James Taylor
7c1b42e3f4
Extract feature slotting into a new class
2011-03-28 20:32:43 -04:00
Jeremy Goecks
cf3dc6ac01
Trackster: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics.
2011-03-30 11:44:08 -04:00
Jeremy Goecks
b752173b99
Trackster: simplify use of jQuery deferreds for getting data.
2011-03-29 16:27:35 -04:00
Jeremy Goecks
08a15195c4
Trackster: use gap to correctly position read connector in Pack mode. Also some code cleanup and commenting.
2011-03-29 13:43:24 -04:00
Jeremy Goecks
202b513f57
Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same.
2011-03-28 15:27:14 -04:00
Kanwei Li
f99b11b73f
UI Tweaks and fixes:
...
- View details icon no longer tooltip; it now links to a page
- Restore folder icon to data libraries
- Make popupmenu link boxes smaller so that link clickthroughs don't activate popup as easily
- Make popupmenu initial position lower after click
2011-03-24 18:26:29 -04:00
Jeremy Goecks
42084999ac
Trackster: put show_insertions and show_differences in track config and fix show_differences, which was broken in previous trackster commit.
2011-03-24 17:12:16 -04:00
Jeremy Goecks
6bb3133d54
Implement a data manager for trackster. Convert DataCache into a DataManager and use jQuery Deferred objects to move data management from the tile level to the track level. Implications of these changes include (a) callbacks are no longer needed when drawing tiles; (a) data is fetched before a tile is drawn; and (c) tile drawing is completely tracked so that actions can be taken after a track has been drawn.
2011-03-24 15:05:28 -04:00
Jeremy Goecks
2f64fc02a4
Trackster: small fix for read drawing and added note about larger issue.
2011-03-24 13:52:04 -04:00
Jeremy Goecks
a01e61e297
Trackster: fix feature track bugs so that intervals are correctly drawn as half-open.
2011-03-18 14:42:08 -04:00
Jeremy Goecks
a567c07863
Trackster: fix issues with navigation input: (a) arrow keys no longer perform navigation and (b) invalid chromosome names are handled well.
2011-03-18 13:51:51 -04:00
James Taylor
d3c884b324
jquery.drag with touch support, trackster now works (well) on the ipad
2011-03-17 19:48:07 -04:00
Kanwei Li
dcfa7af7cc
trackster: Fix BAM reads without cigar string (assume all match); datasets added into a new track browser will now index immediately instead of after changing a chrom
2011-03-11 17:54:06 -05:00
Jeremy Goecks
0c2b732e8e
Make shared visualizations work again and pack trackster.js
2011-03-10 16:42:34 -05:00
Jeremy Goecks
b64c880315
Remove debugging statement.
2011-03-08 10:26:52 -05:00
Jeremy Goecks
6d4519f363
Trackster: enable full keyboard navigation via arrow keys using jquery.scrollTo plugin.
2011-03-08 10:04:39 -05:00
Jeremy Goecks
23a5d3588a
Trackster: remove form from nav controls so that enter key works properly and sets the chrom/low/high.
2011-03-07 22:00:50 -05:00
Jeremy Goecks
ab50ae5b55
Trackster: another pass on reads insertion display. Fixed bugs, add menu item to show/hide insertions, and improve display of insertions. Pack scripts.
2011-03-05 18:33:06 -05:00
Jeremy Goecks
259ec2d649
Trackster: add another parameter to draw() method that determines whether to clear old tiles immediately or after new tiles have been drawn. This parameter enables draw() to clear a track quickly (e.g. when scrolling fast) or slowly (e.g. when using filters). Also included is a long comment about why clearing tiles after often fails and ways to address this issue.
2011-03-04 15:22:17 -05:00
Jeremy Goecks
35a5196daa
Trackster: refactor filtering functionality out of draw() method and do use CSS classes for information transfer. Also remove unused menu code.
2011-03-04 14:29:19 -05:00
Kanwei Li
0472e3eb6e
trackster: Refactor to use one central tile_data method instead of having separate get_data methods for each type of track.
2011-03-03 21:06:33 -05:00
Jeremy Goecks
2864d89238
Trackster: refactor filters code to use functions and styles from tool parameters.
2011-03-03 17:40:35 -05:00
Kanwei Li
cb076fdd9a
trackster: Fix summary_tree and error messages
2011-03-03 16:32:04 -05:00
Jeremy Goecks
52acff3112
Trackster: refactor and enhance track popup menus so that menu items can be dynamically updated. Improve menu descriptions for showing/hiding filters and tools.
2011-03-03 15:38:48 -05:00
Jeremy Goecks
b3edc1b905
Trackster bug fixes for drawing feature tracks in squish and dense mode.
2011-03-03 11:47:10 -05:00
Kanwei Li
dc108dd26f
trackster: reorganize drawing so that it's callback based. Now it will only draw read tracks after reference sequence is downloaded, if applicable.
2011-03-02 18:03:51 -05:00
Jeremy Goecks
ebf81092c4
Trackster: make visual analytics code compatible with HDA/LDDA changes.
2011-03-02 17:15:08 -05:00
Kanwei Li
fac370ce4e
trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks.
2011-03-01 16:39:46 -05:00
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
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
James Taylor