gmungoc [Mon, 24 Jul 2017 12:43:38 +0000 (14:43 +0200)]
spike branch updated from latest features/JAL-2446
gmungoc [Sat, 24 Jun 2017 12:08:35 +0000 (13:08 +0100)]
Merge branch 'features/JAL-2446NCList' into spikes/mungo
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 10:31:51 +0000 (11:31 +0100)]
Merge branch 'features/JAL-2446NCList' into spikes/mungo
Conflicts:
help/html/releases.html
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/features/FeatureStore.java
src/jalview/datamodel/features/NCList.java
src/jalview/datamodel/features/NCNode.java
src/jalview/datamodel/features/SequenceFeatures.java
src/jalview/gui/SeqCanvas.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/urls/UrlLinkDisplay.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/features/FeatureStoreTest.java
test/jalview/datamodel/features/SequenceFeaturesTest.java
test/jalview/urls/UrlLinkDisplayTest.java
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 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 09:35:25 +0000 (10:35 +0100)]
JAL-2526 don't retain lastColumnPosition from an invalidated cursor
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
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 15:28:28 +0000 (16:28 +0100)]
JAL-2446 merged to spike branch
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
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
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
gmungoc [Wed, 7 Jun 2017 09:59:19 +0000 (10:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 6 Jun 2017 10:49:46 +0000 (11:49 +0100)]
JAL-2526 less stringent test for invalid cursor
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
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
gmungoc [Fri, 2 Jun 2017 15:37:06 +0000 (16:37 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Fri, 2 Jun 2017 15:36:22 +0000 (16:36 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
gmungoc [Fri, 2 Jun 2017 15:35:33 +0000 (16:35 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 2 Jun 2017 15:33:44 +0000 (16:33 +0100)]
JAL-2526 additional tests for findPosition with/without cursor/edit
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
gmungoc [Fri, 2 Jun 2017 08:15:29 +0000 (09:15 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
gmungoc [Thu, 1 Jun 2017 15:43:22 +0000 (16:43 +0100)]
JAL-2526 additional calls to sequenceChanged() after edits
gmungoc [Thu, 1 Jun 2017 15:11:45 +0000 (16:11 +0100)]
JAL-2526 zapCursor() renamed sequenceChanged()
gmungoc [Thu, 1 Jun 2017 15:06:39 +0000 (16:06 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Thu, 1 Jun 2017 14:36:41 +0000 (15:36 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
test/jalview/ext/jmol/JmolParserTest.java
gmungoc [Thu, 1 Jun 2017 13:35:10 +0000 (14:35 +0100)]
JAL-2754 Sequence.findFeatures(fromCol, toCol)
Jim Procter [Thu, 1 Jun 2017 13:17:05 +0000 (14:17 +0100)]
Merge branch 'features/JAL-1648_cache_user_inputs' into develop
gmungoc [Thu, 1 Jun 2017 12:33:26 +0000 (13:33 +0100)]
JAL-2563 JAL-2547 amended unit tests for amended setStatusMessage
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
gmungoc [Wed, 31 May 2017 15:15:52 +0000 (16:15 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Wed, 31 May 2017 15:12:17 +0000 (16:12 +0100)]
JAL-2483 JAL-2575 don't sort newly discovered features
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
gmungoc [Wed, 31 May 2017 10:00:53 +0000 (11:00 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Wed, 31 May 2017 09:59:58 +0000 (10:59 +0100)]
JAL-2574 preparation for Sequence.findFeatures(col1, col2)
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 08:04:56 +0000 (09:04 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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
git://source.jalview.org / jalview.git / log