this)});var o,a;this.cv.bind("dragstart",function(){var i=t(this).offset(),n=e.cc.position();a=n.top-i.top,o=n.left-i.left}).bind("drag",function(t,e){i(e.offsetX+o,e.offsetY+a)}).bind("dragend",function(){e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),this.overview.click(function(t){if(e.overview.hasClass("blockaclick"))e.overview.removeClass("blockaclick");else{var n=e.cc.width(),o=e.cc.height(),a=e.oc.width(),r=e.oc.height(),s=t.pageX-e.oc.offset().left-e.ov.width()/2,l=t.pageY-e.oc.offset().top-e.ov.height()/2;i(-s/a*n,-l/r*o),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}}),this.ov.bind("drag",function(t,n){var o=e.cc.width(),a=e.cc.height(),r=e.oc.width(),s=e.oc.height(),l=n.offsetX-e.overview.offset().left,u=n.offsetY-e.overview.offset().top;i(-l/r*o,-u/s*a)}).bind("dragend",function(){e.overview.addClass("blockaclick"),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),t("#overview-border").bind("drag",function(i,n){var o=t(this).offsetParent(),a=o.offset(),r=Math.max(o.width()-(n.offsetX-a.left),o.height()-(n.offsetY-a.top));t(this).css({width:r,height:r}),e.draw_overview()}),t("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,i=this.oc,n=this.ov,o=t.width(),a=t.height(),r=i.width(),s=i.height(),l=t.position();n.css({left:-l.left/o*r,top:-l.top/a*s,width:e.width()/o*r-2,height:e.height()/a*s-2})},draw_overview:function(){var e,i,n,o,a=t("#overview-canvas"),r=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=t("#canvas-container").width(),u=t("#canvas-container").height(),c=this.cv.width(),d=this.cv.height();l<c&&u<d?(n=l/c*r,o=(r-n)/2,e=u/d*r,i=(r-e)/2):l<u?(i=0,e=r,n=Math.ceil(e*l/u),o=(r-n)/2):(n=r,o=0,e=Math.ceil(n*u/l),i=(r-e)/2),a.parent().css({left:o,top:i,width:n,height:e}),a.attr("width",n),a.attr("height",e),t.each(this.app.workflow.nodes,function(i,o){s.fillStyle="#D2C099",s.strokeStyle="#D8B365",s.lineWidth=1;var a=t(o.element),r=a.position(),c=r.left/l*n,d=r.top/u*e,h=a.width()/l*n,f=a.height()/u*e;o.errors?(s.fillStyle="#FFCCCC",s.strokeStyle="#AA6666"):void 0!==o.workflow_outputs&&o.workflow_outputs.length>0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(c,d,h,f),s.strokeRect(c,d,h,f)}),this.update_viewport_overlay()}}),t.extend(n.prototype,{test:function(e,i){clearTimeout(this.timeout);var n=e.pageX,o=e.pageY,a=t(this.panel),r=a.position(),s=a.width(),l=a.height(),u=a.parent(),c=u.width(),d=u.height(),h=u.offset(),f=h.left,p=h.top,m=f+u.width(),v=p+u.height(),g=-(s-c/2),_=-(l-d/2),w=c/2,b=d/2,y=!1;if(n-5<f){if(r.left<w){var x=Math.min(23,w-r.left);a.css("left",r.left+x),y=!0}}else if(n+5>m){if(r.left>g){var x=Math.min(23,r.left-g);a.css("left",r.left-x),y=!0}}else if(o-5<p){if(r.top<b){var x=Math.min(23,b-r.top);a.css("top",r.top+x),y=!0}}else if(o+5>v&&r.top>_){var x=Math.min(23,r.top-g);a.css("top",r.top-x+"px"),y=!0}if(y){i();var a=this;this.timeout=setTimeout(function(){a.test(e,i)},50)}},stop:function(t,e){clearTimeout(this.timeout)}}),e.default=i}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,o){Object.defineProperty(e,"__esModule",{value:!0});var a=i(289),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return n.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var i={output_name:t};return e&&(i.label=e),this.workflow_outputs.push(i),!0}return!1},labelWorkflowOutput:function(t,e){var i=!1,n=null;if(this.isWorkflowOutput(t)){var o=this.getWorkflowOutput(t);n=o.label,o.label=e,i=n!=e}else i=this.addWorkflowOutput(t,e);return i&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),i},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.connectors.length>0&&e.push(i)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var i=t[e];if(i.connectors.length>0&&i.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&i.connectors.length>0&&e.push(i)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&e.push(i)}),e},hasMappedOverInputTerminals:function(){var t=!1;return n.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){o.each(this.input_terminals,function(t,e){e.redraw()}),o.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){o.each(this.input_terminals,function(t,e){e.destroy()}),o.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),o(this.element).remove()},make_active:function(){o(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),o(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,i=new r.default({el:this.element[0],node:e});e.nodeView=i,o.each(t.data_inputs,function(t,e){i.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&i.addRule(),o.each(t.data_outputs,function(t,e){i.addDataOutput(e)}),i.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,i=e.nodeView,a=[];if(o.each(i.outputViews,function(e,i){var o=i.output.name,r=t.data_outputs,s=!1;n.each(r,function(t){t.name==o&&(s=!0)}),!1===s&&a.push(o)}),n.each(a,function(t){n.each(i.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),i.outputViews[t].remove(),delete i.outputViews[t],delete e.output_terminals[t]}),o.each(e.workflow_outputs,function(t,i){i&&!e.output_terminals[i.output_name]&&e.workflow_outputs.splice(t,1)}),o.each(t.data_outputs,function(t,n){i.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):i.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var r=t.post_job_actions;this.post_job_actions=r||{}}e.nodeView.renderToolErrors();var s=i.$("div.inputs"),l=i.newInputsDiv(),u={};n.each(t.data_inputs,function(t){var i=e.nodeView.addDataInput(t,l);u[t.name]=i}),n.each(n.difference(n.values(i.terminalViews),n.values(u)),function(t){t.el.terminal.destroy()}),i.terminalViews=u,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&i.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=o(this.element).find(".toolFormBody");e.find("div").remove();var i="<div style='color: red; text-style: italic;'>"+t+"</div>";this.config_form=i,e.html(i),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=s}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=i(290),l=o(s),u=i(292),c=o(u);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return n("<div/>").addClass("inputs")},updateMaxWidth:function(t){this.output_width=Math.max(this.output_width,t)},addRule:function(){this.tool_body.append(n("<div/>").addClass("rule"))},addDataInput:function(t,e){var i=!0;e||(e=this.$(".inputs"),i=!1);var n=this.terminalViews[t.name],o="dataset_collection"==t.input_type?l.default.InputCollectionTerminalView:l.default.InputTerminalView;if(!n||n instanceof o||(n.el.terminal.destroy(),n=null),n){var a=n.el.terminal;a.update(t),a.destroyInvalidConnections()}else n=new o({node:this.node,input:t});this.terminalViews[t.name]=n;var r=n.el,s=new c.default.DataInputView({terminalElement:r,input:t,nodeView:this,skipResize:i}),u=s.$el;return e.append(u.prepend(n.terminalElements())),n},addDataOutput:function(t){var e=t.collection?l.default.OutputCollectionTerminalView:l.default.OutputTerminalView,i=new e({node:this.node,output:t}),n=new c.default.DataOutputView({output:t,terminalElement:i.el,nodeView:this});this.outputViews[t.name]=n,this.tool_body.append(n.$el.append(i.terminalElements()))},redrawWorkflowOutputs:function(){r.each(this.outputViews,function(t){t.redrawWorkflowOutput()})},updateDataOutput:function(t){this.node.output_terminals[t.name].update(t)}})}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(291),s=a(r),l=i(224),u=a(l);window.workflow_globals=window.workflow_globals||{};var c=t.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(t){this.$el.tooltip({delay:500,title:"Run tool in parallel over 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e=t.node,i=t.input,n=i.name,o=this.terminalForInput(i);o.multiple||this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.input_terminals[n]=o},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(t,e){var i=this.el.terminal;return o(e.drag).hasClass("output-terminal")&&i.canAccept(e.drag.terminal)},onDropStart:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(t,e){var i=this.el.terminal;new u.default(e.drag.terminal,i).redraw()},onHover:function(){var t=this.el,e=t.terminal;if(e.connectors.length>0){var i=o("<div class='callout'></div>").css({display:"none"}).appendTo("body").append(o("<div class='button'></div>").append(o("<div/>").addClass("fa-icon-button fa 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t=o(e.proxy).offsetParent().offset(),i=e.offsetX-t.left,n=e.offsetY-t.top;o(e.proxy).css({left:i,top:n}),e.proxy.terminal.redraw(),window.workflow_globals.canvas_manager.update_viewport_overlay()};i(),o("#canvas-container").get(0).scroll_panel.test(t,i)},onDragStart:function(t,e){o(e.available).addClass("input-terminal-active"),window.workflow_globals.workflow.check_changes_in_active_form();var i=o('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new s.default.OutputTerminal({element:i});var n=new u.default;return n.dragging=!0,n.connect(this.el.terminal,i.terminal),i},onDragEnd:function(t,e){var i=e.proxy.terminal.connectors[0];i&&i.destroy(),o(e.proxy).remove(),o(e.available).removeClass("input-terminal-active"),o("#canvas-container").get(0).scroll_panel.stop()}}),g=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.extensions;return new s.default.OutputTerminal({element:this.el,datatypes:e})}}),_=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.collection_type,i=t.collection_type_source;return new s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:i,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:g,InputCollectionTerminalView:m,OutputCollectionTerminalView:_}}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,i,n){function o(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(t){return!1},canMapOver:function(t){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},r={isCollection:!0,canMatch:function(t){return a!==t},canMapOver:function(t){return!1},toString:function(){return"AnyCollectionType[]"},append:function(t){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(t){return t===this}};t.extend(o.prototype,{append:function(t){return t===a?this:t===r?otherCollectionType:new o(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==a&&(t===r||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===a)return!1;if(t===r)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new o(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var s=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||a,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),l=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){n.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),n.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),u=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||n.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),n.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||n.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var t;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:t=!1:t=!0:t=!1,t},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(n.first(n.values(this.node.output_terminals)).mapOver()):n.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var i=this.datatypes[e];if("input"==i)return!0;var n=new Array;if(n=n.concat(t.datatypes),t.node.post_job_actions)for(var o in t.node.post_job_actions){var a=t.node.post_job_actions[o];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=t.name||!a.action_arguments||n.push(a.action_arguments.newtype)}for(var r in n){var s=n[r];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(n[r],i))return!0}}return!1},_otherCollectionType:function(t){var e=a;t.isCollection&&(e=t.collectionType);var i=t.mapOver();return i.isCollection&&(e=i.append(e)),e}}),d=c.