diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js index a0d7da79d4d..96451d1d74b 100644 --- a/client/galaxy/scripts/mvc/tool/tools.js +++ b/client/galaxy/scripts/mvc/tool/tools.js @@ -531,9 +531,7 @@ var ToolLinkView = BaseView.extend({ Galaxy.upload.show(); }); } - - // regular tools - if ( this.model.id !== 'upload1' && this.model.get( 'model_class' ) === 'Tool' ) { + else if ( this.model.get( 'model_class' ) === 'Tool' ) { // regular tools var self = this; $link.find('a').on('click', function(e) { e.preventDefault(); diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js index d5318a2797d..265d0bf07d8 100644 --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -3259,7 +3259,7 @@ extend(LabelTrack.prototype, Track.prototype, { new_div = $("
").addClass('label-container'); while ( position < view.high ) { var screenPosition = Math.floor( ( position - view.low ) / range * width ); - new_div.append( $("
").addClass('label').text(util.commatize( position )).css( { + new_div.append( $("
").addClass('pos-label').text(commatize( position )).css( { left: screenPosition })); position += tickDistance; diff --git a/client/galaxy/style/less/trackster.less b/client/galaxy/style/less/trackster.less index eabdfcf527a..d68ccbb2553 100644 --- a/client/galaxy/style/less/trackster.less +++ b/client/galaxy/style/less/trackster.less @@ -18,7 +18,7 @@ /* Used to push nav into title bar: */ height: 0; } - + text-align: center; } @@ -202,7 +202,7 @@ padding: 0px 2px; text-align: left; margin: 2px; - + /* Make header opaque when focused on. */ &:hover { background-color: #DDDDDD; @@ -232,7 +232,7 @@ overflow: hidden; } -.overlay { +.overlay { position: absolute; left: 0; top: 0; @@ -241,7 +241,7 @@ .track-tile { position: absolute; background: white; - + canvas { position: relative; z-index: @base-index; @@ -292,7 +292,7 @@ } .label-track { - font-size: 10px; + font-size: 10px; border: none; padding: 0; margin: 0; @@ -300,11 +300,11 @@ overflow: hidden; .label-container { - position: relative; + position: relative; height: 1.3em; } - .label { + .pos-label { position: absolute; border-left: solid #999 1px; padding: 1px; @@ -344,7 +344,7 @@ .nav-labeltrack { border-top: solid #999 1px; border-bottom: solid #333 1px; -} +} // Styles for tools and filters. input { @@ -544,7 +544,7 @@ input { top: 0px; background-color: #ccf; opacity: 0.5; - z-index: @overlay-index; + z-index: @overlay-index; } .mouse-pos { @@ -565,7 +565,7 @@ input { height: 12px; } -// Highlight for element(s) being dragged. This definition must be after definition of draggable +// Highlight for element(s) being dragged. This definition must be after definition of draggable // elements (e.g. track, group) in order to take precedence. .dragging { border: 1px solid blue; diff --git a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py index 381630e9d8a..33365131980 100644 --- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py +++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py @@ -104,7 +104,7 @@ def main(): f.write('
%s\n
    ' % (s)) for i, data in enumerate( flist ): f.write('
  1. %s
    2. \n' % (os.path.split(data)[-1], os.path.split(data)[-1])) - f.write("
") + f.write("
") f.close() diff --git a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py index f24b9ce9aac..8f48a8aed37 100644 --- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py +++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py @@ -72,7 +72,7 @@ def main(): f.write('
%s\n
    ' % (s)) for i, data in enumerate( flist ): f.write('
  1. %s
    2. \n' % (os.path.split(data)[-1], os.path.split(data)[-1])) - f.write("
") + f.write("
") f.close() diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py index 86d5dc02852..d7fce87ecb2 100644 --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -19,6 +19,7 @@ DATABASE = { 'repo': 'lib/galaxy/model/migrate', 'old_config_file': 'universe_wsgi.ini', 'default_sqlite_file': './database/universe.sqlite', + 'config_override': 'GALAXY_CONFIG_', }, "tool_shed": { @@ -26,6 +27,7 @@ DATABASE = { 'config_file': 'config/tool_shed.ini', 'old_config_file': 'tool_shed_wsgi.ini', 'default_sqlite_file': './database/community.sqlite', + 'config_override': 'TOOL_SHED_CONFIG_', }, "install": { @@ -33,6 +35,7 @@ DATABASE = { 'old_config_file': 'universe_wsgi.ini', 'config_prefix': 'install_', 'default_sqlite_file': './database/install.sqlite', + 'config_override': 'GALAXY_INSTALL_CONFIG_', }, } @@ -92,11 +95,12 @@ def get_config( argv, cwd=None ): config_file = read_config_file_arg( argv, default, old_default ) repo = database_defaults[ 'repo' ] config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX ) + config_override = database_defaults.get( 'config_override', 'GALAXY_CONFIG_' ) default_sqlite_file = database_defaults[ 'default_sqlite_file' ] if cwd: config_file = os.path.join( cwd, config_file ) - properties = load_app_properties( ini_file=config_file ) + properties = load_app_properties( ini_file=config_file, config_prefix=config_override ) if ("%sdatabase_connection" % config_prefix) in properties: db_url = properties[ "%sdatabase_connection" % config_prefix ] diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index 401997feeb4..adda277f5c6 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -918,9 +918,9 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ): # _tools_by_id and _tool_versions_by_id self.register_tool( new_tool ) message = "Reloaded the tool:
" - message += "name: %s
" % old_tool.name - message += "id: %s
" % old_tool.id - message += "version: %s" % old_tool.version + message += "name: %s
" % escape( old_tool.name ) + message += "id: %s
