gmungoc [Fri, 30 Jun 2017 07:44:08 +0000 (08:44 +0100)]
JAL-2574 renamed findFeatures as findOverlappingFeatures to minimise
confusion
gmungoc [Fri, 30 Jun 2017 04:39:33 +0000 (05:39 +0100)]
Merge branch 'develop' into bug/JAL-2541cutWithFeatures
gmungoc [Wed, 28 Jun 2017 14:16:17 +0000 (15:16 +0100)]
Merge branch 'bug/JAL-2600resizeflicker' into develop
kiramt [Wed, 28 Jun 2017 11:49:17 +0000 (12:49 +0100)]
JAL-2600 Tidies
kiramt [Wed, 28 Jun 2017 11:45:50 +0000 (12:45 +0100)]
JAL-2600 updates following review
gmungoc [Wed, 28 Jun 2017 07:27:10 +0000 (08:27 +0100)]
JAL-2541 clean unit test of cut/undo (ungapped sequence)
gmungoc [Tue, 27 Jun 2017 20:16:00 +0000 (21:16 +0100)]
JAL-2541 more useful assert message
gmungoc [Tue, 27 Jun 2017 16:35:24 +0000 (17:35 +0100)]
Merge branch 'features/JAL-2446NCList' into bug/JAL-2541cutWithFeatures
(Undo fails outstanding to resolve)
Conflicts:
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
test/jalview/datamodel/SequenceTest.java
gmungoc [Tue, 27 Jun 2017 13:27:36 +0000 (14:27 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/appletgui/SeqPanel.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
kiramt [Tue, 27 Jun 2017 13:18:01 +0000 (14:18 +0100)]
JAL-2600 Tidies
kiramt [Tue, 27 Jun 2017 13:16:56 +0000 (14:16 +0100)]
JAL-2600 Abandoned fastpaint for resize; now full repaint, single call
gmungoc [Tue, 27 Jun 2017 13:03:09 +0000 (14:03 +0100)]
JAL-2602 check for null or empty description when copying consensus
gmungoc [Tue, 27 Jun 2017 13:01:47 +0000 (14:01 +0100)]
JAL-1858 highlights on wrapped panel - work in progress
gmungoc [Tue, 27 Jun 2017 12:59:46 +0000 (13:59 +0100)]
JAL-147 scroll wrapped panel by one width's worth at a time
kiramt [Tue, 27 Jun 2017 08:36:37 +0000 (09:36 +0100)]
JAL-2600 Add in IdCanvas and checks for 0 size images
kiramt [Tue, 27 Jun 2017 07:12:00 +0000 (08:12 +0100)]
JAL-2600 vertical fast paint too
kiramt [Tue, 27 Jun 2017 06:47:55 +0000 (07:47 +0100)]
JAL-2600 fast painting on resize
kiramt [Mon, 26 Jun 2017 13:33:15 +0000 (14:33 +0100)]
JAL-2600 reinstate original behaviour
gmungoc [Mon, 26 Jun 2017 07:29:52 +0000 (08:29 +0100)]
JAL-1858 ensure full redraw on 'remove all selections'
gmungoc [Sat, 24 Jun 2017 12:08:00 +0000 (13:08 +0100)]
JAL-2589 unit test updated
gmungoc [Sat, 24 Jun 2017 12:06:12 +0000 (13:06 +0100)]
JAL-2547 fix case of gap followed by enclosing contact feature position
gmungoc [Sat, 24 Jun 2017 08:29:18 +0000 (09:29 +0100)]
JAL-1858 null img when doing full repaint of wrapped alignment
gmungoc [Sat, 24 Jun 2017 08:16:34 +0000 (09:16 +0100)]
JAL-1858 don't fastpaint highlights if wrapped format
gmungoc [Sat, 24 Jun 2017 05:48:27 +0000 (06:48 +0100)]
JAL-1858 refactored method to redraw previous/new highlighted positions
gmungoc [Fri, 23 Jun 2017 15:05:53 +0000 (16:05 +0100)]
JAL-1858 handle hidden columns when computing region to redraw
gmungoc [Fri, 23 Jun 2017 12:13:02 +0000 (13:13 +0100)]
JAL-1858 'fastPaint' of minimal region for highlights; todo: hidden
columns
gmungoc [Thu, 22 Jun 2017 15:45:53 +0000 (16:45 +0100)]
JAL-2481 JAL-2593 JAL-2526 further optimisation of feature/index finding
gmungoc [Thu, 22 Jun 2017 09:46:39 +0000 (10:46 +0100)]
JAL-2480 simpler and safer test to avoid adding duplicates
gmungoc [Wed, 21 Jun 2017 15:26:56 +0000 (16:26 +0100)]
JAL-2480 tidy generic initialisations, SequenceFeatures.varargToTypes
gmungoc [Wed, 21 Jun 2017 12:46:50 +0000 (13:46 +0100)]
JAL-2541 save/Undo only 'diffs' for features with Cut command
gmungoc [Wed, 21 Jun 2017 11:29:47 +0000 (12:29 +0100)]
JAL-2451 remove unused flag
gmungoc [Wed, 21 Jun 2017 11:00:04 +0000 (12:00 +0100)]
JAL-2541 adjust end of contact feature spanning cut region
