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
e85d70ffa4
Trackster refactoring: (a) move ReadTrack-specific code out of FeatureTrack and into ReadTrack; (b) move VCFTrack-specific code of out FeatureTrack and into VcfTTrack. This makes it easier to modify drawing for each track type but creates some repeated code in draw_tile() for different classes that needs to be cleaned up.
2011-02-21 15:54:22 -05:00
Jeremy Goecks
7bd07d7121
Trackster: save and restore mode for feature and read tracks.
2011-02-21 14:00:39 -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:
...
- 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
dcc0d780bc
trackster: Recalc slots no matter what level it's on since it's fast enough
2011-02-09 13:24:35 -05:00
Kanwei Li
b5f72b0afe
Make left and right panels openable to 1000px, up from 400px
2011-02-08 18:07:27 -05:00
Kanwei Li
d56e7e4191
trackster:
...
- Fix packing overlap issue due to font calculation being different in dummy context vs drawing context
- Refactor incremental_slots for simplicity/readability
- Properly add padding to text label for "pack"-view feature tracks
2011-02-08 17:45:03 -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
...
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
Kanwei Li
4ed00252db
trackster: fix farb color picker playing badly with tipsy
2011-02-07 18:11:44 -05:00
Kanwei Li
31a66567ec
trackster: move summary count text darker and aligned at the top for better visibility in most cases, and only draw if there is some padding so that numbers don't bunch up
2011-02-07 16:59:12 -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
7ad70716af
trackster: use new jquery defereds to ensure draw happens after predraw_init in line tracks, eliminates failure to draw before scrolling
2011-02-06 14:44:14 -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
b2863ca4af
trackster: tiny tweaks
2011-02-06 11:29:04 -05:00
James Taylor
e80a525fe9
trackster: color picker shows on click, not hover, and below the input element
2011-02-06 10:27:53 -05:00
James Taylor
ca61aa3a54
trackster: packed scripts
2011-02-06 02:21:10 -05:00
James Taylor
1dbbf1818e
trackster: color picker for color track config params
2011-02-06 02:20:31 -05:00
James Taylor
c3af1a8990
trackster: save line track height properly
2011-02-06 00:41:03 -05:00
James Taylor
8e2b990331
trackster: refactor track configuration to be data/configuration driven -- easier to extend
2011-02-06 00:39:09 -05:00
James Taylor
7b7b8a4ebd
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2011-02-05 15:38:11 -05:00
James Taylor
8085f39738
Fix problem with adding filters when no data is returned, eliminates one of the problems drawing feature track tiles
2011-02-05 15:37:56 -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
Kanwei Li
c40d9c895a
trackster: Fix infinite data query loop when chrom is null or 'None'
2011-02-04 21:02:23 -05:00
James Taylor
76c7f4de77
trackster: fix for track height calculation
2011-02-04 14:48:39 -05:00
James Taylor
9cb37c5c3d
Disable overview canvas saving for now, need to do this right
2011-02-04 14:29:23 -05:00
James Taylor
877614d0c1
trackster: give tile tracks a background that shows when loading tiles
2011-02-04 14:17:07 -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
James Taylor
290fd6fc68
trackster: do not init tracks with null chromosome, use correct low and high when testing tiles in delayed draw, calculate position in show_tile without tile_index (which cna change)
2011-02-03 17:01:17 -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
James Taylor
c3ba5a2a95
trackster: merge
2011-02-03 14:57:49 -05:00
James Taylor
3f14341b0f
trackster: clean up positioning of tiles somewhat
2011-02-03 14:54:40 -05:00
James Taylor
1f2c38f346
trackster: better supression of drags starting in scrollbar using the draginit event
2011-02-03 13:15:34 -05:00
James Taylor
051e7760f8
trackster: capture horizontal mouse wheel events for scrolling (left right drags on mac touch pads)
2011-02-03 11:46:14 -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:
...
- 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
a439076698
trackster: allow line track height to be resized (hover over track, control appears at bottom right). TODO: needs to be saved with track config.
2011-01-30 23:44:57 -05:00
Jeremy Goecks