" % escape( old_tool.id ) + message += "version: %s" % escape( old_tool.version ) status = 'done' return message, status @@ -952,9 +952,9 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ): del self.data_manager_tools[ tool_id ] # TODO: do we need to manually remove from the integrated panel here? message = "Removed the tool:
" - message += "name: %s
" % tool.name - message += "id: %s
" % tool.id - message += "version: %s" % tool.version + message += "name: %s
" % escape( tool.name ) + message += "id: %s
" % escape( tool.id ) + message += "version: %s" % escape( tool.version ) status = 'done' return message, status diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py index 37821a3415c..b4e4fc29331 100644 --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -98,7 +98,7 @@ class Admin( object ): toolbox = self.app.toolbox tool_id = None if params.get( 'reload_tool_button', False ): - tool_id = params.get('tool_id', None) + tool_id = kwd.get( 'tool_id', None ) galaxy.queue_worker.send_control_task(trans.app, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} ) message, status = trans.app.toolbox.reload_tool_by_id( tool_id) return trans.fill_template( '/admin/reload_tool.mako', diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 7fba23d9ce2..d3627565091 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -250,8 +250,10 @@ class ToolShedRepositoriesController( BaseAPIController ): action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) return tool_shed_repository_dict - - return map( to_dict, installed_tool_shed_repositories ) + if installed_tool_shed_repositories: + return map( to_dict, installed_tool_shed_repositories ) + message = "No repositories were installed, possibly because the selected repository has already been installed." + return dict( status="ok", message=message ) @expose_api def install_repository_revisions( self, trans, payload, **kwd ): diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 6b4a9f2d2f6..e4f47df8aae 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -216,7 +216,8 @@ class RepositoriesController( BaseAPIController ): repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=encoded_repository_metadata_id ) - repository_metadata_dict[ 'valid_tools' ] = repository_metadata.metadata[ 'tools' ] + if 'tools' in repository_metadata.metadata: + repository_metadata_dict[ 'valid_tools' ] = repository_metadata.metadata[ 'tools' ] # Get the repo_info_dict for installing the repository. repo_info_dict, \ includes_tools, \ diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py index 67e5620789a..21da0a06f3d 100644 --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -16,6 +16,7 @@ from galaxy.webapps.util import build_template_error_formatters from galaxy.webapps.tool_shed.framework.middleware import hg from galaxy import util from galaxy.config import process_is_uwsgi +from galaxy.util.properties import load_app_properties log = logging.getLogger( __name__ ) @@ -49,6 +50,10 @@ def add_ui_controllers( webapp, app ): def app_factory( global_conf, **kwargs ): """Return a wsgi application serving the root object""" # Create the Galaxy tool shed application unless passed in + kwargs = load_app_properties( + kwds=kwargs, + config_prefix='TOOL_SHED_CONFIG_' + ) if 'app' in kwargs: app = kwargs.pop( 'app' ) else: diff --git a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py index cdc1aa56cb2..a7117efccbc 100644 --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -5,6 +5,7 @@ import os import sqlalchemy import sys import tempfile +import urlparse from paste.auth.basic import AuthBasicAuthenticator from paste.httpheaders import AUTH_TYPE from paste.httpheaders import REMOTE_USER @@ -49,11 +50,11 @@ class Hg( object ): # a clone or a pull. However, we do not want to increment the times_downloaded count if we're only setting repository # metadata. if cmd == 'getbundle' and not self.setting_repository_metadata: - common, _ = environ[ 'HTTP_X_HGARG_1' ].split( '&' ) + hg_args = urlparse.parse_qs( environ[ 'HTTP_X_HGARG_1' ] ) # The 'common' parameter indicates the full sha-1 hash of the changeset the client currently has checked out. If # this is 0000000000000000000000000000000000000000, then the client is performing a fresh checkout. If it has any # other value, the client is getting updates to an existing checkout. - if common == 'common=0000000000000000000000000000000000000000': + if 'common' in hg_args and hg_args[ 'common' ][-1] == '0000000000000000000000000000000000000000': # Increment the value of the times_downloaded column in the repository table for the cloned repository. if 'PATH_INFO' in environ: # Instantiate a database connection diff --git a/static/maps/mvc/tool/tools.js.map b/static/maps/mvc/tool/tools.js.map index f0f3cbcf043..71599f745d5 100644 --- a/static/maps/mvc/tool/tools.js.map +++ b/static/maps/mvc/tool/tools.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/tool/tools.js b/static/scripts/mvc/tool/tools.js index a1ad8fc3d8f..1fe371d0526 100644 --- a/static/scripts/mvc/tool/tools.js +++ b/static/scripts/mvc/tool/tools.js @@ -1,2 +1,2 @@ -define(["libs/underscore","viz/trackster/util","mvc/dataset/data","mvc/tool/tools-form","templates/tool_form.handlebars","templates/tool_link.handlebars","templates/panel_section.handlebars","templates/tool_search.handlebars"],function(a,b,c,d,e,f,g,h){var i={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},j=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new 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b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new p(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve(new c.DatasetCollection(a))}),f}});a.extend(p.prototype,i);var q=(Backbone.View.extend({}),Backbone.Collection.extend({model:p})),r=Backbone.Model.extend(i),s=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof r?