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._otherCollectionType(e);i.isCollection&&this.setMapOver(i)}},attachable:function(t){var e=this._otherCollectionType(t),i=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(i.isCollection&&i.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(n.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!i.isCollection&&this._producesAcceptableDatatype(t)}}),h=c.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?n.each(t.collection_types,function(t){e.push(new o(t))}):e.push(r),this.collectionTypes=e},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._effectiveMapOver(e);this.setMapOver(i)}},_effectiveMapOver:function(t){var e=this.collectionTypes,i=this._otherCollectionType(t);if(!n.some(e,function(t){return t.canMatch(i)}))for(var o in e){var r=e[o];if(i.canMapOver(r)){var s=i.effectiveMapOver(r);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var t=this.mapOver();return n.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var i=this._effectiveCollectionTypes(),o=this.mapOver();if(n.some(i,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(o.isCollection)return!1;if(n.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),f=l.extend({initialize:function(t){if(l.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=r}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=r}e.collectionType!=this.collectionType.collectionType&&n.each(this.connectors,function(t){t.destroy()}),this.collectionType=e}});e.default={InputTerminal:d,OutputTerminal:u,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:o,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:r}}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var n=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),o=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,n=e.name,o=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(n=n+" ("+e.extensions.join(", ")+")"),this.$el.html(n),this.calloutView=null,["tool","subworkflow"].indexOf(o.type)>=0){var r=new a({label:n,output:e,node:o});this.calloutView=r,this.$el.append(r.el),this.$el.hover(function(){r.hoverImage()},function(){r.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,n=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(i("<div class='buttons'></div>").append(i("<img/>").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;n.isWorkflowOutput(t)?(n.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(n.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});e.default={DataInputView:n,DataOutputView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}function a(t){var e=t.model.attributes,i=e.workflow,n=e.node;e.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:n.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),e.inputs.unshift({type:"text",name:"__label",label:"Label",value:n.label,help:"Add a step label.",fixed:!0,onchange:function(e){var o=!1;for(var a in i.nodes){var r=i.nodes[a];if(r.label&&r.label==e&&r.id!=n.id){o=!0;break}}var s=t.data.match("__label");t.element_list[s].model.set("error_text",o&&"Duplicate label. Please fix this before saving the workflow."),t.trigger("change")}})}function r(t,e,i,n){var o=n.node.post_job_actions;e=e||[],e.push(t);for(var a in t.inputs){var s=t.inputs[a];if(s.action){if(s.name="pja__"+i+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var u=o[s.action+i];if(u){for(var c in e)e[c].expanded=!0;s.pja_arg?s.value=u.action_arguments&&u.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&r(s,e.slice(0),i,n)}}function s(t,e){var i=[],n=[],o=e.datatypes,a=e.node,s=e.workflow;for(var l in o)i.push({0:o[l],1:o[l]});for(l in a.input_terminals)n.push(a.input_terminals[l].name);i.sort(function(t,e){return t.label>e.label?1:t.label<e.label?-1:0}),i.unshift({0:"Sequences",1:"Sequences"}),i.unshift({0:"Roadmaps",1:"Roadmaps"}),i.unshift({0:"Leave unchanged",1:"__empty__"});var u,c={title:"Configure Output: '"+t+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(u=a.getWorkflowOutput(t))&&u.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(e){s.attemptUpdateOutputLabel(a,t,e)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>'+n.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:i,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return r(c,[],t,e),c}function l(t){var e=t.model.attributes,i=e.inputs,n=e.node,o=n.post_job_actions,a=n.output_terminals&&Object.keys(n.output_terminals)[0];if(a){i.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(o["EmailAction"+a])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),i.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(o["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var r in n.output_terminals)i.push(s(r,e))}}Object.defineProperty(e,"__esModule",{value:!0});var u=i(3),c=o(u),d=i(20),h=o(d),f=i(63),p=o(f),m=t.View.extend({initialize:function(t){var e=this,i=t.node;this.form=new h.default(c.default.merge(t,{onchange:function(){c.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:i.id,type:i.type,content_id:i.content_id,inputs:e.form.data.create()},success:function(t){i.update_field_data(t)}})}})),a(this.form),this.form.render()}}),v=t.View.extend({initialize:function(t){var e=this,i=t.node;this.form=new p.default(c.default.merge(t,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(t,i){e._customize(i),t.resolve()},buildmodel:function(t,e){e.model.get("postchange")(t,e)},postchange:function(t,o){var a=o.model.attributes,r={tool_id:a.id,tool_version:a.version,type:"tool",inputs:n.extend(!0,{},o.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",r),c.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:r,success:function(n){o.model.set(n.config_form),e._customize(o),o.update(n.config_form),o.errors(n.config_form),i.update_field_data(n),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",n),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",e),t.reject()}})}}))},_customize:function(t){var e=t.model.attributes;c.default.deepeach(e.inputs,function(t){t.type&&(-1!=["data","data_collection"].indexOf(t.type)?(t.type="hidden",t.info="Data input '"+t.name+"' ("+c.default.textify(t.extensions)+")",t.value={__class__:"RuntimeValue"}):t.fixed||(t.collapsible_value={__class__:"RuntimeValue"},t.is_workflow=t.options&&0===t.options.length||-1!=["integer","float"].indexOf(t.type)))}),c.default.deepeach(e.inputs,function(t){"conditional"===t.type&&(t.test_param.collapsible_value=void 0)}),l(t),a(t)}});e.default={Default:m,Tool:v}}).call(e,i(1),i(0))}],[284]);
\ No newline at end of file
diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js
index 48c251ea000..d2c6a84d112 100644
--- a/static/scripts/mvc/history/hdca-li.js
+++ b/static/scripts/mvc/history/hdca-li.js
@@ -1 +1 @@
-define("mvc/history/hdca-li",["exports","mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-view","mvc/base-mvc","mvc/history/history-item-li","utils/localization"],function(e,t,i,n,s,l,a){"use strict";function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var c=o(t),r=o(i),d=o(n),u=(o(s),o(l)),p=o(a),h=r.default.DCListItemView,m=h.extend({className:h.prototype.className+" history-content",_setUpListeners:function(){h.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:tags change:populated change:visible":function(e,t){this.render()}})},_getFoldoutPanelClass:function(){var e=this.model.get("collection_type");switch(e){case"list":return d.default.ListCollectionView;case"paired":return d.default.PairCollectionView;case"list:paired":return d.default.ListOfPairsCollectionView;case"list:list":return d.default.ListOfListsCollectionView}throw new TypeError("Unknown collection_type: "+e)},_swapNewRender:function(e){h.prototype._swapNewRender.call(this,e);var t=this.model.get("populated")?c.default.OK:c.default.RUNNING;return this.$el.addClass("state-"+t),this.$el},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){var e=_.extend({},h.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}});return _.extend({},h.prototype.templates,{warnings:e,titleBar:function(e){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+e.hid+'</span>\n                <span class="name">'+_.escape(e.name)+'</span>\n            </div>\n            <div class="subtitle"></div>\n            '+u.default.nametagTemplate(e)+"\n        </div>\n    "}})}(),e.default={HDCAListItemView:m}});
\ No newline at end of file
+define("mvc/history/hdca-li",["exports","mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-view","mvc/base-mvc","mvc/history/history-item-li","utils/localization"],function(e,t,s,i,n,a,r){"use strict";function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var l=o(t),d=o(s),c=o(i),p=(o(n),o(a)),u=o(r),h=d.default.DCListItemView,m=h.extend({className:h.prototype.className+" history-content",_setUpListeners:function(){var e=this;h.prototype._setUpListeners.call(this);var t=function(t,s){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){var e=this.model.get("collection_type");switch(e){case"list":return c.default.ListCollectionView;case"paired":return c.default.PairCollectionView;case"list:paired":return c.default.ListOfPairsCollectionView;case"list:list":return c.default.ListOfListsCollectionView}throw new TypeError("Unknown collection_type: "+e)},_swapNewRender:function(e){h.prototype._swapNewRender.call(this,e);var t,s=this.model.jobStatesSummary;t=s?s.new()?"loading":s.errored()?"error":s.terminal()?"ok":s.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?l.default.OK:l.default.RUNNING,this.$el.addClass("state-"+t);var i=this.stateDescription();return this.$(".state-description").html(i),this.$el},stateDescription:function(){var e,t=this.model,s=t.get("element_count"),i=t.get("job_source_type"),n=this.model.get("collection_type");e="list"==n?"list":"paired"==n?"dataset pair":"list:paired"==n?"list of pairs":"nested list";var a="";1==s?a=" with 1 item":s&&(a=" with "+s+" items");var r=t.jobStatesSummary,o=""+e+a;if(i&&"Job"!=i){if(r&&r.hasDetails()){var l=r.new(),d=l?null:r.jobCount();if(l)return'\n                        <div class="progress state-progress">\n                            <span class="note">Creating jobs.<span class="blinking">..</span></span>\n                            <div class="progress-bar info" style="width:100%">\n                        </div>';if(r.errored())return"a "+e+" with "+r.numInError()+" / "+d+" jobs in error";if(r.terminal())return"a "+o;var c=r.states().running||0,p=(r.states().ok||0)/(1*d),u=c/(1*d),h=1-p-u;return'\n                        <div class="progress state-progress">\n                            <span class="note">'+(d&&d>1?d+" jobs":"a job")+" generating a "+e+'</span>\n                            <div class="progress-bar ok" style="width:'+100*p+'%"></div>\n                            <div class="progress-bar running" style="width:'+100*u+'%"></div>\n                            <div class="progress-bar new" style="width:'+100*h+'%">\n                        </div>'}return'\n                    <div class="progress state-progress">\n                        <span class="note">Loading job data for '+e+'.<span class="blinking">..</span></span>\n                        <div class="progress-bar info" style="width:100%">\n                    </div>'}return"a "+o},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){var e=_.extend({},h.prototype.templates.warnings,{hidden:function(e){e.visible||(0,u.default)("This collection has been hidden")}});return _.extend({},h.prototype.templates,{warnings:e,titleBar:function(e){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+e.hid+'</span>\n                <span class="name">'+_.escape(e.name)+'</span>\n            </div>\n            <div class="state-description">\n            </div>\n            '+p.default.nametagTemplate(e)+"\n        </div>\n    "}})}(),e.default={HDCAListItemView:m}});
