Kanwei Li
2d0ade7288
Update jQuery to 1.5.1, and also jquery.form as old one was incompatible with 1.5
2011-02-24 17:23:16 -05:00
Jeremy Goecks
bc9955b6fd
Trackster: (a) refactoring back down to a single draw_tile method for FeatureTracks but each track now has a draw_element() method for drawing individual elements; (b) when mode is Auto, enable squish mode when possible to bridge from summary tree to pack.
2011-02-22 11:00:03 -05:00
Jeremy Goecks
b7f921f38d
Trackster: enhancements to read track display: insertions and deletions now shown correctly, and some efficiency improvements made using overlap calculations. Added function to compute the type of overlap between two regions.
2011-02-21 11:49:24 -05:00
Kanwei Li
0143be5e83
Use jStorage ( http://www.jstorage.info/ ) instead of jStore. Tested to be working on IE7 and IE8, where the latter was failing. Fixes links not showing up in history pane to expand histories.
2011-02-18 15:06:34 -05:00
Jeremy Goecks
77795a02a1
Trackster: fix max chrom length.
2011-02-15 19:20:39 -05:00
Kanwei Li
c075b3d119
trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization.
2011-02-15 19:09:38 -05:00
Jeremy Goecks
906d9e98bc
Trackster: better handling when data has a message -- (a) if there's data, show it; and (b) add border to all canvas elements so that they line up when messages are shown and error borders are drawn.
2011-02-14 19:40:40 -05:00
Jeremy Goecks
5e4755172a
Trackster: increase summary tree track height so that max label does not overlap data.
2011-02-14 15:53:39 -05:00
Kanwei Li
09e5692b27
trackster:
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- Fix bug where tiles were not aligning correctly because of inconsistent w_scale
- Fix tracks with errors or no data not having right background
- Refactoring
2011-02-11 16:55:14 -05:00
Dannon Baker
031b0fca6e
workflows: jquery1.5 fix, quotations.
2011-02-10 13:58:48 -05:00
Kanwei Li
b5f72b0afe
Make left and right panels openable to 1000px, up from 400px
2011-02-08 18:07:27 -05:00
Jeremy Goecks
bf8648675f
Fix bug in changeset 36c27bfbb7a8; remove debugging statement.
2011-02-08 16:48:41 -05:00
Jeremy Goecks
a41e40ce60
Trackster: standardization and better handling of track heights. This fixes overly large spacing for zoomed-out interval_index tracks and does away with the no_detail parameter, which is not sufficient for setting track height. Also fixed bug in
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BAM display label spacing.
2011-02-08 15:21:19 -05:00
Dannon Baker
b40c7e5b40
workflows: Fixed jquery 1.5 errors related to workflow saving and flagging of outputs. Repack.
2011-02-08 13:36:12 -05:00
Jeremy Goecks
ea5d68bb76
Partially addressing packing bugs that cause features to be drawn overlapping. Pack scripts.
2011-02-07 15:22:23 -05:00
James Taylor
2af69d58b4
merge
2011-02-07 11:38:34 -05:00
Jeremy Goecks
fa0d2bea2c
Trackster: refactor interval index drawing. Modified interval index squish mode to display blocks and treat intervals as half-open. Also use constants to standardize the drawing height of different modes across tracks.
2011-02-07 09:23:57 -05:00
James Taylor
17352f3de5
jquery updated to 1.5, fixed minor bugs in use of jStore and some dom manipulation in workflows (both problems in our code, not backward incompatibility). Please help test.
2011-02-06 14:42:11 -05:00
James Taylor
ca61aa3a54
trackster: packed scripts
2011-02-06 02:21:10 -05:00
Kanwei Li
02e154a8e7
trackster: Reference track should not have the new loading background and min-height
2011-02-04 21:13:36 -05:00
Jeremy Goecks
0e9ba8e2cb
Trackster: support large (10,000+) sets of chromosomes/contigs, as is often the case for lower coverage genomes. Subsets of chromosomes are loaded into in the chrom select and there are options to move to the previous/next set of chromosomes. If user enters chrom not loaded into navigation box, chrom is loaded and then navigation is performed.
2011-02-04 11:33:30 -05:00
Jeremy Goecks
fdb7690687
Trackseter: fix bug that prevented draw(force) from working.
2011-02-03 17:13:49 -05:00
Jeremy Goecks
3337323c55
Trackster bug fixes: (a) fix read packing bug caused by bad guide and (b) better clean up of old tiles/canvases.