(c=a,c.hide()):a instanceof p&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(s.prototype,i);var t=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length");if(a.append(f(this.model.toJSON())),"upload1"===this.model.id&&a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()}),"upload1"!==this.model.id&&"Tool"===this.model.get("model_class")){var b=this;a.find("a").on("click",function(a){a.preventDefault();var c=new d.View({id:b.model.id,version:b.model.get("version")});c.deferred.execute(function(){Galaxy.app.display(c)})})}return this.$el.append(a),this}}),x=v.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("").text(this.model.attributes.text)),this}}),y=v.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){v.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(g(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof p){var c=new w({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof r){var d=new x({model:a});d.render(),b.append(d.$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")}}),z=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(h(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),A=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new z({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof s){var c=new y({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof p){var d=new w({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof r){var e=new x({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),B=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(e(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new A({collection:this.collection}),this.tool_form_view=new B},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 a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:j,IntegerToolParameter:m,SelectToolParameter:o,Tool:p,ToolCollection:q,ToolSearch:t,ToolPanel:u,ToolPanelView:A,ToolFormView:B}}); +define(["libs/underscore","viz/trackster/util","mvc/dataset/data","mvc/tool/tools-form","templates/tool_form.handlebars","templates/tool_link.handlebars","templates/panel_section.handlebars","templates/tool_search.handlebars"],function(a,b,c,d,e,f,g,h){var i={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},j=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new j(this.toJSON())},set_value:function(a){this.set("value",a||"")}}),k=Backbone.Collection.extend({model:j}),l=j.extend({}),m=j.extend({set_value:function(a){this.set("value",parseInt(a,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),n=m.extend({set_value:function(a){this.set("value",parseFloat(a))}}),o=j.extend({get_samples:function(){return a.map(this.get("options"),function(a){return a[0]})}});j.subModelTypes={integer:m,"float":n,data:l,select:o};var p=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(b){this.set("inputs",new k(a.map(b.inputs,function(a){var b=j.subModelTypes[a.type]||j;return new b(a)})))},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return a.inputs=this.get("inputs").map(function(a){return a.toJSON()}),a},remove_inputs:function(a){var b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new p(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve(new c.DatasetCollection(a))}),f}});a.extend(p.prototype,i);var q=(Backbone.View.extend({}),Backbone.Collection.extend({model:p})),r=Backbone.Model.extend(i),s=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof r?(c=a,c.hide()):a instanceof p&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(s.prototype,i);var t=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length");if(a.append(f(this.model.toJSON())),"upload1"===this.model.id)a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var b=this;a.find("a").on("click",function(a){a.preventDefault();var c=new d.View({id:b.model.id,version:b.model.get("version")});c.deferred.execute(function(){Galaxy.app.display(c)})})}return this.$el.append(a),this}}),x=v.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("").text(this.model.attributes.text)),this}}),y=v.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){v.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(g(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof p){var c=new w({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof r){var d=new x({model:a});d.render(),b.append(d.$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")}}),z=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(h(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),A=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new z({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof s){var c=new y({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof p){var d=new w({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof r){var e=new x({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),B=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(e(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new A({collection:this.collection}),this.tool_form_view=new B},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 a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:j,IntegerToolParameter:m,SelectToolParameter:o,Tool:p,ToolCollection:q,ToolSearch:t,ToolPanel:u,ToolPanelView:A,ToolFormView:B}}); //# sourceMappingURL=../../../maps/mvc/tool/tools.