\ No newline at end of file
diff --git a/static/scripts/mvc/history/history-contents.js b/static/scripts/mvc/history/history-contents.js
index 847d3c3a6ad..9e95edffb05 100644
--- a/static/scripts/mvc/history/history-contents.js
+++ b/static/scripts/mvc/history/history-contents.js
@@ -1 +1 @@
-define("mvc/history/history-contents",["exports","mvc/base/controlled-fetch-collection","mvc/history/hda-model","mvc/history/hdca-model","mvc/history/history-preferences","mvc/base-mvc","utils/ajax-queue"],function(t,e,i,n,r,o,s){"use strict";function d(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(t,"__esModule",{value:!0});var a=d(e),l=d(i),c=d(n),u=d(r),h=d(o),f=d(s),y=a.default.PaginatedCollection,p=y.extend(h.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(t,e){e=e||{},y.prototype.initialize.call(this,t,e),this.history=e.history||null,this.setHistoryId(e.historyId||null),this.includeDeleted=e.includeDeleted||this.includeDeleted,this.includeHidden=e.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},model:function(t,e){if("dataset"===t.history_content_type)return new l.default.HistoryDatasetAssociation(t,e);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new c.default.HistoryListDatasetCollection(t,e);case"paired":return new c.default.HistoryPairDatasetCollection(t,e);case"list:paired":return new c.default.HistoryListPairedDatasetCollection(t,e);case"list:list":return new c.default.HistoryListOfListsDatasetCollection(t,e)}var i="Unknown collection_type: "+t.collection_type;return console.warn(i,t),{validationError:i}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},setHistoryId:function(t){this.historyId=t,this._setUpWebStorage()},_setUpWebStorage:function(t){if(this.historyId)return this.storage=new u.default.HistoryPrefs({id:u.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(t){this.storage.includeDeleted(t)},"include-hidden":function(t){this.storage.includeHidden(t)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:_.extend(_.clone(y.prototype.comparators),{name:h.default.buildComparator("name",{ascending:!0}),"name-dsc":h.default.buildComparator("name",{ascending:!1}),hid:h.default.buildComparator("hid",{ascending:!1}),"hid-asc":h.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(t){return!t.inReadyState()})},runningAndActive:function(){return this.filter(function(t){return!t.inReadyState()&&t.get("visible")&&!t.get("deleted")})},getByHid:function(t){return this.findWhere({hid:t})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},hidden:function(){return this.filter(function(t){return t.hidden()})},deleted:function(){return this.filter(function(t){return t.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(t){return t.get("visible")&&!t.get("deleted")})},setIncludeDeleted:function(t,e){if(_.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,_.result(e,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,e){if(_.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,e=e||{},_.result(e,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var e=u.default.HistoryPrefs.get(this.historyId).toJSON();_.isEmpty(e.expandedIds)||(t.details=_.values(e.expandedIds).join(","))}return y.prototype.fetch.call(this,t)},_buildFetchData:function(t){return _.extend(y.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:y.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var e=y.prototype._buildFetchFilters.call(this,t)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),_.defaults(e,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(t,e){return t&&((e=e||{filters:{}}).remove=!1,e.filters={"update_time-ge":t.toISOString(),visible:""}),this.fetch(e)},fetchDeleted:function(t){var e=this;return t=t||{},t.filters=_.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){e.trigger("fetching-deleted-done",e)})},fetchHidden:function(t){var e=this;return(t=t||{}).filters=_.extend(t.filters,{visible:!1}),t.remove=!1,e.trigger("fetching-hidden",e),e.fetch(t).always(function(){e.trigger("fetching-hidden-done",e)})},fetchAllDetails:function(t){var e={details:"all"};return(t=t||{}).data=_.extend(t.data||{},e),this.fetch(t)},fetchCollectionCounts:function(t){return t=t||{},t.keys=["type_id","element_count"].join(","),t.filters=_.extend(t.filters||{},{history_content_type:"dataset_collection"}),t.remove=!1,this.fetch(t)},_filterAndUpdate:function(t,e){var i=this,n=i.model.prototype.idAttribute,r=[e];return i.fetch({filters:t,remove:!1}).then(function(t){return t=t.reduce(function(t,e,r){var o=i.get(e[n]);return o?t.concat(o):t},[]),i.ajaxQueue("save",r,t)})},ajaxQueue:function(t,e,i){return i=i||this.models,new f.default.AjaxQueue(i.slice().reverse().map(function(i,n){var r=_.isString(t)?i[t]:t;return function(){return r.apply(i,e)}})).deferred},progressivelyFetchDetails:function(t){function e(s){s=s||0;var d=_.extend(_.clone(t),{view:"summary",keys:o,limit:r,offset:s,reset:0===s,remove:!1});_.defer(function(){n.fetch.call(n,d).fail(i.reject).done(function(t){i.notify(t,r,s),t.length!==r?(n.allFetched=!0,i.resolve(t,r,s)):e(s+r)})})}t=t||{};var i=jQuery.Deferred(),n=this,r=t.limitPerCall||n.limitPerProgressiveFetch,o=l.default.HistoryDatasetAssociation.prototype.searchAttributes.join(",");return e(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return _.isObject(t)&&t.id&&_.contains(e,t.model_class)},copy:function(t){var e,i,n;_.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var r=this,o=jQuery.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:e,source:n,type:i})}).done(function(t){r.add([t],{parse:!0})}).fail(function(t,s,d){r.trigger("error",r,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},createHDCA:function(t,e,i,n,r){return this.model({history_content_type:"dataset_collection",collection_type:e,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:t}).save(r)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return _.has(t.attributes,"annotation")})},matches:function(t){return this.filter(function(e){return e.matches(t)})},clone:function(){var t=Backbone.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:p}});
\ No newline at end of file
+define("mvc/history/history-contents",["exports","mvc/base/controlled-fetch-collection","mvc/history/hda-model","mvc/history/hdca-model","mvc/history/history-preferences","mvc/history/job-states-model","mvc/base-mvc","utils/ajax-queue"],function(t,e,i,n,o,r,s,a){"use strict";function l(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(t,"__esModule",{value:!0});var d=l(e),c=l(i),u=l(n),h=l(o),f=l(r),y=l(s),m=l(a),p=d.default.PaginatedCollection,g=p.extend(y.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(t,e){this.on({"sync add":this.trackJobStates}),e=e||{},p.prototype.initialize.call(this,t,e),this.history=e.history||null,this.setHistoryId(e.historyId||null),this.includeDeleted=e.includeDeleted||this.includeDeleted,this.includeHidden=e.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var t=this;this.each(function(e){if(!e.has("job_states_summary")&&"dataset_collection"===e.attributes.history_content_type){var i=e.attributes.job_source_type,n=e.attributes.job_source_id;if(i){t.jobStateSummariesCollection.add({id:n,model:i,history_id:t.history_id,collection_id:e.attributes.id});var o=t.jobStateSummariesCollection.get(n);e.jobStatesSummary=o}}})},model:function(t,e){if("dataset"===t.history_content_type)return new c.default.HistoryDatasetAssociation(t,e);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new u.default.HistoryListDatasetCollection(t,e);case"paired":return new u.default.HistoryPairDatasetCollection(t,e);case"list:paired":return new u.default.HistoryListPairedDatasetCollection(t,e);case"list:list":return new u.default.HistoryListOfListsDatasetCollection(t,e)}var i="Unknown collection_type: "+t.collection_type;return console.warn(i,t),{validationError:i}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(t){this.stopPolling(),this.historyId=t,t&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new f.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=t,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(t){return this.storage=new h.default.HistoryPrefs({id:h.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(t){this.storage.includeDeleted(t)},"include-hidden":function(t){this.storage.includeHidden(t)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:_.extend(_.clone(p.prototype.comparators),{name:y.default.buildComparator("name",{ascending:!0}),"name-dsc":y.default.buildComparator("name",{ascending:!1}),hid:y.default.buildComparator("hid",{ascending:!1}),"hid-asc":y.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(t){return!t.inReadyState()})},runningAndActive:function(){return this.filter(function(t){return!t.inReadyState()&&t.get("visible")&&!t.get("deleted")})},getByHid:function(t){return this.findWhere({hid:t})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},hidden:function(){return this.filter(function(t){return t.hidden()})},deleted:function(){return this.filter(function(t){return t.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(t){return t.get("visible")&&!t.get("deleted")})},setIncludeDeleted:function(t,e){if(_.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,_.result(e,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,e){if(_.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,e=e||{},_.result(e,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var e=h.default.HistoryPrefs.get(this.historyId).toJSON();_.isEmpty(e.expandedIds)||(t.details=_.values(e.expandedIds).join(","))}return p.prototype.fetch.call(this,t)},_buildFetchData:function(t){return _.extend(p.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:p.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var e=p.prototype._buildFetchFilters.call(this,t)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),_.defaults(e,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(t,e){return t&&((e=e||{filters:{}}).remove=!1,e.filters={"update_time-ge":t.toISOString(),visible:""}),this.fetch(e)},fetchDeleted:function(t){var e=this;return t=t||{},t.filters=_.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){e.trigger("fetching-deleted-done",e)})},fetchHidden:function(t){var e=this;return(t=t||{}).filters=_.extend(t.filters,{visible:!1}),t.remove=!1,e.trigger("fetching-hidden",e),e.fetch(t).always(function(){e.trigger("fetching-hidden-done",e)})},fetchAllDetails:function(t){var e={details:"all"};return(t=t||{}).data=_.extend(t.data||{},e),this.fetch(t)},_filterAndUpdate:function(t,e){var i=this,n=i.model.prototype.idAttribute,o=[e];return i.fetch({filters:t,remove:!1}).then(function(t){return t=t.reduce(function(t,e,o){var r=i.get(e[n]);return r?t.concat(r):t},[]),i.ajaxQueue("save",o,t)})},ajaxQueue:function(t,e,i){return i=i||this.models,new m.default.AjaxQueue(i.slice().reverse().map(function(i,n){var o=_.isString(t)?i[t]:t;return function(){return o.apply(i,e)}})).deferred},progressivelyFetchDetails:function(t){function e(s){s=s||0;var a=_.extend(_.clone(t),{view:"summary",keys:r,limit:o,offset:s,reset:0===s,remove:!1});_.defer(function(){n.fetch.call(n,a).fail(i.reject).done(function(t){i.notify(t,o,s),t.length!==o?(n.allFetched=!0,i.resolve(t,o,s)):e(s+o)})})}t=t||{};var i=jQuery.Deferred(),n=this,o=t.limitPerCall||n.limitPerProgressiveFetch,r=c.default.HistoryDatasetAssociation.prototype.searchAttributes.join(",");return e(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return _.isObject(t)&&t.id&&_.contains(e,t.model_class)},copy:function(t){var e,i,n;_.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var o=this,r=jQuery.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:e,source:n,type:i})}).done(function(t){o.add([t],{parse:!0})}).fail(function(t,s,a){o.trigger("error",o,r,{},"Error copying contents",{type:i,id:e,source:n})});return r},createHDCA:function(t,e,i,n,o){return this.model({history_content_type:"dataset_collection",collection_type:e,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:t}).save(o)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return _.has(t.attributes,"annotation")})},matches:function(t){return this.filter(function(e){return e.matches(t)})},clone:function(){var t=Backbone.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:g}});
