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Author SHA1 Message Date
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
Daniel Blankenberg 4432911038 Better handling of errors on rerun when grouping constructs have been added or removed. 2011-04-01 18:10:47 -04:00
Jeremy Goecks 11ec423833 Do not use from_work_dir in Tophat because it causes set_metadata to fail on BAM output when run on a cluster. 2011-04-01 11:36:55 -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
Kanwei Li fc550cdbab Remove array_tree datatype; add tabix 2011-03-31 18:58:02 -04:00
Jeremy Goecks 30bb64bbca Trackster visual analytics: enable datasets that cannot be indexed--and hence cannot be subseted--to be used as tool inputs. 2011-03-31 17:22:10 -04:00
Jeremy Goecks 3ec9a1c91f Trackster visual analytics: add support for static select parameters. 2011-03-31 15:07:02 -04:00
Dannon Baker 5aaeabe8ad mapping change: For data libraries of sufficient size, eager loading related to getting the root_folder of a library was causing huge delays. This should reduce the delay in viewing a library of ~500 items by about 90%. 2011-03-31 14:09:47 -04:00
James Taylor 8b9c1c4627 Merge 2011-03-31 14:08:00 -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
Dannon Baker c5dda01276 workflows api: patch from Tobias Wohlfrom <twohlfrom@illumina.com> 
Fixed label output in workflow API in order to map the input datasets.
 2011-03-31 11:27:49 -04:00
Daniel Blankenberg 955acd87e1 Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool. 2011-03-31 10:16:40 -04:00
Daniel Blankenberg ba71264790 Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool. 2011-03-31 10:16:40 -04:00
James Taylor a127f8c677 Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-30 18:30:35 -04:00
James Taylor 950b6e6abe Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-30 18:30:35 -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 6800ad1ff5 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
Jeremy Goecks 3a9351eda1 Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations. 2011-03-30 17:20:10 -04:00
James Taylor 6d1f5d8554 Fix accidently introduced tabs 2011-03-30 13:09:42 -04:00
James Taylor 98959235ad Fix accidently introduced tabs 2011-03-30 13:09:42 -04:00
James Taylor 84117841d6 Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-30 13:01:41 -04:00
James Taylor 90b267b0b9 Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-30 13:01:41 -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
Daniel Blankenberg 9229e32e52 Minor fix for 5283:41a416e61021. 2011-03-30 10:40:09 -04:00
Dannon Baker e49d224f1e Removing a debug print from previous commit. 2011-03-30 10:38:45 -04:00
Daniel Blankenberg 3b5562fcfd Minor fix for 5283:41a416e61021. 2011-03-30 10:34:21 -04:00
Dannon Baker d628f1a843 Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata. 2011-03-30 07:14:20 -04:00
James Taylor affd7e292b Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-29 18:40:24 -04:00
James Taylor 354171fcbd Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-29 18:40:24 -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
James Taylor aaf804e11a 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
Jeremy Goecks 8031354029 Fix read id bug in Trackster BAM data provider. 2011-03-29 14:28:17 -04:00
Kelly Vincent d3d26a7149 Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds 2011-03-29 13:59:07 -04:00
James Taylor f09185dc71 Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-29 13:56:57 -04:00
James Taylor 55211d0268 Automated merge with https://bitbucket.org/galaxy/galaxy-central 2011-03-29 13:56:57 -04:00
James Taylor 8fa49921f8 Extract LinePainter from LineTrack 2011-03-29 13:56:44 -04:00
James Taylor 4f07835e77 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
Nate Coraor 37cc99a9c1 Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment. 2011-03-29 08:18:49 -04:00
James Taylor fe79a2ecaf Extract SummaryTree painter, abstract canvas creation into CanvasManager class 2011-03-28 21:35:29 -04:00
James Taylor 2b856d969f 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
James Taylor 3d99a8ae81 Extract feature slotting into a new class 2011-03-28 20:32:43 -04:00