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools.js b/static/scripts/mvc/tools.js new file mode 100644 index 00000000000..4a325dfe087 --- /dev/null +++ b/static/scripts/mvc/tools.js @@ -0,0 +1,2 @@ +define(["libs/underscore","viz/trackster/util","mvc/data","mvc/tools/tools-form"],function(a,b,c,d){var e={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},f=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new f(this.toJSON())},set_value:function(a){this.set("value",a||"")}}),g=Backbone.Collection.extend({model:f}),h=f.extend({}),i=f.extend({set_value:function(a){this.set("value",parseInt(a,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),j=i.extend({set_value:function(a){this.set("value",parseFloat(a))}}),k=f.extend({get_samples:function(){return a.map(this.get("options"),function(a){return a[0]})}});f.subModelTypes={integer:i,"float":j,data:h,select:k};var l=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(b){this.set("inputs",new g(a.map(b.inputs,function(a){var b=f.subModelTypes[a.type]||f;return new b(a)})))},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return a.inputs=this.get("inputs").map(function(a){return a.toJSON()}),a},remove_inputs:function(a){var b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new l(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve(new c.DatasetCollection(a))}),f}});a.extend(l.prototype,e);var m=(Backbone.View.extend({}),Backbone.Collection.extend({model:l})),n=Backbone.Model.extend(e),o=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof n?(c=a,c.hide()):a instanceof l&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(o.prototype,e);var p=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:galaxy_config.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length");if(a.append(Handlebars.templates.tool_link(this.model.toJSON())),"upload1"===this.model.id)a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var b=this;a.find("a").on("click",function(a){a.preventDefault();var c=new d.View({id:b.model.id,version:b.model.get("version")});c.deferred.execute(function(){Galaxy.app.display(c)})})}return this.$el.append(a),this}}),t=r.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("").text(this.model.attributes.text)),this}}),u=r.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){r.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof l){var c=new s({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof n){var d=new t({model:a});d.render(),b.append(d.$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")}}),v=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(Handlebars.templates.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new v({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof o){var c=new u({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof l){var d=new s({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof n){var e=new t({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),x=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection}),this.tool_form_view=new x},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 a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:f,IntegerToolParameter:i,SelectToolParameter:k,Tool:l,ToolCollection:m,ToolSearch:p,ToolPanel:q,ToolPanelView:w,ToolFormView:x}}); +//# sourceMappingURL=../../maps/mvc/tools.js.map \ No newline at end of file diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js index 4715afd0636..404ab0f0a9a 100644 --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,3 +1,3 @@ define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/dataset/data","mvc/tool/tools","utils/config","ui/editable-text"],function(a,b,c,d,e,f,g,h,i,j){var k=a.extend,l={},m=function(a,b){l[a.attr("id")]=b},n=function(a,b,c,d){c=".group",l[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=l[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var m=l[e.attr("id")];if(b.offsetYg)return $(this).insertAfter(e),m.remove_drawable(k),void m.container.add_drawable(k)}for(e=null,h=0;h=f&&b.offsetY<=g)return b.offsetY-f0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},o=20,p=100,q=12e3,r=400,s=5e3,t=100,u="Cannot display dataset due to an error. ",v="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",w="No data for this chrom/contig.",x="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",z="Ready for display",A=10,B=["Histogram","Line","Filled","Intensity"],C=function(a,b,d){if(C.id_counter||(C.id_counter=0),this.id=C.id_counter++,this.view=a,this.container=b,this.drag_handle_class=d.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=j.ConfigSettingCollection.from_models_and_saved_values(this.config_params,d.prefs),this.config.get_value("name")||this.config.set_value("name",d.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,d.header!==!1){var e=new c.TrackHeaderView({model:this,id:this.id});this.header_div=e.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};C.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],k(C.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return this.enabled&&this.config.get_value("content_visible")?!0:!1},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(a){this.old_name=this.config.get_value("name"),this.config.set_value("name",a)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var a=this.view;this.container_div.hide(0,function(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(a,b,c){C.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};k(D.prototype,C.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),m(this.container_div,this),m(this.content_div,this),n(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new g.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after($("
")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};k(E.prototype,C.prototype,D.prototype,{action_icons_def:[C.prototype.action_icons_def[0],C.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?(a.filters_manager.clear_filters(),a._restore_filter_managers()):(a.setup_multitrack_filtering(),a.request_draw({clear_tile_cache:!0})),a.filters_manager.toggle()}},C.prototype.action_icons_def[2]],build_container_div:function(){var a=$("
").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Q),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof U&&h++}if(e&&this.drawables[0]instanceof S?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a0){this.saved_filters_managers=[];for(var a=0;a").addClass("top-container").appendTo(c),this.browser_content_div=$("