\ No newline at end of file
diff --git a/static/scripts/mvc/history/history-model.js b/static/scripts/mvc/history/history-model.js
index b09a15d1438..9dcabb6ccad 100644
--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -1 +1 @@
-define("mvc/history/history-model",["exports","mvc/history/history-contents","mvc/history/history-preferences","mvc/base/controlled-fetch-collection","utils/utils","mvc/base-mvc","utils/localization"],function(t,e,n,i,r,s,o){"use strict";function u(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(t,"__esModule",{value:!0});var a=u(e),c=(u(n),u(i)),d=u(r),l=u(s),h=u(o),f=Backbone.Model.extend(l.default.LoggableMixin).extend(l.default.mixin(l.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:a.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(t,e){e=e||{},this.logger=e.logger||null,this.log(this+".initialize:",t,e),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:e.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(t,e,n,i,r){this.clearUpdateTimeout()},"change:id":function(t,e){this.contents&&(this.contents.historyId=e)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,jQuery.makeArray(arguments))}}):this},contentsShown:function(){var t=this.get("contents_active"),e=t.active||0;return e+=this.contents.includeDeleted?t.deleted:0,e+=this.contents.includeHidden?t.hidden:0},nice_size:function(){var t=this.get("size");return t?d.default.bytesToString(t,!0,2):(0,h.default)("(empty)")},toJSON:function(){return _.extend(Backbone.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():Backbone.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var t=this.get("non_ready_jobs");return t?t.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var t=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:$.param({keys:t.join(",")})})},refresh:function(t){var e=this;t=t||{};var n=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return e.contents.fetchPage(e.contents.currentPage)}:function(){return e.contents.fetchUpdated(n)})().done(function(n,i,r){var s;try{s=new Date(r.getResponseHeader("Date"))}catch(t){}e.lastUpdateTime=s||new Date,e.checkForUpdates(t)})},checkForUpdates:function(t){var e=this;t=t||{};var n=this.UPDATE_DELAY;if(this.id){var i=function(){e.clearUpdateTimeout(),e.updateTimeoutId=setTimeout(function(){e.refresh(t)},n)};this.numOfUnfinishedShownContents()>0?i():this._fetchContentRelatedAttributes().done(function(t){e.numOfUnfinishedJobs()>0?i():e.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(t,e){var n=Backbone.Model.prototype.parse.call(this,t,e);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(t,e){var n=this;return(t=t||{}).view="dev-detailed",this.fetch(t).then(function(t){return n.contents.history=n,n.contents.setHistoryId(t.id),n.fetchContents(e)})},fetchContents:function(t){t=t||{};var e=this;return e.lastUpdateTime=new Date,e.contents.fetchCurrentPage(t)},_delete:function(t){return this.get("deleted")?jQuery.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?jQuery.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):jQuery.when()},copy:function(t,e,n){if(t=void 0===t||t,!this.id)throw new Error("You must set the history ID before copying it.");var i={history_id:this.id};t&&(i.current=!0),e&&(i.name=e),n||(i.all_datasets=!1),i.view="dev-detailed";var r=this,s=jQuery.post(this.urlRoot,i);return t?s.then(function(t){return new f(t).setAsCurrent().done(function(){r.trigger("copied",r,t)})}):s.done(function(t){r.trigger("copied",r,t)})},setAsCurrent:function(){var t=this,e=jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return e.done(function(){t.trigger("set-as-current",t)}),e},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),g=c.default.InfinitelyScrollingCollection,p=g.extend(l.default.LoggableMixin).extend({_logNamespace:"history",model:f,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(t,e){e=e||{},this.log("HistoryCollection.initialize",t,e),g.prototype.initialize.call(this,t,e),this.includeDeleted=e.includeDeleted||!1,this.currentHistoryId=e.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(t){this.debug("change:deleted",this.includeDeleted,t.get("deleted")),!this.includeDeleted&&t.get("deleted")&&this.remove(t)},copied:function(t,e){this.setCurrent(new f(e,[]))},"set-as-current":function(t){var e=this.currentHistoryId;this.trigger("no-longer-current",e),this.currentHistoryId=t.id}})},_buildFetchData:function(t){return _.extend(g.prototype._buildFetchData.call(this,t),{view:"dev-detailed"})},_buildFetchFilters:function(t){var e=g.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted?n.deleted=null:(n.deleted=!1,n.purged=!1),_.defaults(e,n)},fetchFirst:function(t){var e=this,n=$.when();return this.currentHistoryId&&(n=g.prototype.fetchFirst.call(e,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),n.then(function(){return t=t||{},t.offset=0,e.fetchMore(t)})},comparators:_.extend(_.clone(g.prototype.comparators),{name:l.default.buildComparator("name",{ascending:!0}),"name-dsc":l.default.buildComparator("name",{ascending:!1}),size:l.default.buildComparator("size",{ascending:!1}),"size-asc":l.default.buildComparator("size",{ascending:!0})}),sort:function(t){var e=(t=t||{}).silent,n=this.remove(this.get(this.currentHistoryId));return g.prototype.sort.call(this,_.defaults({silent:!0},t)),this.unshift(n,{silent:!0}),e||this.trigger("sort",this,t),this},create:function(t,e,n,i){var r=this;return jQuery.getJSON(Galaxy.root+"history/create_new_current").done(function(t){r.setCurrent(new f(t,[],n||{}))})},setCurrent:function(t,e){return e=e||{},this.unshift(t,e),this.currentHistoryId=t.get("id"),e.silent||this.trigger("new-current",t,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:f,HistoryCollection:p}});
\ No newline at end of file
+define("mvc/history/history-model",["exports","mvc/history/history-contents","mvc/history/history-preferences","mvc/base/controlled-fetch-collection","utils/utils","mvc/base-mvc","utils/localization"],function(t,e,n,i,r,s,o){"use strict";function u(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(t,"__esModule",{value:!0});var c=u(e),a=(u(n),u(i)),d=u(r),l=u(s),h=u(o),f=Backbone.Model.extend(l.default.LoggableMixin).extend(l.default.mixin(l.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:c.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(t,e){e=e||{},this.logger=e.logger||null,this.log(this+".initialize:",t,e),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:e.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(t,e,n,i,r){this.clearUpdateTimeout()},"change:id":function(t,e){this.contents&&(this.contents.historyId=e)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,jQuery.makeArray(arguments))}}):this},contentsShown:function(){var t=this.get("contents_active"),e=t.active||0;return e+=this.contents.includeDeleted?t.deleted:0,e+=this.contents.includeHidden?t.hidden:0},nice_size:function(){var t=this.get("size");return t?d.default.bytesToString(t,!0,2):(0,h.default)("(empty)")},toJSON:function(){return _.extend(Backbone.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():Backbone.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var t=this.get("non_ready_jobs");return t?t.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var t=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:$.param({keys:t.join(",")})})},refresh:function(t){var e=this;t=t||{};var n=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return e.contents.fetchPage(e.contents.currentPage)}:function(){return e.contents.fetchUpdated(n)})().done(function(n,i,r){var s;try{s=new Date(r.getResponseHeader("Date"))}catch(t){}e.lastUpdateTime=s||new Date,e.checkForUpdates(t)})},checkForUpdates:function(t){var e=this;t=t||{};var n=this.UPDATE_DELAY;if(this.id){var i=function(){e.clearUpdateTimeout(),e.updateTimeoutId=setTimeout(function(){e.refresh(t)},n)};this.numOfUnfinishedShownContents()>0?i():this._fetchContentRelatedAttributes().done(function(t){e.numOfUnfinishedJobs()>0?i():e.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,e){var n=Backbone.Model.prototype.parse.call(this,t,e);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(t,e){var n=this;return(t=t||{}).view="dev-detailed",this.fetch(t).then(function(t){return n.contents.history=n,n.contents.setHistoryId(t.id),n.fetchContents(e)})},fetchContents:function(t){t=t||{};var e=this;return e.lastUpdateTime=new Date,e.contents.fetchCurrentPage(t)},_delete:function(t){return this.get("deleted")?jQuery.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?jQuery.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):jQuery.when()},copy:function(t,e,n){if(t=void 0===t||t,!this.id)throw new Error("You must set the history ID before copying it.");var i={history_id:this.id};t&&(i.current=!0),e&&(i.name=e),n||(i.all_datasets=!1),i.view="dev-detailed";var r=this,s=jQuery.post(this.urlRoot,i);return t?s.then(function(t){return new f(t).setAsCurrent().done(function(){r.trigger("copied",r,t)})}):s.done(function(t){r.trigger("copied",r,t)})},setAsCurrent:function(){var t=this,e=jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return e.done(function(){t.trigger("set-as-current",t)}),e},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),g=a.default.InfinitelyScrollingCollection,p=g.extend(l.default.LoggableMixin).extend({_logNamespace:"history",model:f,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(t,e){e=e||{},this.log("HistoryCollection.initialize",t,e),g.prototype.initialize.call(this,t,e),this.includeDeleted=e.includeDeleted||!1,this.currentHistoryId=e.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(t){this.debug("change:deleted",this.includeDeleted,t.get("deleted")),!this.includeDeleted&&t.get("deleted")&&this.remove(t)},copied:function(t,e){this.setCurrent(new f(e,[]))},"set-as-current":function(t){var e=this.currentHistoryId;this.trigger("no-longer-current",e),this.currentHistoryId=t.id}})},_buildFetchData:function(t){return _.extend(g.prototype._buildFetchData.call(this,t),{view:"dev-detailed"})},_buildFetchFilters:function(t){var e=g.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted?n.deleted=null:(n.deleted=!1,n.purged=!1),_.defaults(e,n)},fetchFirst:function(t){var e=this,n=$.when();return this.currentHistoryId&&(n=g.prototype.fetchFirst.call(e,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),n.then(function(){return t=t||{},t.offset=0,e.fetchMore(t)})},comparators:_.extend(_.clone(g.prototype.comparators),{name:l.default.buildComparator("name",{ascending:!0}),"name-dsc":l.default.buildComparator("name",{ascending:!1}),size:l.default.buildComparator("size",{ascending:!1}),"size-asc":l.default.buildComparator("size",{ascending:!0})}),sort:function(t){var e=(t=t||{}).silent,n=this.remove(this.get(this.currentHistoryId));return g.prototype.sort.call(this,_.defaults({silent:!0},t)),this.unshift(n,{silent:!0}),e||this.trigger("sort",this,t),this},create:function(t,e,n,i){var r=this;return jQuery.getJSON(Galaxy.root+"history/create_new_current").done(function(t){r.setCurrent(new f(t,[],n||{}))})},setCurrent:function(t,e){return e=e||{},this.unshift(t,e),this.currentHistoryId=t.get("id"),e.silent||this.trigger("new-current",t,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:f,HistoryCollection:p}});
