kiramt [Wed, 12 Jul 2017 07:03:52 +0000 (08:03 +0100)]
JAl-2588 test updates
kiramt [Wed, 12 Jul 2017 06:17:25 +0000 (07:17 +0100)]
JAL-2588 Added tests
kiramt [Tue, 11 Jul 2017 11:15:09 +0000 (12:15 +0100)]
JAL-2588 (and JAL-2610, JAL-2603) mid refactor
kiramt [Wed, 28 Jun 2017 11:03:29 +0000 (12:03 +0100)]
JAL-2603 Putative fix
kiramt [Wed, 28 Jun 2017 09:59:17 +0000 (10:59 +0100)]
Merge remote-tracking branch 'origin/develop' into feature/2588
kiramt [Wed, 28 Jun 2017 09:55:50 +0000 (10:55 +0100)]
JAL-2588 Gap colour scheme now shown in overview
gmungoc [Thu, 15 Jun 2017 13:22:11 +0000 (14:22 +0100)]
JAL-2563 test updated for fix
gmungoc [Thu, 15 Jun 2017 13:08:32 +0000 (14:08 +0100)]
Merge branch 'bug/JAL-2386groupConservationColouring' into develop
kiramt [Thu, 15 Jun 2017 10:54:40 +0000 (11:54 +0100)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2591
gmungoc [Thu, 15 Jun 2017 10:34:37 +0000 (11:34 +0100)]
JAL-2418 typos
gmungoc [Thu, 15 Jun 2017 09:26:40 +0000 (10:26 +0100)]
Merge branch 'bug/JAL-2589gapColour' into develop
gmungoc [Mon, 12 Jun 2017 16:11:27 +0000 (17:11 +0100)]
JAL-2577 mirror select/hide by annotation in split frame applet, and on
Cancel
kiramt [Mon, 12 Jun 2017 15:00:20 +0000 (16:00 +0100)]
JAL-2591 Updates following code review
gmungoc [Mon, 12 Jun 2017 09:36:36 +0000 (10:36 +0100)]
JAL-2577 mirror hide/select columns by annotation across split frame
Jim Procter [Sun, 11 Jun 2017 02:24:29 +0000 (12:24 +1000)]
JAL-2418 updated release branch/version and release date before forking release branch
gmungoc [Fri, 9 Jun 2017 14:21:35 +0000 (15:21 +0100)]
JAL-2589 render colour scheme gap colour in overview
gmungoc [Fri, 9 Jun 2017 09:58:52 +0000 (10:58 +0100)]
JAL-2594 avoid stack trace creating feature on gapped region
kiramt [Thu, 8 Jun 2017 17:12:41 +0000 (18:12 +0100)]
JAL-2588 Consistent gap colour when in None colour scheme
kiramt [Thu, 8 Jun 2017 15:15:51 +0000 (16:15 +0100)]
Merge branch 'bug/JAL-2589gapColour' into feature/2588
gmungoc [Thu, 8 Jun 2017 14:19:04 +0000 (15:19 +0100)]
JAL-2386 JAL-2570 use ResidueShader copy constructor in SequenceGroup
copy constructor for 'like but yet unlike' colouring of new group
kiramt [Thu, 8 Jun 2017 14:01:35 +0000 (15:01 +0100)]
Merge branch 'bug/JAL-2586' into develop
kiramt [Thu, 8 Jun 2017 14:01:02 +0000 (15:01 +0100)]
JAL-2586 Clarification to URL link code
kiramt [Thu, 8 Jun 2017 10:38:08 +0000 (11:38 +0100)]
JAL-2591 made redraw volatile
kiramt [Thu, 8 Jun 2017 10:15:28 +0000 (11:15 +0100)]
JAL-2591 Refactor HiddenColumns to use ArrayList instead of Vector
kiramt [Thu, 8 Jun 2017 09:55:52 +0000 (10:55 +0100)]
JAL-2591 More HiddenColumns refactoring. Tests passing.