").addClass("content").appendTo(c),this.bottom_container=$("
").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,m(this.viewport_container,d),this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container);$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(Galaxy.root+"visualization/list_current_history_datasets",Galaxy.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(Y(a,d,d))})})});this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("
").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){d.location_span.hide(),d.chrom_select.hide(),d.nav_input.val(d.chrom+":"+d.low+"-"+d.high),d.nav_input.css("display","inline-block"),d.nav_input.select(),d.nav_input.focus(),d.nav_input.autocomplete({source:function(a,b){var c=[],e=$.map(d.get_tracks(U),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.when.apply($,e).done(function(){b($.map(c,function(a){return{label:a[0],value:a[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(a){d.zoom_in(a.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(a,b){this.current_x=b.offsetX}).bind("drag",function(a,b){var c=b.offsetX-this.current_x;this.current_x=b.offsetX;var e=Math.round(c/d.viewport_container.width()*(d.max_high-d.max_low));d.move_delta(-e)}),this.overview_close.click(function(){d.reset_overview()}),this.viewport_container.bind("draginit",function(a){return a.clientX>d.viewport_container.width()-16?!1:void 0}).bind("dragstart",function(a,b){b.original_low=d.low,b.current_height=a.clientY,b.current_x=b.offsetX}).bind("drag",function(a,b){var c=$(this),e=b.offsetX-b.current_x,f=c.scrollTop()-(a.clientY-b.current_height);c.scrollTop(f),b.current_height=a.clientY,b.current_x=b.offsetX;var g=Math.round(e/d.viewport_container.width()*(d.high-d.low));d.move_delta(g)}),this.top_labeltrack.bind("dragstart",function(){return $("
").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(a,b){$(b.proxy).css({left:Math.min(a.pageX,b.startX)-d.container.offset().left,width:Math.abs(a.pageX-b.startX)});var c=Math.min(a.pageX,b.startX)-d.container.offset().left,e=Math.max(a.pageX,b.startX)-d.container.offset().left,f=d.high-d.low,g=d.viewport_container.width();d.update_location(Math.round(c/g*f)+d.low,Math.round(e/g*f)+d.low)}).bind("dragend",function(a,b){var c=Math.min(a.pageX,b.startX),e=Math.max(a.pageX,b.startX),f=d.high-d.low,g=d.viewport_container.width(),h=d.low;d.low=Math.round(c/g*f)+h,d.high=Math.round(e/g*f)+h,$(b.proxy).remove(),d.request_redraw()}),this.add_label_track(new P(this,{content_div:this.top_labeltrack})),$(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){d.resize_window()},500)}),$(document).bind("redraw",function(){d.redraw()}),this.reset(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});k(F.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(d.commatize(a)+" - "+d.commatize(b)),this.nav_input.val(this.chrom+":"+d.commatize(a)+"-"+d.commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=t;var b=this,c=$.Deferred();return $.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new R(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='"}a.prev_chroms&&(e+='"),a.next_chroms&&(e+='"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-t});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+t});var e=$.grep(d.chrom_data,function(b){return b.chrom===a})[0];if(void 0===e)return void d.load_chroms({chrom:a},function(){d.change_chrom(a,b,c)});if(a!==d.chrom){d.chrom=a,d.chrom_select.val(d.chrom),d.max_high=e.len-1,d.reset();for(var f=0,g=d.drawables.length;g>f;f++){var h=d.drawables[f];h.init&&h.init()}d.reference_track&&d.reference_track.init()}void 0===b&&void 0===c?(d.low=0,d.high=d.max_high):(d.low=void 0!==b?Math.max(b,0):0,void 0===c?(d.low=Math.max(d.low-15,0),d.high=d.low+30):d.high=Math.min(c,d.max_high)),d.request_redraw()}},go_to:function(a){a=a.replace(/,/g,""),a=a.replace(/:|\-/g," ");var b=a.split(/\s+/),c=b[0],d=b[1]?parseInt(b[1],10):void 0,e=b[2]?parseInt(b[2],10):void 0;this.change_chrom(c,d,e)},move_fraction:function(a){var b=this,c=b.high-b.low;this.move_delta(a*c)},move_delta:function(a){var b=this,c=b.high-b.low;b.low-ab.max_high?(b.high=b.max_high,b.low=b.max_high-c):(b.high-=a,b.low-=a),b.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){b.request_redraw()},200);var d=b.chrom_select.val();this.trigger_navigate(d,b.low,b.high,!0)},add_drawable:function(a){D.prototype.add_drawable.call(this,a),a.init(),this.changed(),this.update_intro_div();var b=this;a.config.on("change",function(){b.changed()})},add_label_track:function(a){a.view=this,a.init(),this.label_tracks.push(a)},remove_drawable:function(a,b){if(D.prototype.remove_drawable.call(this,a),b){var c=this;a.container_div.hide(0,function(){$(this).remove(),c.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(b,c){var d=this,e=c?[c]:d.drawables;a.each(e,function(c){var e=a.find(d.tracks_to_be_redrawn,function(a){return a[0]===c});e?e[1]=b:d.tracks_to_be_redrawn.push([c,b])}),this.requested_redraw||(requestAnimationFrame(function(){d._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var b=this.low,c=this.high;bthis.