2011-02-03 15:33:45 -05:00
Jeremy Goecks
a2a9898841
Trackster: avoid drawing tiles multiple times by checking cache in delayed_draw.
2011-02-03 09:34:39 -05:00
Kanwei Li
6cb8336f30
Backend changes to implicitly converted datasets:
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- Library dataset LDDAs can now be implicitly converted to another format. For this to happen, an HDA is created by copying the LDDA info, and the HDA is then used as the tool input parameter. The implicitly converted dataset table will map the LDDA to the resulting converted output HDA.
- Added set_output_history optional param to tool.execute to specify whether output dataset is added to the current (or specified) history. Defaults to true but is set to false for implicitly converted datasets so that it does not show up as a hidden history item, which show up in features like "extract workflow from history".
Initial pass at UI for adding data library datasets to trackster using the "Select Library, then Select Datasets" paradigm currently also used for adding history datasets. Currently uses browse_library.mako code but this will need to be enhanced for trackster's purposes.
2011-02-01 20:07:17 -05:00
Jeremy Goecks
fe8c2d8cef
Trackster bug fixes: (a) correct message returned by check_dataset_state and (b) modify payload returned by interal_index datasets to place score in earlier position, making it easier to work with.
2011-01-31 10:02:01 -05:00
James Taylor
b0b2c5f4b6
pack scripts
2011-01-30 23:45:58 -05:00
James Taylor
828cab0ed6
Packed scripts
2011-01-29 21:14:38 -05:00
Jeremy Goecks
52b908e808
Fix bugs from changesets b242befbcd1f and e58f1dc1f5ee: (a) provide default value for is_child attribute for backward compatibility; and (b) check whether dataset has data on a chromosome when initializing.
2011-01-27 18:30:47 -05:00
Jeremy Goecks
206bbf51c2
Trackster: add support for child tracks. Each track in a view can now have child tracks; child tracks have a different icon and are themselves draggable and sortable amongst each other. However, child tracks follow parents when parents are sorted/dragged. Child tracks are used for nicely displaying tracks generated by visual analytics framework.
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Also better handling of tool execution errors when doing visual analytics.
2011-01-27 12:59:21 -05:00
Jeremy Goecks
c63bc7cf1b
Trackster: (a) fix cigar parsing bug that prevented sequence data from being displayed correctly; (b) extend cigar parsing to handle all operations; (c) UI hints for zooming out/in.
2011-01-24 16:40:20 -05:00
Jeremy Goecks
f13b3beaf2
Improve data fetching and caching in trackster. Detailed data is now reused when possible and initialization sequence is simplified and unneeded data requests are removed.
2011-01-24 14:49:28 -05:00
Dannon Baker
89be044152
Workflows containing tools that are not loaded will now open in the editor instead of failing on the dictionary lookup.
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The offending nodes are marked as having an error state, and the workflow cannot be saved.
This will enable users to at least look at and try to recover a workflow by removing (and potentially replacing) the offending steps, as well as providing a better view of what's actually wrong with the workflow.
2011-01-21 15:50:21 -05:00
Jeremy Goecks
13c2f73f34
Trackster improvements: (a) track name uses config data rather than dataset name; (b) track ids are encoded; (c) dashed lines to connect paired reads (solid lines denote skipped bases in reads).
2011-01-20 19:10:33 -05:00
Jeremy Goecks
a0d252acb0
Trackster: fixed bugs and refactored code to better support BAM visualization. Bugs fixed: (a) multi-mapping reads now display correctly; (b) no_detail display for interval index works; and (c) paired reads now have independent CIGAR strings. Also, BAI payload now mirrors interval_index payload so that both datatypes can be handled in the same code.
2011-01-18 15:54:13 -05:00
Jeremy Goecks
33aa20daf3
Fix type in 4858:459a8b52dc90.
2011-01-17 11:05:59 -05:00
Jeremy Goecks
70eb8c4131
Fix bug in 4856:3b741c9cd4e7 so that data is displayed correctly when clicking on the view icon.
2011-01-17 09:08:17 -05:00
Jeremy Goecks
f141710463
Show Galaxy masthead as often as possible using the following approaches: (a) when the galaxy_main frame is not present, all links targeting the galaxy_main frame include the parameter and value 'use_panels=True'; (b) logout links target galaxy_main rather than _top; and (c) enable custom dbkeys page is work with and without frames. Also enable 'Saved Histories' grid to work outside of galaxy_main panel.
