James Taylor
f9db75311d
trackster: fix bug with fetching same data many times by putting deferred in data cache immediately, still problematic because many deferred callbacks are queued up and the tile is drawn multiple times, debug statement demonstrates this, needs more refactoring to get it right
2011-04-02 23:12:02 -04:00
James Taylor
474ee073bb
trackster: disabling subsetting in data manager, breaks line tracks
2011-04-02 18:30:13 -04:00
James Taylor
2f233b446b
trackster: drawing labels on left at start of chrom works again, tweaks to feature track padding
2011-04-02 17:35:27 -04:00
James Taylor
d89596f1a8
trackster: everything now contained in three distinct modules using CommonJS exports/require style, more fixing coupling and global variables
2011-04-02 16:02:30 -04:00
James Taylor
1b5bc59367
Use extend everywhere instead of $.extend
2011-04-02 14:46:42 -04:00
James Taylor
e41c38fedf
trackster: draw intron/exon structure in dense mode, also restore border top for all tracks
2011-04-02 14:36:52 -04:00
James Taylor
3f3af03da3
trackster: draw inverted fishbones for genes with UTRs but no introns (one block with meaningful thick region)
2011-04-02 13:34:08 -04:00
James Taylor
9b7ef47d98
trackster: fixing tabs again
2011-04-02 13:02:43 -04:00
James Taylor
c41719902d
trackster: thick region should not be drawn when thick_stat == thick_end (this indicates no thick region). Non-coding genes draw correctly now
2011-04-02 13:01:25 -04:00
James Taylor
2eb08910af
trackster: encapsulate tracks in a closure to ensure global variables are not leaking, eliminated many global variables and moved others to the painters (where they should become configurable). Should have no globals that are shared between Tracks and Painters. Also, some drawing tweaks: thicker dense display, cleaner axis line for line tracks, when in auto mode, the actual mode is displayed in parens
2011-04-02 12:20:22 -04:00
James Taylor
f0063baf57
trackster: making extensions to CanvasRenderingContext regular functions, extending built-ins is verboten, breaks encapsulation
2011-04-02 10:05:24 -04:00
Kanwei Li
bff6742992
pack js
2011-03-31 19:01:12 -04:00
Kanwei Li
7b89893c4b
Merge james' trackster changes
2011-03-31 18:58:25 -04:00
Jeremy Goecks
3ec9a1c91f
Trackster visual analytics: add support for static select parameters.
2011-03-31 15:07:02 -04:00
James Taylor
2a96970ef3
Remove left_offset stuff from ReadTracks, fix some other stuff related to padding and height calculation, read tracks now work fine
2011-03-31 13:05:24 -04:00
James Taylor
693009f153
Extracted feature painters for generic linked features, VCF, and reads. Not all types have been completely tested yet
2011-03-30 18:30:22 -04:00
James Taylor
6d1f5d8554
Fix accidently introduced tabs
2011-03-30 13:09:42 -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
James Taylor
a2deb073d8
Streamlining feature track drawing in preparation for pulling out a Painter, cleaning up Painter interface (not quite a common interface yet)
2011-03-29 18:40:18 -04:00
Jeremy Goecks
b752173b99
Trackster: simplify use of jQuery deferreds for getting data.
2011-03-29 16:27:35 -04:00
James Taylor
8fa49921f8
Extract LinePainter from LineTrack
2011-03-29 13:56:44 -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
James Taylor
fe79a2ecaf
Extract SummaryTree painter, abstract canvas creation into CanvasManager class
2011-03-28 21:35:29 -04:00
James Taylor
7c1b42e3f4
Extract feature slotting into a new class
2011-03-28 20:32:43 -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
James Taylor