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&df&&this.overview_box.css("left",e-(g-f)/2),this.overview_highlight&&this.overview_highlight.css({left:e,width:f}),a.each(this.tracks_to_be_redrawn,function(a){var b=a[0],c=a[1];b&&b._draw(c)}),this.tracks_to_be_redrawn=[],a.each(this.label_tracks,function(a){a._draw()})},zoom_in:function(a){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var b=this.high-this.low,c=b/2+this.low,d=b/this.zoom_factor/2;a&&(c=a/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(c-d),this.high=Math.round(c+d),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var a=this.high-this.low,b=a/2+this.low,c=a*this.zoom_factor/2;this.low=Math.round(b-c),this.high=Math.round(b+c),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(a){if(this.overview_drawable){if(this.overview_drawable.dataset.id===a.dataset.id)return;this.overview_viewport.find(".track").remove()}var b=a.copy({content_div:this.overview_viewport}),c=this;b.header_div.hide(),b.is_overview=!0,c.overview_drawable=b,this.overview_drawable.postdraw_actions=function(){c.overview_highlight.show().height(c.overview_drawable.content_div.height()),c.overview_viewport.height(c.overview_drawable.content_div.height()+c.overview_box.outerHeight()),c.overview_close.show(),c.resize_window()},c.overview_drawable.request_draw(),this.changed()},reset_overview:function(){$(".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 G=i.Tool.extend({defaults:{track:null},initialize:function(a){i.Tool.prototype.initialize.call(this,a);var b=!0;void 0!==a.tool_state&&void 0!==a.tool_state.hidden&&(b=a.tool_state.hidden),this.set("hidden",b),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(){return a.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),H=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("
").addClass("param-label").text(b.get("label")).appendTo(a),$("
").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("
").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),I=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide(),parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).keydown(function(a){a.stopPropagation()});$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new H({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("
").addClass("param-row").appendTo(parent_div),c=$("").attr("value","Run on complete dataset").appendTo(b),d=$("").attr("value","Run on visible region").appendTo(b);d.click(function(){a.run_on_region()}),c.click(function(){a.run_on_dataset()}),tool.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var a=0;a").append(d),this.data=e,this.stale=!1};K.prototype.predisplay_actions=function(){};var L=function(a,b,c,d,e){K.call(this,a,b,c,d,e)};L.prototype.predisplay_actions=function(){};var M=function(a,b,c,d,e,f,g,h,i,j,k){K.call(this,a,b,c,d,e),this.mode=f,this.all_slotted=h,this.feature_mapper=i,this.has_icons=!1,this.incomplete_features=j,this.other_tiles_features_drawn={},this.seq_data=k};k(M.prototype,K.prototype),M.prototype.predisplay_actions=function(){};var N=function(a,c,d){k(d,{drag_handle_class:"draghandle"}),C.call(this,a,c,d),this.dataset=null,d.dataset&&(this.dataset=d.dataset instanceof Backbone.Model?d.dataset:new h.Dataset(d.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in d?d.data_query_wait:s,this.data_manager="data_manager"in d?d.data_manager:new b.GenomeDataManager({dataset:this.dataset,genome:new b.Genome({key:a.dbkey,chroms_info:{chrom_info:a.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=$("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};k(N.prototype,C.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},C.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},C.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="Tool:"+c.tool.get("name")+"
Dataset:"+c.config.get_value("name")+'
Region(s): ',e=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},f=function(){var d,e=$('select[name="regions"] option:selected').val(),f=new b.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),g=a.map($(".bookmark"),function(a){return new b.GenomeRegion({from_str:$(a).children(".position").text()})});d="cur"===e?[f]:"bookmarks"===e?g:[f].concat(g),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+$.param({dataset_id:c.dataset.id,hda_ldda:c.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(d).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:d,buttons:{No:e,Yes:f}})}},C.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&C.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("
");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(a.content_div).height()}).bind("drag",function(b,c){var d=Math.min(Math.max(c.original_height+c.deltaY,a.min_height_px),a.max_height_px);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof P?"LabelTrack":this instanceof R?"ReferenceTrack":this instanceof S?"LineTrack":this instanceof W?"ReadTrack":this instanceof V?"VariantTrack":this instanceof Q?"CompositeTrack":this instanceof U?"FeatureTrack":""},show_message:function(a){return this.tiles_div.remove(),$("").addClass("message").html(a).appendTo(this.content_div)},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(), -b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(v)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(w)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(x),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(z),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(u);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(void 0!==c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var O=function(c,d,e){N.call(this,c,d,e);var f=this;if(n(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new G(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(A),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new I({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};k(O.prototype,C.prototype,N.prototype,{action_icons_def:N.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(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();k(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,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 a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(r*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(c.config.get_value(f)):(g=$("