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Important: these changes only guarantee that use_panels is appended to page requests when necessary. It does not guarantee that controller methods work with use_panels or that methods behave correctly with and without panels.
2011-01-16 15:48:58 -05:00
Jeremy Goecks
41f937d166
Cleanup from changeset 4815:761738c53c8f: (1) fix bug that was loading jquery twice and hence causing problems; and (2) move setting of modal's min-width from init function into modal code itself.
2011-01-10 11:21:08 -05:00
Jeremy Goecks
e490ab0c38
Trackster: fix bug that prevented 'Dense' mode from working. Also tweaked BAM density display, performed some refactoring, and added some documention.
2011-01-06 23:36:30 -05:00
Jeremy Goecks
76b8710677
Enhancements to visual analytics: (1) refactoring of tracks controller to enable more efficient dataset indexing and reuse of code; (2) new features in track browser: custom wait times, programmatic track renaming, strict synchronization b/t slider and parameter values, and labeling for tracking parameter values.
2011-01-06 12:12:43 -05:00
Jeremy Goecks
3e98171846
Speed and usability improvements for visual analytics. New track now appears immediately when user runs tool, and track data is pulled directly from file to avoid indexing delay.
2010-12-21 13:23:18 -05:00
Dannon Baker
fb30a7db55
Fixed the javascript error on workflow saving introduced by the workflow parameter display.
2010-12-15 20:38:40 -05:00
Dannon Baker
c8e438f6d0
Repacked galaxy.workflow_editor.canvas.js.
2010-12-15 13:10:57 -05:00
Kanwei Li
5962f0ab2e
trackster: Add bigWig display to trackster. Automatically converts wig to bigwig if needed (NOTE: datatypes_conf.xml.sample has been edited to add the new converter, you must update datatypes_conf.xml to use it). The converter requires that wigToBigWig be in the PATH, but no other tools are needed to view bigwig files as they are provided by bx_python.
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- Fix track preferences not being applied
- Fix chroms not being selectable when a new track browser is created
- Fix ReferenceTrack not working with filters
- Fix visual analytics error when tool configuration has changed
2010-12-10 14:59:43 -05:00
Jeremy Goecks
59bc7f7669
Add dynamically-generated tracks to trackster as child tracks; this enables comparison between original track and track generated from running a tool on a subset of original track's data. Child tracks are not currently saved, however. Also added many comments to trackster code and refactored tools and filters out of Track class and into TiledTrack class.
2010-12-06 15:26:38 -05:00
Greg Von Kuster
51e9ae9296
Add a sequencer emulator webapp for demonstration purposes.
2010-12-03 11:43:08 -05:00
Jeremy Goecks
c1b0c1e27e
Add basic visual analytics framework to Galaxy/trackster. When viewing a dataset in trackster, a user can adjust parameters and rerun the tool used to create the dataset and view the new, corresponding dataset in trackster.
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Basic steps are:
-create subset of input data
-run tool with input data subset
-convert new output for display in trackster
-display in trackster
Although framework is applicable to any tool, only cufflinks wrapper has been augmented to work in visual analytics framework. Specifically, min and max values have been added to cufflinks' numerical parameters.
Currently, when a tool is run in trackster, all of a tool's input and output datasets are associated with the original dataset's history, though they are hidden.
Enhancements that were made to support visual analytics include:
-add UI for setting tool parameters in trackster;
-add tool_data method to trackster controller that reruns a tool and produce;
-refactoring of GFFReaderWrapper code for efficiency;
-enabling a tool's output datasets to be directed to a particular history rather than only the current history;
-optional 'min' and 'max' attributes for tool integer and float parameters;
-enable trackster data providers to write a region of data--defined by chrom, start, and end--to a file;
-styles for tool parameters and dynamic filters.
2010-12-02 10:32:55 -05:00
Kanwei Li
5db2483fdb
Make tool_search always the top option even after toggle. Extend make_popup_menus() to create 'label' elements when no href is specified. Added download link for original dataset when there is a dropdown for the download. Call make_popup_menus() when loading embedded items in pages.
2010-11-18 19:42:14 -05:00
Kanwei Li
cd44249bd5
Explicitly convert autocomplete dropdown values on refresh_on_change
2010-11-18 15:25:25 -05:00
Kanwei Li