\ No newline at end of file
diff --git a/static/scripts/mvc/history/history-view.js b/static/scripts/mvc/history/history-view.js
index be6b47c052d..3b8b20faed6 100644
--- a/static/scripts/mvc/history/history-view.js
+++ b/static/scripts/mvc/history/history-view.js
@@ -1 +1 @@
-define("mvc/history/history-view",["exports","mvc/list/list-view","mvc/history/history-model","mvc/history/history-contents","mvc/history/history-preferences","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/ui/error-modal","ui/fa-icon-button","mvc/base-mvc","utils/localization","ui/search-input"],function(e,t,s,i,n,o,l,r,a,d,c,h){"use strict";function u(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var g=u(t),m=u(s),f=u(i),p=(u(n),u(o)),v=u(l),y=(u(r),u(a)),w=u(d),I=u(c),T=u(h),C=g.default.ModelListPanel,b=C.extend({_logNamespace:"history",HDAViewClass:p.default.HDAListItemView,HDCAViewClass:v.default.HDCAListItemView,collectionClass:f.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:C.prototype.className+" history-panel",emptyMsg:(0,T.default)("This history is empty"),noneFoundMsg:(0,T.default)("No matching datasets found"),searchPlaceholder:(0,T.default)("search datasets"),FETCH_COLLECTION_COUNTS_DELAY:2e3,initialize:function(e){C.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.detailedFetchTimeoutId=null},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return C.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this._clearDetailedFetchTimeout(),this},_clearDetailedFetchTimeout:function(){this.detailedFetchTimeoutId&&(clearTimeout(this.detailedFetchTimeoutId),this.detailedFetchTimeoutId=null)},_setUpListeners:function(){var e=this;C.prototype._setUpListeners.call(this),this.on({error:function(e,t,s,i,n){this.errorHandler(e,t,s,i,n)},"loading-done":function(){e.detailedFetchTimeoutId=_.delay(function(){e.detailedFetchTimeoutId=null,e.model.contents.fetchCollectionCounts()},e.FETCH_COLLECTION_COUNTS_DELAY)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,t,s){var i=this;return s=_.extend(s||{silent:!0}),this.info("loadHistory:",e,t,s),this.setModel(new m.default.History({id:e})),s.silent=!0,this.trigger("loading"),this.model.fetchWithContents(t,s).always(function(){i.render(),i.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):$.when()},_setUpCollectionListeners:function(){return C.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(e,t,s){var i=$('<div class="loading-indicator"/>');this.$el.html(i.text(e).slideDown(_.isUndefined(t)?this.fxSpeed:t))},_hideLoadingIndicator:function(e){this.$(".loading-indicator").slideUp(_.isUndefined(e)?this.fxSpeed+200:e,function(){$(this).remove()})},_buildNewRender:function(){var e=C.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,w.default)({title:(0,T.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),$())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('<div class="contents-loading-indicator"><span class="fa fa-2x fa-spinner fa-spin"/></div>'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);$(".tooltip").remove(),t.empty(),this.views=[];var s=this._filterCollection();return s.length?(this._renderPagination(e),this.views=this._renderSomeItems(s,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!s.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var s=this,i=[];return t.append(e.map(function(e){var t=s._createItemView(e);return i.push(t),s._renderItemView$el(t)})),i},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&C.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=C.prototype._getItemViewOptions.call(this,e);return _.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return C.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),C.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=C.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:_.extend(_.clone(C.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.clearUpdateTimeout();var t=$(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var s=this.model.contents;return s.setIncludeDeleted(e,t),this.trigger("show-deleted",e),s.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,s){e=void 0!==e?e:!this.model.contents.includeHidden;var i=this.model.contents;return i.setIncludeHidden(e,s),this.trigger("show-hidden",e),i.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())this.searchItems(e);else{this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,s,i){t.renderItems(),t.trigger("search:loading-progress",s,i)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})}},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(e,t,s){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,s),_.isString(e)&&_.isString(t)){var i=e,n=t;return y.default.errorModal(i,n,s)}return t&&502===t.status?y.default.badGatewayErrorModal():y.default.ajaxErrorModal(e,t,s)}},clearMessages:function(e){return(_.isUndefined(e)?this.$messages().children('[class$="message"]'):$(e.currentTarget)).fadeOut(this.fxSpeed,function(){$(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(_.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});b.prototype.templates=function(){var e=I.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%- history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,T.default)("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,T.default)("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,T.default)("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,T.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,T.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>",'<div class="list-pagination form-inline"></div>',"</div>"],"history"),t=I.default.wrapTemplate(['<button class="prev" <%- pages.current === 1 ? "disabled" : "" %>>previous</button>','<select class="pages form-control" ','title="',(0,T.default)("Click to open and select a page. Begin typing a page number to select it"),'">',"<% _.range( 1, pages.last + 1 ).forEach( function( i ){ %>",'<option value="<%- i - 1 %>" <%- i === pages.current ? "selected" : "" %>>',"<%- view.ordinalIndicator( i ) %> of <%- pages.last %> pages","</option>","<% }); %>","</select>",'<button class="next" <%- pages.current === pages.last ? "disabled" : "" %>>next</button>'],"pages");return _.extend(_.clone(C.prototype.templates),{el:function(){return'<div>\n            <div class="controls"></div>\n            <ul class="list-items"></ul>\n            <div class="empty-message infomessagesmall"></div>\',\n        </div>'},controls:e,pagination:t})}(),e.default={HistoryView:b}});
\ No newline at end of file
+define("mvc/history/history-view",["exports","mvc/list/list-view","mvc/history/history-model","mvc/history/history-contents","mvc/history/history-preferences","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/ui/error-modal","ui/fa-icon-button","mvc/base-mvc","utils/localization","ui/search-input"],function(e,t,s,i,n,o,r,l,a,c,d,h){"use strict";function u(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var g=u(t),f=u(s),m=u(i),p=(u(n),u(o)),v=u(r),y=(u(l),u(a)),w=u(c),I=u(d),b=u(h),P=g.default.ModelListPanel,C=P.extend({_logNamespace:"history",HDAViewClass:p.default.HDAListItemView,HDCAViewClass:v.default.HDCAListItemView,collectionClass:m.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:P.prototype.className+" history-panel",emptyMsg:(0,b.default)("This history is empty"),noneFoundMsg:(0,b.default)("No matching datasets found"),searchPlaceholder:(0,b.default)("search datasets"),initialize:function(e){P.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return P.prototype.freeModel.call(this),this.model&&this.model.stopPolling(),this},_setUpListeners:function(){P.prototype._setUpListeners.call(this),this.on({error:function(e,t,s,i,n){this.errorHandler(e,t,s,i,n)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,t,s){var i=this;return s=_.extend(s||{silent:!0}),this.info("loadHistory:",e,t,s),this.setModel(new f.default.History({id:e})),s.silent=!0,this.trigger("loading"),this.model.fetchWithContents(t,s).always(function(){i.render(),i.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):$.when()},_setUpCollectionListeners:function(){return P.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(e,t,s){var i=$('<div class="loading-indicator"/>');this.$el.html(i.text(e).slideDown(_.isUndefined(t)?this.fxSpeed:t))},_hideLoadingIndicator:function(e){this.$(".loading-indicator").slideUp(_.isUndefined(e)?this.fxSpeed+200:e,function(){$(this).remove()})},_buildNewRender:function(){var e=P.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,w.default)({title:(0,b.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),$())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('<div class="contents-loading-indicator"><span class="fa fa-2x fa-spinner fa-spin"/></div>'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);$(".tooltip").remove(),t.empty(),this.views=[];var s=this._filterCollection();return s.length?(this._renderPagination(e),this.views=this._renderSomeItems(s,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!s.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var s=this,i=[];return t.append(e.map(function(e){var t=s._createItemView(e);return i.push(t),s._renderItemView$el(t)})),i},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&P.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=P.prototype._getItemViewOptions.call(this,e);return _.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return P.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),P.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=P.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:_.extend(_.clone(P.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=$(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var s=this.model.contents;return s.setIncludeDeleted(e,t),this.trigger("show-deleted",e),s.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,s){e=void 0!==e?e:!this.model.contents.includeHidden;var i=this.model.contents;return i.setIncludeHidden(e,s),this.trigger("show-hidden",e),i.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())this.searchItems(e);else{this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,s,i){t.renderItems(),t.trigger("search:loading-progress",s,i)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})}},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(e,t,s){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,s),_.isString(e)&&_.isString(t)){var i=e,n=t;return y.default.errorModal(i,n,s)}return t&&502===t.status?y.default.badGatewayErrorModal():y.default.ajaxErrorModal(e,t,s)}},clearMessages:function(e){return(_.isUndefined(e)?this.