").text(c.config.get_value(f)).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,a),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof L});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof L||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",o)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(B,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.LinePainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new L(this,d,e,g,a.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var P=function(a,b){N.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};k(P.prototype,N.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),e=Math.floor(a.low/c)*c,f=this.view.container.width(),g=$("
").addClass("label-container");e").addClass("label").text(d.commatize(e)).css({left:h})),e+=c}this.content_div.children(":first").remove(),this.content_div.append(g)}});var Q=function(b,c,d){if(O.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof U||a instanceof W)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};k(Q.prototype,O.prototype,{display_modes:B,config_params:a.union(C.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(a){$(".tooltip").remove(),a.show_group()}}].concat(O.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 b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),N.prototype.on_resize.call(this)},change_mode:function(a){O.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=O.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new K(this,d,e,h,f)}});var S=function(a,b,c){this.mode="Histogram",O.call(this,a,b,c)};k(S.prototype,C.prototype,O.prototype,{display_modes:B,config_params:a.union(C.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(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var T=function(a,b,c){this.mode="Heatmap",O.call(this,a,b,c)};k(T.prototype,C.prototype,O.prototype,{display_modes:["Heatmap"],config_params:a.union(C.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 a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(a){a.data})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new K(this,d,e,g,a.data)}});var U=function(a,b,c){O.call(this,a,b,c),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()};k(U.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.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:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,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(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof L});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;kq?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new J(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new J(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new M(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var V=function(a,b,c){O.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};k(V.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.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(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new K(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[N.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof L}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var W=function(a,b,c){U.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};k(W.prototype,C.prototype,O.prototype,U.prototype,{config_params:a.union(C.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var X={CompositeTrack:Q,DrawableGroup:E,DiagonalHeatmapTrack:T,FeatureTrack:U,LineTrack:S,ReadTrack:W,VariantTrack:V,VcfTrack:V},Y=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new X[d](b,c,a)};return{TracksterView:F,DrawableGroup:E,LineTrack:S,FeatureTrack:U,DiagonalHeatmapTrack:T,ReadTrack:W,VariantTrack:V,CompositeTrack:Q,object_from_template:Y}}); +b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(v)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(w)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(x),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(z),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(u);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(void 0!==c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var O=function(c,d,e){N.call(this,c,d,e);var f=this;if(n(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new G(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(A),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new I({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};k(O.prototype,C.prototype,N.prototype,{action_icons_def:N.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(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();k(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,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 a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(r*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(c.config.get_value(f)):(g=$("
").text(c.config.get_value(f)).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,a),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof L});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof L||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",o)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(B,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.LinePainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new L(this,d,e,g,a.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var P=function(a,b){N.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};k(P.prototype,N.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),d=Math.floor(a.low/c)*c,e=this.view.container.width(),f=$("