kiramt [Wed, 7 Jun 2017 17:04:43 +0000 (18:04 +0100)]
JAL-2591 Further refactoring (still incomplete)
kiramt [Wed, 7 Jun 2017 14:32:30 +0000 (15:32 +0100)]
JAL-2591 More refactoring (incomplete)
kiramt [Wed, 7 Jun 2017 10:32:20 +0000 (11:32 +0100)]
JAL-2591 Hidden columns regions can be output to string + test
kiramt [Wed, 7 Jun 2017 09:58:04 +0000 (10:58 +0100)]
JAL-2591 updated HiddenColumns::findHiddenRegionPositions + test
kiramt [Wed, 7 Jun 2017 09:25:18 +0000 (10:25 +0100)]
JAL-2591 Overview changes ported to applet
kiramt [Wed, 7 Jun 2017 09:25:03 +0000 (10:25 +0100)]
JAL-2591 More rationalising of hiddencols
gmungoc [Wed, 7 Jun 2017 09:22:24 +0000 (10:22 +0100)]
JAL-2386 ensure group conservation shading is applied from slider
kiramt [Wed, 7 Jun 2017 07:14:48 +0000 (08:14 +0100)]
JAL-2591 Increased granularity of overview panel update checks
kiramt [Wed, 7 Jun 2017 06:58:34 +0000 (07:58 +0100)]
JAL-2591 simplifying hidden columns usage
kiramt [Tue, 6 Jun 2017 14:56:04 +0000 (15:56 +0100)]
JAL-2591 Removed getHiddenRegions()==null checks which are always false
kiramt [Tue, 6 Jun 2017 14:44:04 +0000 (15:44 +0100)]
JAL-2591 Added readwrite locking on HiddenColumns
gmungoc [Tue, 6 Jun 2017 14:00:25 +0000 (15:00 +0100)]
JAL-2589 correct colour for Gap in Score and User Defined schemes
kiramt [Tue, 6 Jun 2017 06:35:27 +0000 (07:35 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2576' into bug/JAL-2591
Jim Procter [Mon, 5 Jun 2017 20:53:25 +0000 (21:53 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 5 Jun 2017 20:51:05 +0000 (21:51 +0100)]
JAL-2590 release notes
Jim Procter [Mon, 5 Jun 2017 20:49:36 +0000 (21:49 +0100)]
Merge branch 'bug/JAL-2590' into develop
Jim Procter [Mon, 5 Jun 2017 20:49:14 +0000 (21:49 +0100)]
JAL-2590 patch for rendering eggnog trees with polytomies (also see
Jim Procter [Mon, 5 Jun 2017 20:06:40 +0000 (21:06 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 5 Jun 2017 20:06:22 +0000 (21:06 +0100)]
JAL-2576 release notes
kiramt [Mon, 5 Jun 2017 19:45:06 +0000 (20:45 +0100)]
JAL-2588 Naive implementation of gaps as grey in overview
Jim Procter [Mon, 5 Jun 2017 19:44:23 +0000 (20:44 +0100)]
Merge branch 'bug/JAL-2576' into develop
Jim Procter [Mon, 5 Jun 2017 19:41:34 +0000 (20:41 +0100)]
Merge branch 'bug/JAL-2586' into develop
kiramt [Mon, 5 Jun 2017 13:19:58 +0000 (14:19 +0100)]
JAL-2586 Checkstyle flagged fix of unintended fall through
kiramt [Mon, 5 Jun 2017 06:51:49 +0000 (07:51 +0100)]
JAL-2571 Missed (alwaysRun=true) for @BeforeMethod
Jim Procter [Sun, 4 Jun 2017 15:12:13 +0000 (16:12 +0100)]
JAL-2228 java 1.7 compliance
Jim Procter [Sun, 4 Jun 2017 12:27:45 +0000 (13:27 +0100)]
JAL-2291 updated docs
Jim Procter [Sun, 4 Jun 2017 12:18:38 +0000 (13:18 +0100)]
JAL-2291 only hide/show columns intersecting with currently selected region.
Jim Procter [Sun, 4 Jun 2017 12:18:27 +0000 (13:18 +0100)]
JAL-2291 get bitset representing hidden columns
Jim Procter [Sun, 4 Jun 2017 11:17:31 +0000 (12:17 +0100)]
JAL-2291 use HiddenColumns.hideMarkedBits and take union of selection and sequence under popup
Jim Procter [Sun, 4 Jun 2017 11:05:49 +0000 (12:05 +0100)]
JAL-2291 method taking a BitSet for hiding columns
Jim Procter [Sun, 4 Jun 2017 11:04:31 +0000 (12:04 +0100)]
JAL-2291 bug fix - BitSet.set is [start,end+1)
Jim Procter [Sun, 4 Jun 2017 11:02:16 +0000 (12:02 +0100)]
JAL-2291 fixed broken asserts for SequenceI.getInsertionsAsBits
Jim Procter [Sun, 4 Jun 2017 09:43:01 +0000 (10:43 +0100)]
JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequence that was right-clicked on.
Jim Procter [Sun, 4 Jun 2017 09:41:56 +0000 (10:41 +0100)]
JAL-2291 SequenceI.getInsertionsAsBits for convenient logical operations
Jim Procter [Sun, 4 Jun 2017 09:03:39 +0000 (10:03 +0100)]
JAL-2582 comment about IDs being lost if they resembl ensembl IDs but can’t be resolved to a genomic ID.
Jim Procter [Sun, 4 Jun 2017 09:01:54 +0000 (10:01 +0100)]
JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.