$messages().children('[class$="message"]'):$(e.currentTarget)).fadeOut(this.fxSpeed,function(){$(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(_.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});C.prototype.templates=function(){var e=I.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%- history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,b.default)("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,b.default)("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,b.default)("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,b.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,b.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>",'<div class="list-pagination form-inline"></div>',"</div>"],"history"),t=I.default.wrapTemplate(['<button class="prev" <%- pages.current === 1 ? "disabled" : "" %>>previous</button>','<select class="pages form-control" ','title="',(0,b.default)("Click to open and select a page. Begin typing a page number to select it"),'">',"<% _.range( 1, pages.last + 1 ).forEach( function( i ){ %>",'<option value="<%- i - 1 %>" <%- i === pages.current ? "selected" : "" %>>',"<%- view.ordinalIndicator( i ) %> of <%- pages.last %> pages","</option>","<% }); %>","</select>",'<button class="next" <%- pages.current === pages.last ? "disabled" : "" %>>next</button>'],"pages");return _.extend(_.clone(P.prototype.templates),{el:function(){return'<div>\n            <div class="controls"></div>\n            <ul class="list-items"></ul>\n            <div class="empty-message infomessagesmall"></div>\',\n        </div>'},controls:e,pagination:t})}(),e.default={HistoryView:C}});
\ No newline at end of file
diff --git a/static/scripts/mvc/history/job-states-model.js b/static/scripts/mvc/history/job-states-model.js
new file mode 100644
index 00000000000..e8bd8f48723
--- /dev/null
+++ b/static/scripts/mvc/history/job-states-model.js
@@ -0,0 +1 @@
+define("mvc/history/job-states-model",["exports","libs/backbone","utils/ajax-queue"],function(t,e,n){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(e),r=function(t){return t&&t.__esModule?t:{default:t}}(n),u=["new","queued","running"],o=["error","deleted"],a=i.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(o)},states:function(){return this.get("states")||{}},anyWithState:function(t){return(this.states()[t]||0)>0},anyWithStates:function(t){var e=this.states();for(var n in t)if((e[t[n]]||0)>0)return!0;return!1},numWithStates:function(t){var e=this.states(),n=0;for(var i in t)n+=e[t[i]]||0;return n},numInError:function(){return this.numWithStates(o)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(u)},jobCount:function(){var t=this.states(),e=0;for(var n in t)e+=t[n];return e},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),s=i.Collection.extend({model:a,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var t=this.models.filter(function(t){return!t.terminal()}),e=t.map(function(t){return t.get("id")}).join(","),n=t.map(function(t){return t.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+e+"&types="+n},monitor:function(){var t=this;if(this.clearUpdateTimeout(),this.active){var e=function(){t.updateTimeoutId=setTimeout(function(){t.monitor()},2e3)},n=this.models.filter(function(t){return!t.terminal()});if(n.length,!1){var i=n.map(function(t){return function(){return t.fetch()}});return new r.default.AjaxQueue(i).done(e)}n.length>0?this.fetch({remove:!1}).done(e):e()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:a,JobStatesSummaryCollection:s,FETCH_STATE_ON_ADD:!1}});
\ No newline at end of file
diff --git a/static/scripts/mvc/history/multi-panel.js b/static/scripts/mvc/history/multi-panel.js
index ba361baf2f9..a4f8442ccee 100644
--- a/static/scripts/mvc/history/multi-panel.js
+++ b/static/scripts/mvc/history/multi-panel.js
@@ -1 +1 @@
-define("mvc/history/multi-panel",["exports","utils/localization","mvc/history/history-model","mvc/history/history-view-edit","mvc/history/copy-dialog","mvc/ui/error-modal","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(e,t,n,i,o,r,l,s){"use strict";function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var c=a(t),d=a(n),u=a(i),h=a(o),f=a(r),p=a(l),m=a(s),g=Backbone.View.extend(p.default.LoggableMixin).extend({_logNamespace:"history",tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(e){e=e||{},this.purgeAllowed=!_.isUndefined(e.purgeAllowed)&&e.purgeAllowed,this.panel=e.panel||this.createPanel(e),this.setUpListeners()},createPanel:function(e){return new u.default.HistoryViewEdit(_.defaults(e,{model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0,$scrollContainer:function(){return this.$el}}))},setUpListeners:function(){var e=this;this.once("rendered",function(){e.trigger("rendered:initial",e)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var e=this;this.listenTo(this.panel,{rendered:function(){e.trigger("rendered",e)},"view:expanded view:rendered":function(e){e.$(".rerun-btn").off()}},this)},inView:function(e,t){var n=this.$el.offset().left;return!(n+this.$el.width()<e)&&!(n>t)},$panel:function(){return this.$(".history-panel")},render:function(e){e=void 0!==e?e:"fast";var t=this.model?this.model.toJSON():{};return this.$el.html(this.template(t)),this.renderPanel(e),this.panel.$el.css("display","flex"),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(e){return e=_.extend(e||{},{isCurrentHistory:this.currentHistory}),$(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:e,view:this}),this.controlsRightTemplate({history:e,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',e.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function(e){return e=void 0!==e?e:"fast",this.panel.setElement(this.$panel()).render(e),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var e=this;this.model._delete().done(function(t){e.render()})},"click .undelete-history":function(){var e=this;this.model.undelete().done(function(t){e.render()})},"click .purge-history":function(){if(confirm((0,c.default)("This will permanently remove the data. Are you sure?"))){var e=this;this.model.purge().done(function(t){e.render()})}},"click .copy-history":"copy"},copy:function(){(0,h.default)(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',(0,c.default)("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',(0,c.default)("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',(0,c.default)("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',(0,c.default)("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',(0,c.default)("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',(0,c.default)("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryViewColumn("+(this.panel?this.panel:"")+")"}}),v=Backbone.View.extend(p.default.LoggableMixin).extend({_logNamespace:"history",className:"multi-panel-history",initialize:function(e){e=e||{},this.log(this+".init",e),this.$el.addClass(this.className),this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.perPage=e.perPage||10,this.hdaQueue=new m.default.NamedAjaxQueue([],!1),this.collection=null,this.columnMap={},this.columnOptions=e.columnOptions||{},this.historySearch=null,this.datasetSearch=null,this.setCollection(e.histories),this.setUpListeners()},setUpListeners:function(){var e=this;this.on("end-of-scroll",function(){e.collection.fetchMore()})},setCollection:function(e){return this.stopListening(this.collection),this.collection=e||new d.default.HistoryCollection,this.setUpCollectionListeners(),this.createColumns(),this.hdaQueue.clear(),this.trigger("new-collection",this),this},addModels:function(e,t,n){n=n||{};var i=this;return(e=_.isArray(e)?e:[e]).forEach(function(e){i.addColumn(e,!1)}),this},setUpCollectionListeners:function(){var e=this;e.listenTo(e.collection,{error:e.errorHandler,add:e.addModels,"all-fetched":e._postFetchAll,"new-current":e.addAsCurrentColumn,"set-as-current":e.setCurrentHistory,"change:deleted change:purged":e.handleDeletedHistory,sort:function(){e.renderColumns(0)}})},_postFetchAll:function(e){if(this.$(".histories-loading-indicator").remove(),!this.historySearch){var t=this.$(".outer-middle");t.scrollLeft(t.scrollLeft()+24)}},setCurrentHistory:function(e){this.log("setCurrentHistory:",e);var t=_.findWhere(this.columnMap,{currentHistory:!0});t&&(t.currentHistory=!1,t.$el.height(""));var n=this.columnMap[this.collection.currentHistoryId];return n.currentHistory=!0,this.collection.sort(),this._recalcFirstColumnHeight(),n},handleDeletedHistory:function(e){if(e.get("deleted")||e.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,e);var t=this,n=t.columnMap[e.id];if(!n)return;n.model.id===this.collection.currentHistoryId||t.collection.includeDeleted||t.removeColumn(n)}},errorHandler:function(e,t,n){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,n),_.isString(e)&&_.isString(t)){var i=e,o=t;return f.default.errorModal(i,o,n)}return t&&502===t.status?f.default.badGatewayErrorModal():f.default.ajaxErrorModal(e,t,n)}},_ajaxErrorHandler:function(){f.default.ajaxErrorModal.apply(null,_.toArray(arguments))},create:function(e){return this.collection.create({current:!0})},createColumns:function(e,t){t=t||this.options.columnOptions;var n=this;n.columnMap={},n.collection.each(function(e,i){var o=n.createColumn(e,t);n.columnMap[e.id]=o})},createColumn:function(e,t){t=_.extend({},t,{model:e,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var n=new g(t);return e.id===this.collection.currentHistoryId&&(n.currentHistory=!0),this.setUpColumnListeners(n),this.datasetSearch&&(n.panel.searchItems(this.datasetSearch),this.queueHdaFetchDetails(n)),n},addColumn:function(e,t){t=void 0===t||t;var n=this.createColumn(e);return this.columnMap[e.id]=n,t&&this.renderColumns(),n},addAsCurrentColumn:function(e,t,n){var i=this,o=this.addColumn(e,!1);return this.setCurrentHistory(e),o.once("rendered",function(){i.queueHdaFetch(o)}),o},removeColumn:function(e,t){if(t=void 0===t||t,this.log("removeColumn",e),e){var n=this,i=this.options.columnWidth+this.options.columnGap;e.$el.fadeOut("fast",function(){t&&($(this).remove(),n.$(".middle").width(n.$(".middle").width()-i),n.checkColumnsInView(),n._recalcFirstColumnHeight()),n.stopListening(e.panel),n.stopListening(e),delete n.columnMap[e.model.id],e.remove()})}},setUpColumnListeners:function(e){var t=this;t.listenTo(e,{"in-view":t.queueHdaFetch}),t.listenTo(e.panel,{"view:draggable:dragstart":function(e,n,i,o){t._dropData=JSON.parse(e.dataTransfer.getData("text")),t.currentColumnDropTargetOn()},"view:draggable:dragend":function(e,n,i,o){t._dropData=null,t.currentColumnDropTargetOff()},"droptarget:drop":function(e,n,i){var o=t._dropData.filter(function(e){return i.model.contents.isCopyable(e)});t._dropData=null;var r=new m.default.NamedAjaxQueue;0!==i.model.contents.currentPage&&r.add({name:"fetch-front-page",fn:function(){return i.model.contents.fetchPage(0)}}),o.reverse().forEach(function(e){r.add({name:"copy-"+e.id,fn:function(){return i.model.contents.copy(e)}})}),r.start(),r.done(function(e){i.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},sortedFilteredColumns:function(e){return(e=e||this.filters)&&e.length?this.sortedColumns().filter(function(t,n){return t.currentHistory||_.every(e.map(function(e){return e.call(t)}))}):this.sortedColumns()},sortedColumns:function(){var e=this;return this.collection.map(function(t,n){return e.columnMap[t.id]})},render:function(e){e=void 0!