").addClass("label-container");d").addClass("pos-label").text(commatize(d)).css({left:g})),d+=c}this.content_div.children(":first").remove(),this.content_div.append(f)}});var Q=function(b,c,d){if(O.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof U||a instanceof W)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};k(Q.prototype,O.prototype,{display_modes:B,config_params:a.union(C.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(a){$(".tooltip").remove(),a.show_group()}}].concat(O.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 b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),N.prototype.on_resize.call(this)},change_mode:function(a){O.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=O.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new K(this,d,e,h,f)}});var S=function(a,b,c){this.mode="Histogram",O.call(this,a,b,c)};k(S.prototype,C.prototype,O.prototype,{display_modes:B,config_params:a.union(C.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(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var T=function(a,b,c){this.mode="Heatmap",O.call(this,a,b,c)};k(T.prototype,C.prototype,O.prototype,{display_modes:["Heatmap"],config_params:a.union(C.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 a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(a){a.data})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new K(this,d,e,g,a.data)}});var U=function(a,b,c){O.call(this,a,b,c),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()};k(U.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.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:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,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(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof L});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;kq?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new J(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new J(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new M(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var V=function(a,b,c){O.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};k(V.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.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(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new K(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[N.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof L}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var W=function(a,b,c){U.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};k(W.prototype,C.prototype,O.prototype,U.prototype,{config_params:a.union(C.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:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,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 X={CompositeTrack:Q,DrawableGroup:E,DiagonalHeatmapTrack:T,FeatureTrack:U,LineTrack:S,ReadTrack:W,VariantTrack:V,VcfTrack:V},Y=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new X[d](b,c,a)};return{TracksterView:F,DrawableGroup:E,LineTrack:S,FeatureTrack:U,DiagonalHeatmapTrack:T,ReadTrack:W,VariantTrack:V,CompositeTrack:Q,object_from_template:Y}}); //# sourceMappingURL=../../../maps/viz/trackster/tracks.js.map \ No newline at end of file diff --git a/static/style/blue/trackster.css b/static/style/blue/trackster.css index 0cecd3168a5..19babb880fb 100644 --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -1 +1 @@ -.viewport-container{overflow-x:hidden;overflow-y:auto;background:white}.trackster-nav-container{width:100%;text-align:center}.trackster-nav-container.stand-alone{height:0}.trackster-nav{padding:0 0;color:#333;font-weight:bold;background:#ccc;display:inline-block;top:-2em;background:transparent;border:none}.trackster-nav.stand-alone{position:relative}.chrom-nav{width:15em}.content{font:10px verdana;position:relative}.nav-controls{text-align:center;padding:1px 0}.nav-controls input{margin:0 5px}#zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer}#zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center 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.track-content{border:none;background:white}.reference-track{border:none;margin:0;padding:0;line-height:1}.reference-track .track-content{min-height:0}.right-float{float:right;margin-left:5px}.top-labeltrack{position:relative;border-bottom:solid #999 1px}.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px}input{font:10px 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no-repeat}.icon-button.toggle{background:transparent url('../images/fugue/toggle-bw.png') no-repeat}.icon-button.toggle:hover{background:transparent url('../images/fugue/toggle.png') no-repeat}.icon-button.toggle-expand{background:transparent url('../images/fugue/toggle-expand-bw.png') no-repeat}.icon-button.toggle-expand:hover{background:transparent url('../images/fugue/toggle-expand.png') no-repeat}.icon-button.gear{background:transparent url('../images/fugue/gear-bw.png') no-repeat}.icon-button.gear:hover{background:transparent url('../images/fugue/gear.png') no-repeat}.icon-button.application-dock-270{background:transparent url('../images/fugue/application-dock-270-bw.png') no-repeat}.icon-button.application-dock-270:hover{background:transparent url('../images/fugue/application-dock-270.png') no-repeat}.icon-button.ui-slider-050{background:transparent url('../images/fugue/ui-slider-050-bw.png') no-repeat}.icon-button.ui-slider-050:hover{background:transparent 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8px;background-color:black;color:white}.zoom-area{position:absolute;top:0;background-color:#ccf;opacity:.5;z-index:2}.mouse-pos{position:absolute;top:0;background-color:black;opacity:.15;height:100%;width:1px}.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px}.dragging{border:1px solid blue} \ No newline at end of file diff --git a/templates/admin/reload_tool.mako b/templates/admin/reload_tool.mako index 15d22ff38f2..c29a233e2e5 100644 --- a/templates/admin/reload_tool.mako +++ b/templates/admin/reload_tool.mako @@ -31,7 +31,7 @@ $().ready(function() {