gmungoc [Wed, 21 Jun 2017 10:59:28 +0000 (11:59 +0100)]
JAL-2480 clarify that findOverlaps excludes spanning contact features
gmungoc [Wed, 21 Jun 2017 08:37:34 +0000 (09:37 +0100)]
JAL-2524 don't render up to a hidden marker beyond the visible region
gmungoc [Tue, 20 Jun 2017 10:21:26 +0000 (11:21 +0100)]
JAL-2541 clearer comments
gmungoc [Tue, 20 Jun 2017 10:08:09 +0000 (11:08 +0100)]
JAL-2541 length check in deleteChars to avoid index out of bounds
gmungoc [Tue, 20 Jun 2017 09:36:54 +0000 (10:36 +0100)]
Merge branch 'features/JAL-2446NCList' into bug/JAL-2541cutWithFeatures
Conflicts:
src/jalview/datamodel/Sequence.java
gmungoc [Tue, 20 Jun 2017 09:35:25 +0000 (10:35 +0100)]
JAL-2526 don't retain lastColumnPosition from an invalidated cursor
gmungoc [Tue, 20 Jun 2017 09:33:28 +0000 (10:33 +0100)]
JAL-2541 working Cut/Undo with feature relocation
gmungoc [Tue, 20 Jun 2017 09:29:46 +0000 (10:29 +0100)]
JAL-2526 better names for fields
gmungoc [Tue, 20 Jun 2017 09:28:43 +0000 (10:28 +0100)]
JAL-2480 make fiels of Range private
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
gmungoc [Thu, 15 Jun 2017 13:06:15 +0000 (14:06 +0100)]
JAL-2541 revised cut with features (work in progress)
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 [Wed, 14 Jun 2017 08:04:14 +0000 (09:04 +0100)]
JAL-2598 Sequence.getSequence return a copy of the char array
gmungoc [Tue, 13 Jun 2017 08:07:40 +0000 (09:07 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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
gmungoc [Fri, 9 Jun 2017 09:32:45 +0000 (10:32 +0100)]
JAL-2480 tidy javadoc
gmungoc [Fri, 9 Jun 2017 09:32:20 +0000 (10:32 +0100)]
JAL-2593 avoid redundant rendering of co-located features
gmungoc [Thu, 8 Jun 2017 15:14:43 +0000 (16:14 +0100)]
JAL-2526 correct boundary conditions for sequence left/right of cursor
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.
gmungoc [Thu, 8 Jun 2017 08:27:34 +0000 (09:27 +0100)]
JAL-2526 cache first/last residue column positions in cursor
gmungoc [Thu, 8 Jun 2017 08:26:59 +0000 (09:26 +0100)]
JAL-2526 setStatusMessage avoid redundant findPosition from
SearchResults
gmungoc [Thu, 8 Jun 2017 08:23:09 +0000 (09:23 +0100)]
JAL-2526 reuse findIndex result if start==end
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
gmungoc [Wed, 7 Jun 2017 09:59:19 +0000 (10:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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
gmungoc [Tue, 6 Jun 2017 10:49:46 +0000 (11:49 +0100)]
JAL-2526 less stringent test for invalid cursor
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
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
gmungoc [Mon, 5 Jun 2017 13:00:48 +0000 (14:00 +0100)]
JAL-2505 comments updated
gmungoc [Mon, 5 Jun 2017 13:00:08 +0000 (14:00 +0100)]
JAL-2480 remove redundant method, further test coverage
gmungoc [Mon, 5 Jun 2017 08:41:02 +0000 (09:41 +0100)]
JAL-2505 explicit (and final) contactFeature property
gmungoc [Mon, 5 Jun 2017 08:03:10 +0000 (09:03 +0100)]
Merge branch 'features/JAL-2526sequenceCursor' into
features/JAL-2446NCList
Conflicts:
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:57:27 +0000 (08:57 +0100)]
Merge branch 'features/JAL-2446NCList' into
features/JAL-2574findFeaturesByColumn
Conflicts:
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:54:11 +0000 (08:54 +0100)]
Merge branch 'features/JAL-2446NCList' into
features/JAL-2526sequenceCursor
Conflicts:
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:52:40 +0000 (08:52 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/datamodel/SequenceI.java
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
git://source.jalview.org / jalview.git / log