==e?e:this.fxSpeed;var t=this;return t.log(t+".render"),t.$el.html(t.mainTemplate(t)),t.renderColumns(e),t.setUpBehaviors(),t.trigger("rendered",t),t},renderColumns:function(e){e=_.isNumber(e)?e:this.fxSpeed;var t=this,n=t.sortedFilteredColumns(),i=t.$(".middle").empty();return t._addColumns(n,e),t.collection.allFetched||i.append(t.loadingIndicatorTemplate(t)),t.trigger("columns-rendered",n,t),t.datasetSearch&&n.length<=1||(t.checkColumnsInView(),t._recalcFirstColumnHeight()),n},_addColumns:function(e,t){t=_.isNumber(t)?t:this.fxSpeed;var n=this.$(".middle"),i=n.children(".history-column").length;n.width(this._calcMiddleWidth(e.length+i)),e.forEach(function(e,i){e.delegateEvents().render(t).$el.appendTo(n)})},_calcMiddleWidth:function(e){return e*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16},queueHdaFetch:function(e){var t=e.model.contents;if(0===t.length&&e.model.contentsShown()){var n={silent:!0},i=_.values(t.storage.allExpanded()).join();i&&(n.details=i),this.hdaQueue.add({name:e.model.id,fn:function(){return t.fetchCurrentPage(n).done(function(){e.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(e){var t=e.model.contents;!(0===t.length&&e.model.contentsShown())&&t.haveDetails()||(this.hdaQueue.add({name:e.model.id,fn:function(){return t.progressivelyFetchDetails().done(function(){e.panel._renderEmptyMessage()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(e){return this.$(".header .header-info").text(e)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(e){window.location=Galaxy.root},_clickToggleDeletedHistories:function(e){this.toggleDeletedHistories($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleDeletedHistories:function(e){window.location=e?Galaxy.root+"history/view_multiple?include_deleted_histories=True":Galaxy.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(e){this.toggleDeletedDatasets($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleDeletedDatasets:function(e){e=void 0!==e&&e,this.sortedFilteredColumns().forEach(function(t,n){_.delay(function(){t.panel.toggleShowDeleted(e,!1)},200*n)})},_clickToggleHiddenDatasets:function(e){this.toggleHiddenDatasets($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleHiddenDatasets:function(e){e=void 0!==e&&e,this.sortedFilteredColumns().forEach(function(t,n){_.delay(function(){t.panel.toggleShowHidden(e,!1)},200*n)})},_chooseOrder:function(e){var t=this,n=t.collection,i=$(e.currentTarget).data("order");t.$(".current-order").text(t.orderDescriptions[i]),t.toggleOptionsPopover(),n.setOrder(i);var o=n.slice(0,1);n.fetchFirst().done(function(){n.unshift(o,{silent:!0}),t.createColumns(),t.hdaQueue.clear(),t.render()}),t.once("columns-rendered",t._scrollLeft)},_scrollLeft:function(e){e=_.isNumber(e)?e:0,this.$(".outer-middle").scrollLeft(e)},setUpBehaviors:function(){var e=this;e._moreOptionsPopover(),e.$("#search-histories").searchInput({name:"search-histories",placeholder:(0,c.default)("search histories"),onfirstsearch:function(t){e.$("#search-histories").searchInput("toggle-loading"),e.renderInfo((0,c.default)("loading all histories for search")),e.collection.fetchAll().done(function(){e.$("#search-histories").searchInput("toggle-loading"),e.renderInfo("")})},onsearch:function(t){e.historySearch=t,e.filters=[function(){return this.model.matchesAll(e.historySearch)}],e.renderColumns(0)},onclear:function(t){e.historySearch=null,e.filters=[],e.renderColumns(0)}}),e.$("#search-datasets").searchInput({name:"search-datasets",placeholder:(0,c.default)("search all datasets"),onfirstsearch:function(t){e.hdaQueue.clear(),e.$("#search-datasets").searchInput("toggle-loading"),e.datasetSearch=t,e.sortedFilteredColumns().forEach(function(n){n.panel.searchItems(t),e.queueHdaFetchDetails(n)}),e.hdaQueue.progress(function(t){e.renderInfo([(0,c.default)("searching"),t.curr+1,(0,c.default)("of"),t.total].join(" "))}),e.hdaQueue.deferred.done(function(){e.renderInfo(""),e.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(t){e.datasetSearch=t,e.sortedFilteredColumns().forEach(function(e){e.panel.searchItems(t)})},onclear:function(t){e.datasetSearch=null,e.sortedFilteredColumns().forEach(function(e){e.panel.clearSearch()})}}),$(window).resize(function(){e._recalcFirstColumnHeight()});var t=_.debounce(function(){var t=e._viewport();e.checkColumnsInView(t),e.checkForEndOfScroll(t)},100);this.$(".middle").parent().scroll(t)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},toggleOptionsPopover:function(e){this.$(".open-more-options.btn").popover("toggle")},_recalcFirstColumnHeight:function(){var e=this.$(".history-column").first(),t=this.$(".middle").height(),n=e.find(".panel-controls").height();e.height(t).find(".inner").height(t-n)},_viewport:function(){var e=this.$(".middle").parent(),t=e.offset().left;return{left:t,right:t+e.width()}},columnsInView:function(e){var t=e||this._viewport();return this.sortedFilteredColumns().filter(function(e){return e.currentHistory||e.inView(t.left,t.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(e){e.trigger("in-view",e)})},checkForEndOfScroll:function(e){e=e||this._viewport();var t=this.$(".middle");t.parent().scrollLeft()+e.right>=t.width()-16&&this.trigger("end-of-scroll")},currentColumnDropTargetOn:function(){var e=this.columnMap[this.collection.currentHistoryId];e&&(e.panel.dataDropped=function(e){},e.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var e=this.columnMap[this.collection.currentHistoryId];e&&(e.panel.dataDropped=u.default.HistoryViewEdit.prototype.dataDrop,e.panel.dropTarget=!1,e.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="done btn btn-default" tabindex="1">',(0,c.default)("Done"),"</button>",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="create-new btn btn-default" tabindex="4">',(0,c.default)("Create new"),"</button> ","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container"></div>'].join(""),{variable:"view"}),loadingIndicatorTemplate:_.template(['<div class="histories-loading-indicator">','<span class="fa fa-spin fa-spinner"></span>',(0,c.default)("Loading histories"),"...","</div>"].join(""),{variable:"view"}),orderDescriptions:{update_time:(0,c.default)("most recent first"),"update_time-asc":(0,c.default)("least recent first"),name:(0,c.default)("name, a to z"),"name-dsc":(0,c.default)("name, z to a"),size:(0,c.default)("size, large to small"),"size-asc":(0,c.default)("size, small to large")},optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,c.default)("Order histories by")+" ",'<span class="current-order"><%- view.orderDescriptions[ view.collection.order ] %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.orderDescriptions, function( text, order ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%- order %>">',"<%- text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',(0,c.default)("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',(0,c.default)("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',(0,c.default)("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});e.default={MultiPanelColumns:v}});
\ No newline at end of file
+define("mvc/history/multi-panel",["exports","utils/localization","mvc/history/history-model","mvc/history/history-view-edit","mvc/history/job-states-model","mvc/history/copy-dialog","mvc/ui/error-modal","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(e,t,n,i,o,r,l,s,a){"use strict";function c(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var d=c(t),u=c(n),h=c(i),f=c(o),p=c(r),m=c(l),g=c(s),v=c(a),y=Backbone.View.extend(g.default.LoggableMixin).extend({_logNamespace:"history",tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(e){e=e||{},this.purgeAllowed=!_.isUndefined(e.purgeAllowed)&&e.purgeAllowed,this.panel=e.panel||this.createPanel(e),this.setUpListeners()},createPanel:function(e){return new h.default.HistoryViewEdit(_.defaults(e,{model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0,$scrollContainer:function(){return this.$el}}))},setUpListeners:function(){var e=this;this.once("rendered",function(){e.trigger("rendered:initial",e)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var e=this;this.listenTo(this.panel,{rendered:function(){e.trigger("rendered",e)},"view:expanded view:rendered":function(e){e.$(".rerun-btn").off()}},this)},inView:function(e,t){var n=this.$el.offset().left;return!(n+this.$el.width()<e)&&!(n>t)},$panel:function(){return this.$(".history-panel")},render:function(e){e=void 0!==e?e:"fast";var t=this.model?this.model.toJSON():{};return this.$el.html(this.template(t)),this.renderPanel(e),this.panel.$el.css("display","flex"),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(e){return e=_.extend(e||{},{isCurrentHistory:this.currentHistory}),$(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:e,view:this}),this.controlsRightTemplate({history:e,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',e.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function(e){return e=void 0!==e?e:"fast",this.panel.setElement(this.$panel()).render(e),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var e=this;this.model._delete().done(function(t){e.render()})},"click .undelete-history":function(){var e=this;this.model.undelete().done(function(t){e.render()})},"click .purge-history":function(){if(confirm((0,d.default)("This will permanently remove the data. Are you sure?"))){var e=this;this.model.purge().done(function(t){e.render()})}},"click .copy-history":"copy"},copy:function(){(0,p.default)(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',(0,d.default)("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',(0,d.default)("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',(0,d.default)("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',(0,d.default)("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',(0,d.default)("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',(0,d.default)("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryViewColumn("+(this.panel?this.panel:"")+")"}}),w=Backbone.View.extend(g.default.LoggableMixin).extend({_logNamespace:"history",className:"multi-panel-history",initialize:function(e){e=e||{},this.log(this+".init",e),this.$el.addClass(this.className),this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.perPage=e.perPage||10,this.hdaQueue=new v.default.NamedAjaxQueue([],!1),this.collection=null,this.columnMap={},this.columnOptions=e.columnOptions||{},this.historySearch=null,this.datasetSearch=null,this.setCollection(e.histories),this.setUpListeners()},setUpListeners:function(){var e=this;this.on("end-of-scroll",function(){e.collection.fetchMore()})},setCollection:function(e){return this.stopListening(this.collection),this.collection=e||new u.default.HistoryCollection,this.setUpCollectionListeners(),this.createColumns(),this.hdaQueue.clear(),this.trigger("new-collection",this),this},addModels:function(e,t,n){n=n||{};var i=this;return(e=_.isArray(e)?e:[e]).forEach(function(e){i.addColumn(e,!1)}),this},setUpCollectionListeners:function(){var e=this;e.listenTo(e.collection,{error:e.errorHandler,add:e.addModels,"all-fetched":e._postFetchAll,"new-current":e.addAsCurrentColumn,"set-as-current":e.setCurrentHistory,"change:deleted change:purged":e.handleDeletedHistory,sort:function(){e.renderColumns(0)}})},_postFetchAll:function(e){if(this.$(".histories-loading-indicator").remove(),!this.historySearch){var t=this.