Jim Procter [Fri, 2 Jun 2017 16:11:15 +0000 (17:11 +0100)]
Merge branch 'bug/JAL-2578' into develop
Jim Procter [Fri, 2 Jun 2017 16:04:38 +0000 (17:04 +0100)]
Merge branch 'bug/JAL-2577' into develop
Jim Procter [Fri, 2 Jun 2017 15:58:12 +0000 (16:58 +0100)]
Merge branch 'features/JAL-2228_featureSetCounts_minRangeTweak' into develop
tcofoegbu [Fri, 2 Jun 2017 14:29:25 +0000 (15:29 +0100)]
JAL-2473 revised default minimum dimension for Alignment Frame windows
Jim Procter [Fri, 2 Jun 2017 13:12:21 +0000 (14:12 +0100)]
JAL-2228 always create zero score annotations, since select/hide annotation filter ignores null positions in rows
Jim Procter [Fri, 2 Jun 2017 13:11:30 +0000 (14:11 +0100)]
JAL-2228 always set minimum for count to zero for annotation row
kiramt [Fri, 2 Jun 2017 13:10:57 +0000 (14:10 +0100)]
JAL-2576 Proposed fix
kiramt [Fri, 2 Jun 2017 13:00:13 +0000 (14:00 +0100)]
JAL-2577 Don't allow viewport ranges below 0. Unit tests updated.
kiramt [Fri, 2 Jun 2017 08:59:22 +0000 (09:59 +0100)]
JAL-2578 Moved hidden columns reveal to before selection adjustment
Jim Procter [Thu, 1 Jun 2017 13:17:05 +0000 (14:17 +0100)]
Merge branch 'features/JAL-1648_cache_user_inputs' into develop
Jim Procter [Wed, 31 May 2017 21:02:55 +0000 (22:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 21:02:41 +0000 (22:02 +0100)]
JAL-2418 release notes for JAL-2547, JAL-2563, JAL-1256
Jim Procter [Wed, 31 May 2017 20:23:52 +0000 (21:23 +0100)]
Merge branch 'JAL-2571' into develop
Jim Procter [Wed, 31 May 2017 20:21:59 +0000 (21:21 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 20:10:33 +0000 (21:10 +0100)]
JAL-2398 - updated groovy script for direct field modification
Jim Procter [Wed, 31 May 2017 20:07:04 +0000 (21:07 +0100)]
JAL-2418 JAL-2563 release notes
Jim Procter [Wed, 31 May 2017 20:06:31 +0000 (21:06 +0100)]
JAL-2418 typo
Jim Procter [Wed, 31 May 2017 20:05:39 +0000 (21:05 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
tcofoegbu [Wed, 31 May 2017 10:46:22 +0000 (11:46 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 31 May 2017 10:46:08 +0000 (11:46 +0100)]
JAL-2375 fix unit test to reflect improvement
tcofoegbu [Wed, 31 May 2017 10:08:24 +0000 (11:08 +0100)]
Fixed failing tests
tcofoegbu [Wed, 31 May 2017 09:59:45 +0000 (10:59 +0100)]
JAL-2533 updated unit test to reflect improvement
gmungoc [Wed, 31 May 2017 08:00:46 +0000 (09:00 +0100)]
JAL-2547 handle contact features 'around' a gap correctly
kiramt [Tue, 30 May 2017 18:28:42 +0000 (19:28 +0100)]
JAL-2573 Fixes for alignment < viewport width, and similarly height
gmungoc [Tue, 30 May 2017 15:01:44 +0000 (16:01 +0100)]
JAL-2547 tooltip/AmendFeatures on gap straddled by feature, not for
adjacent feature
kiramt [Tue, 30 May 2017 09:36:34 +0000 (10:36 +0100)]
JAL-2571 Corrected alignment width/height checks to visible only
gmungoc [Tue, 30 May 2017 09:26:46 +0000 (10:26 +0100)]
JAL-2570 don't zap group colour scheme when mapping over split frame
Jim Procter [Mon, 29 May 2017 16:38:34 +0000 (17:38 +0100)]
Merge branch 'bug/JAL-2034contextchange' into develop
Jim Procter [Mon, 29 May 2017 16:35:35 +0000 (17:35 +0100)]
JAL-2388 release notes
tcofoegbu [Mon, 29 May 2017 14:12:17 +0000 (15:12 +0100)]
JAL-1648 improvement on finder searchbox keyboard control - Enter to update search box if popup is displayed otherwise perform find next action
Jim Procter [Mon, 29 May 2017 14:00:18 +0000 (15:00 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:58:33 +0000 (14:58 +0100)]
JAL-2520 properly documented as a fixed bug in release notes
Jim Procter [Mon, 29 May 2017 13:26:21 +0000 (14:26 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:25:40 +0000 (14:25 +0100)]
JAL-2465,JAL-2520,JAL-2533 release notes
Jim Procter [Mon, 29 May 2017 13:19:41 +0000 (14:19 +0100)]
Merge branch 'features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url' into develop
Jim Procter [Mon, 29 May 2017 13:07:47 +0000 (14:07 +0100)]
JAL-2533 update javadoc
Jim Procter [Mon, 29 May 2017 12:51:59 +0000 (13:51 +0100)]
JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL
tcofoegbu [Mon, 29 May 2017 12:05:05 +0000 (13:05 +0100)]
JAL-1648 code fix - enter key should pick selected item on finder searchbox
Jim Procter [Mon, 29 May 2017 11:18:53 +0000 (12:18 +0100)]
Merge branch 'bug/JAL-2536' into develop
git://source.jalview.org / jalview.git / log