Jeremy Goecks
f514b9471e
Create and use ReferenceTrackDataManager to fetch ReferenceTrack data.
2011-04-14 14:34:39 -04:00
Jeremy Goecks
23efa70ebe
Trackster: (a) fix bug in acee660871cd that prevented line tracks from displaying properly and (b) set track height in show_tile rather than draw_tile, which obviates the need for parent_element to be passed to draw_tile.
2011-04-14 14:29:32 -04:00
Jeremy Goecks
254018a930
Trackster: refactor so that summary_tree and Histogram modes use the same code.
2011-04-14 10:37:42 -04:00
Jeremy Goecks
bfbe47327a
Add Tile objects to trackster to support better tracking of Tile data properties; use SummaryTreeTile objects to ensure that feature track coverage histograms are drawn with the same max. Some refactoring of TiledTrack.draw() done as well for simplicity. Finally, fixed typos and GFF display bugs.
2011-04-13 18:09:07 -04:00
Kanwei Li
e2b633fd16
trackster: Don't load huge reference tracks now that we pre-load data, preventing hang
2011-04-12 23:41:06 -04:00
Jeremy Goecks
c967bfa36d
Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules.
2011-04-12 14:40:59 -04:00
Kanwei Li
7a03b066e7
update jquery to 1.5.2, pack scripts
2011-04-12 12:10:48 -04:00
Jeremy Goecks
2b31c9737a
Fix bugs introduced in 03c02d86d011.
2011-04-12 09:35:36 -04:00
Jeremy Goecks
8a44d4f5e5
Trackster: refactor track filters out of TiledTracks and into a FiltersManager object.
2011-04-11 14:17:35 -04:00
Jeremy Goecks
9199fcab12
Trackster: fix (a) bug that was not setting appropriate CSS class for track content divs and (b) padding issues with different track states. Also increase bottom border to better delineate tracks.
2011-04-08 17:07:08 -04:00
James Taylor
edfb5baca9
trackster: remove condition that sets mode to squish when less than four features in tile. mode selection must not change across tiles at the same level.
2011-04-08 16:43:45 -04:00
James Taylor
c42268680a
trackster: Painter class defining common interface for all painters
2011-04-08 14:14:58 -04:00
Jeremy Goecks
60ac2204e8
Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px.
2011-04-05 17:59:43 -04:00
Jeremy Goecks
5f5f659402
Trackster: mode is not reduced if in auto mode.
2011-04-05 14:12:39 -04:00
Jeremy Goecks
6416659211
Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders.
2011-04-05 11:51:48 -04:00
James Taylor
63582942cd
trackster: draw lines to indicate when line tracks overflow the visible region
2011-04-04 23:27:25 -04:00
James Taylor
f21278e49c
trackster: fix read track drawing offsets for all modes
2011-04-04 13:40:09 -04:00
James Taylor
5a6dec9a4a
trackster: some fixes for read tracks
2011-04-03 12:47:39 -04:00
James Taylor
7631db87e6
trackster: typo
2011-04-03 12:40:28 -04:00
James Taylor
51ca021998
trackster: tabs. why won't this editor respect my authority?
2011-04-02 23:13:38 -04:00
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