$(".outer-middle");t.scrollLeft(t.scrollLeft()+24)}},setCurrentHistory:function(e){this.log("setCurrentHistory:",e);var t=_.findWhere(this.columnMap,{currentHistory:!0});t&&(t.currentHistory=!1,t.$el.height(""));var n=this.columnMap[this.collection.currentHistoryId];return n.currentHistory=!0,this.collection.sort(),this._recalcFirstColumnHeight(),n},handleDeletedHistory:function(e){if(e.get("deleted")||e.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,e);var t=this,n=t.columnMap[e.id];if(!n)return;n.model.id===this.collection.currentHistoryId||t.collection.includeDeleted||t.removeColumn(n)}},errorHandler:function(e,t,n){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,n),_.isString(e)&&_.isString(t)){var i=e,o=t;return m.default.errorModal(i,o,n)}return t&&502===t.status?m.default.badGatewayErrorModal():m.default.ajaxErrorModal(e,t,n)}},_ajaxErrorHandler:function(){m.default.ajaxErrorModal.apply(null,_.toArray(arguments))},create:function(e){return this.collection.create({current:!0})},createColumns:function(e,t){t=t||this.options.columnOptions;var n=this;n.columnMap={},n.collection.each(function(e,i){var o=n.createColumn(e,t);n.columnMap[e.id]=o})},createColumn:function(e,t){t=_.extend({},t,{model:e,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var n=new y(t);return e.id===this.collection.currentHistoryId&&(n.currentHistory=!0),this.setUpColumnListeners(n),this.datasetSearch&&(n.panel.searchItems(this.datasetSearch),this.queueHdaFetchDetails(n)),n},addColumn:function(e,t){t=void 0===t||t;var n=this.createColumn(e);return this.columnMap[e.id]=n,t&&this.renderColumns(),n},addAsCurrentColumn:function(e,t,n){var i=this,o=this.addColumn(e,!1);return this.setCurrentHistory(e),o.once("rendered",function(){i.queueHdaFetch(o)}),o},removeColumn:function(e,t){if(t=void 0===t||t,this.log("removeColumn",e),e){var n=this,i=this.options.columnWidth+this.options.columnGap;e.$el.fadeOut("fast",function(){t&&($(this).remove(),n.$(".middle").width(n.$(".middle").width()-i),n.checkColumnsInView(),n._recalcFirstColumnHeight()),n.stopListening(e.panel),n.stopListening(e),delete n.columnMap[e.model.id],e.remove()})}},setUpColumnListeners:function(e){var t=this;t.listenTo(e,{"in-view":t.queueHdaFetch}),t.listenTo(e.panel,{"view:draggable:dragstart":function(e,n,i,o){t._dropData=JSON.parse(e.dataTransfer.getData("text")),t.currentColumnDropTargetOn()},"view:draggable:dragend":function(e,n,i,o){t._dropData=null,t.currentColumnDropTargetOff()},"droptarget:drop":function(e,n,i){var o=t._dropData.filter(function(e){return i.model.contents.isCopyable(e)});t._dropData=null;var r=new v.default.NamedAjaxQueue;0!==i.model.contents.currentPage&&r.add({name:"fetch-front-page",fn:function(){return i.model.contents.fetchPage(0)}}),o.reverse().forEach(function(e){r.add({name:"copy-"+e.id,fn:function(){return i.model.contents.copy(e)}})}),r.start(),r.done(function(e){i.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},sortedFilteredColumns:function(e){return(e=e||this.filters)&&e.length?this.sortedColumns().filter(function(t,n){return t.currentHistory||_.every(e.map(function(e){return e.call(t)}))}):this.sortedColumns()},sortedColumns:function(){var e=this;return this.collection.map(function(t,n){return e.columnMap[t.id]})},render:function(e){e=void 0!==e?e:this.fxSpeed;var t=this;return t.log(t+".render"),t.$el.html(t.mainTemplate(t)),t.renderColumns(e),t.setUpBehaviors(),t.trigger("rendered",t),t},renderColumns:function(e){e=_.isNumber(e)?e:this.fxSpeed;var t=this,n=t.sortedFilteredColumns(),i=t.$(".middle").empty();return t._addColumns(n,e),t.collection.allFetched||i.append(t.loadingIndicatorTemplate(t)),t.trigger("columns-rendered",n,t),t.datasetSearch&&n.length<=1||(t.checkColumnsInView(),t._recalcFirstColumnHeight()),n},_addColumns:function(e,t){t=_.isNumber(t)?t:this.fxSpeed;var n=this.$(".middle"),i=n.children(".history-column").length;n.width(this._calcMiddleWidth(e.length+i)),e.forEach(function(e,i){e.delegateEvents().render(t).$el.appendTo(n)})},_calcMiddleWidth:function(e){return e*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16},queueHdaFetch:function(e){var t=e.model.contents;if(0===t.length&&e.model.contentsShown()){var n={silent:!0},i=_.values(t.storage.allExpanded()).join();i&&(n.details=i),this.hdaQueue.add({name:e.model.id,fn:function(){return t.fetchCurrentPage(n).done(function(){e.panel.renderItems()}).done(function(){f.default.FETCH_STATE_ON_ADD||t.jobStateSummariesCollection.fetch()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(e){var t=e.model.contents;!(0===t.length&&e.model.contentsShown())&&t.haveDetails()||(this.hdaQueue.add({name:e.model.id,fn:function(){return t.progressivelyFetchDetails().done(function(){e.panel._renderEmptyMessage()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(e){return this.$(".header .header-info").text(e)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(e){window.location=Galaxy.root},_clickToggleDeletedHistories:function(e){this.toggleDeletedHistories($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleDeletedHistories:function(e){window.location=e?Galaxy.root+"history/view_multiple?include_deleted_histories=True":Galaxy.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(e){this.toggleDeletedDatasets($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleDeletedDatasets:function(e){e=void 0!==e&&e,this.sortedFilteredColumns().forEach(function(t,n){_.delay(function(){t.panel.toggleShowDeleted(e,!1)},200*n)})},_clickToggleHiddenDatasets:function(e){this.toggleHiddenDatasets($(e.currentTarget).is(":checked")),this.toggleOptionsPopover()},toggleHiddenDatasets:function(e){e=void 0!==e&&e,this.sortedFilteredColumns().forEach(function(t,n){_.delay(function(){t.panel.toggleShowHidden(e,!1)},200*n)})},_chooseOrder:function(e){var t=this,n=t.collection,i=$(e.currentTarget).data("order");t.$(".current-order").text(t.orderDescriptions[i]),t.toggleOptionsPopover(),n.setOrder(i);var o=n.slice(0,1);n.fetchFirst().done(function(){n.unshift(o,{silent:!0}),t.createColumns(),t.hdaQueue.clear(),t.render()}),t.once("columns-rendered",t._scrollLeft)},_scrollLeft:function(e){e=_.isNumber(e)?e:0,this.$(".outer-middle").scrollLeft(e)},setUpBehaviors:function(){var e=this;e._moreOptionsPopover(),e.$("#search-histories").searchInput({name:"search-histories",placeholder:(0,d.default)("search histories"),onfirstsearch:function(t){e.$("#search-histories").searchInput("toggle-loading"),e.renderInfo((0,d.default)("loading all histories for search")),e.collection.fetchAll().done(function(){e.$("#search-histories").searchInput("toggle-loading"),e.renderInfo("")})},onsearch:function(t){e.historySearch=t,e.filters=[function(){return this.model.matchesAll(e.historySearch)}],e.renderColumns(0)},onclear:function(t){e.historySearch=null,e.filters=[],e.renderColumns(0)}}),e.$("#search-datasets").searchInput({name:"search-datasets",placeholder:(0,d.default)("search all datasets"),onfirstsearch:function(t){e.hdaQueue.clear(),e.$("#search-datasets").searchInput("toggle-loading"),e.datasetSearch=t,e.sortedFilteredColumns().forEach(function(n){n.panel.searchItems(t),e.queueHdaFetchDetails(n)}),e.hdaQueue.progress(function(t){e.renderInfo([(0,d.default)("searching"),t.curr+1,(0,d.default)("of"),t.total].join(" "))}),e.hdaQueue.deferred.done(function(){e.renderInfo(""),e.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(t){e.datasetSearch=t,e.sortedFilteredColumns().forEach(function(e){e.panel.searchItems(t)})},onclear:function(t){e.datasetSearch=null,e.sortedFilteredColumns().forEach(function(e){e.panel.clearSearch()})}}),$(window).resize(function(){e._recalcFirstColumnHeight()});var t=_.debounce(function(){var t=e._viewport();e.checkColumnsInView(t),e.checkForEndOfScroll(t)},100);this.$(".middle").parent().scroll(t)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},toggleOptionsPopover:function(e){this.$(".open-more-options.btn").popover("toggle")},_recalcFirstColumnHeight:function(){var e=this.$(".history-column").first(),t=this.$(".middle").height(),n=e.find(".panel-controls").height();e.height(t).find(".inner").height(t-n)},_viewport:function(){var e=this.$(".middle").parent(),t=e.offset().left;return{left:t,right:t+e.width()}},columnsInView:function(e){var t=e||this._viewport();return this.sortedFilteredColumns().filter(function(e){return e.currentHistory||e.inView(t.left,t.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(e){e.trigger("in-view",e)})},checkForEndOfScroll:function(e){e=e||this._viewport();var t=this.$(".middle");t.parent().scrollLeft()+e.right>=t.width()-16&&this.trigger("end-of-scroll")},currentColumnDropTargetOn:function(){var e=this.columnMap[this.collection.currentHistoryId];e&&(e.panel.dataDropped=function(e){},e.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var e=this.columnMap[this.collection.currentHistoryId];e&&(e.panel.dataDropped=h.default.HistoryViewEdit.prototype.dataDrop,e.panel.dropTarget=!1,e.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="done btn btn-default" tabindex="1">',(0,d.default)("Done"),"</button>",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="create-new btn btn-default" tabindex="4">',(0,d.default)("Create new"),"</button> ","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container"></div>'].join(""),{variable:"view"}),loadingIndicatorTemplate:_.template(['<div class="histories-loading-indicator">','<span class="fa fa-spin fa-spinner"></span>',(0,d.default)("Loading histories"),"...","</div>"].join(""),{variable:"view"}),orderDescriptions:{update_time:(0,d.default)("most recent first"),"update_time-asc":(0,d.default)("least recent first"),name:(0,d.default)("name, a to z"),"name-dsc":(0,d.default)("name, z to a"),size:(0,d.default)("size, large to small"),"size-asc":(0,d.default)("size, small to large")},optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,d.default)("Order histories by")+" ",'<span class="current-order"><%- view.orderDescriptions[ view.collection.order ] %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.orderDescriptions, function( text, order ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%- order %>">',"<%- text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',(0,d.default)("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',(0,d.default)("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',(0,d.default)("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});e.default={MultiPanelColumns:w}});
\ No newline at end of file
diff --git a/static/style/blue/base.css b/static/style/blue/base.css
index d44cb03842b..92fcad39392 100644
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1,4 +1,4 @@
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.state-icon:before{content:"\f014"}.has-job-state-mixin.state-noPermission{background:#eee;filter:alpha(opacity=60);-moz-opacity:.6;opacity:.6}.has-job-state-mixin.state-noPermission .state-icon{font-size:20px}.has-job-state-mixin.state-noPermission .state-icon:before{content:"\f023"}.has-job-state-mixin.state-new{background:#eee}.has-job-state-mixin.state-new .state-icon:before{content:"\f017"}.has-job-state-mixin.state-loading{background:#eee}.has-job-state-mixin.state-loading .state-icon{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)}100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)}100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)}100%{-o-transform:rotate(359deg)}}@-ms-keyframes 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