Jim Procter [Tue, 22 Aug 2017 21:10:27 +0000 (22:10 +0100)]
JAL-2681 canonicalise DB source before fetching to avoid fetching the same ref !
Jim Procter [Tue, 22 Aug 2017 21:09:44 +0000 (22:09 +0100)]
JAL-2681 formatting
gmungoc [Tue, 22 Aug 2017 15:03:01 +0000 (16:03 +0100)]
JAL-2680 remove all mappings in test teardown
gmungoc [Tue, 22 Aug 2017 12:36:28 +0000 (13:36 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 21 Aug 2017 14:20:36 +0000 (15:20 +0100)]
JAL-2680 clear down all mappings before test
Jim Procter [Mon, 21 Aug 2017 13:47:51 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into develop
Jim Procter [Mon, 21 Aug 2017 13:47:22 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 21 Aug 2017 13:46:45 +0000 (14:46 +0100)]
JAL-2675 typo in what's new href
Jim Procter [Mon, 21 Aug 2017 13:22:52 +0000 (14:22 +0100)]
JAL-2588 don’t test char==gap until we know the shader won’t colour gaps itself
Jim Procter [Mon, 21 Aug 2017 13:21:58 +0000 (14:21 +0100)]
JAL-2588 field on overview colour finder for default gap colour
gmungoc [Mon, 21 Aug 2017 13:06:46 +0000 (14:06 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/MCview/PDBChain.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Dna.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/SeqPanel.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/Finder.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/io/FeaturesFile.java
src/jalview/io/JSONFile.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/util/RangeComparator.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/jws2/AADisorderClient.java
Jim Procter [Fri, 18 Aug 2017 15:34:03 +0000 (16:34 +0100)]
JAL-2588 JAL-2603 JAL-2610 release notes and docs
Jim Procter [Fri, 18 Aug 2017 14:38:20 +0000 (15:38 +0100)]
Merge branch 'feature/2588' into merge/develop_feature/2588_JAL-2588
Jim Procter [Fri, 18 Aug 2017 13:17:50 +0000 (14:17 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:15:40 +0000 (14:15 +0100)]
JAL-2675 bump version for branch to 2.10.2b1
Jim Procter [Fri, 18 Aug 2017 13:14:17 +0000 (14:14 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:13:28 +0000 (14:13 +0100)]
JAL-1551 formatting
Jim Procter [Fri, 18 Aug 2017 13:08:03 +0000 (14:08 +0100)]
JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.
kiramt [Fri, 18 Aug 2017 10:53:23 +0000 (11:53 +0100)]
Merge remote-tracking branch 'origin/develop' into feature/JAL-2664
kiramt [Fri, 18 Aug 2017 10:44:18 +0000 (11:44 +0100)]
JAL-2664 Adjusted colour of hidden cols/seqs
kiramt [Fri, 18 Aug 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2664 Correct colouring for rows
kiramt [Fri, 18 Aug 2017 08:19:58 +0000 (09:19 +0100)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2665
kiramt [Fri, 18 Aug 2017 08:13:57 +0000 (09:13 +0100)]
JAL-2665 Comments
kiramt [Fri, 18 Aug 2017 08:03:44 +0000 (09:03 +0100)]
JAL-2665 Refactoring (and side-effect fix for JAL-2672)
kiramt [Fri, 18 Aug 2017 06:50:05 +0000 (07:50 +0100)]
JAL-2665 tidies
kiramt [Thu, 17 Aug 2017 15:49:49 +0000 (16:49 +0100)]
JAL-2665 Code tidies
kiramt [Thu, 17 Aug 2017 14:16:28 +0000 (15:16 +0100)]
JAL-2665 Fixed wrapped mode group over >1 panel; and hidden cols
Jim Procter [Thu, 17 Aug 2017 12:08:49 +0000 (13:08 +0100)]
Merge branch 'releases/Release_2_10_2_Branch'
Jim Procter [Thu, 17 Aug 2017 12:07:53 +0000 (13:07 +0100)]
JAL-2418 ahem - correct year for what's new
Jim Procter [Thu, 17 Aug 2017 11:39:46 +0000 (12:39 +0100)]
Merge branch 'releases/Release_2_10_2_Branch'
Jim Procter [Thu, 17 Aug 2017 11:37:50 +0000 (12:37 +0100)]
JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9
Jim Procter [Thu, 17 Aug 2017 10:41:33 +0000 (11:41 +0100)]
JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed
kiramt [Thu, 17 Aug 2017 10:23:51 +0000 (11:23 +0100)]
JAL-2665 partial fix for selection running over 2 wrapped panels
kiramt [Thu, 17 Aug 2017 08:02:34 +0000 (09:02 +0100)]
JAL-2665 Correct position of selection switching from wrap to normal
Jim Procter [Wed, 16 Aug 2017 22:24:37 +0000 (23:24 +0100)]
Merge branch 'releases/Release_2_10_2_Branch'
Jim Procter [Wed, 16 Aug 2017 22:24:25 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 22:24:13 +0000 (23:24 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 22:23:59 +0000 (23:23 +0100)]
JAL-2418 formatting
Jim Procter [Wed, 16 Aug 2017 22:23:53 +0000 (23:23 +0100)]
JAL-2418 occupancy row in What’s New
Jim Procter [Wed, 16 Aug 2017 21:38:01 +0000 (22:38 +0100)]
Merge branch 'releases/Release_2_10_2_Branch'
Jim Procter [Wed, 16 Aug 2017 21:37:37 +0000 (22:37 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 21:30:21 +0000 (22:30 +0100)]
JAL-2418 add GPL to main sources
Jim Procter [Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)]
JAL-2418 source formatting
Jim Procter [Wed, 16 Aug 2017 20:52:55 +0000 (21:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 20:52:36 +0000 (21:52 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 20:52:07 +0000 (21:52 +0100)]
JAL-2418 mirror fonts option doc tweak
kiramt [Wed, 16 Aug 2017 19:53:45 +0000 (20:53 +0100)]
JAL-2665 Working with hidden columns
Jim Procter [Wed, 16 Aug 2017 19:17:43 +0000 (20:17 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 19:17:03 +0000 (20:17 +0100)]
JAL-2418 whats new for 2.10.2
Jim Procter [Wed, 16 Aug 2017 19:16:52 +0000 (20:16 +0100)]
JAL-2418 reclassify some issues to features/bugs resolved
Jim Procter [Wed, 16 Aug 2017 18:23:33 +0000 (19:23 +0100)]
JAL-2418 typos in release notes
Jim Procter [Wed, 16 Aug 2017 18:16:08 +0000 (19:16 +0100)]
JAL-2418 check groovy script one-liners for restoring legacy score model behaviour
kiramt [Wed, 16 Aug 2017 15:34:32 +0000 (16:34 +0100)]
JAL-2665 Added hidden columns group selection - almost working
kiramt [Wed, 16 Aug 2017 14:51:55 +0000 (15:51 +0100)]
JAL-2665 Selecting on wrapped alignments
kiramt [Wed, 16 Aug 2017 13:25:03 +0000 (14:25 +0100)]
JAL-2556 start to account for wrapped alignments
kiramt [Wed, 16 Aug 2017 12:28:13 +0000 (13:28 +0100)]
JAL-2665 Tidy
kiramt [Wed, 16 Aug 2017 11:20:16 +0000 (12:20 +0100)]
JAL-2665 fix resize
kiramt [Wed, 16 Aug 2017 10:40:54 +0000 (11:40 +0100)]
JAL-2556 Code tidy
kiramt [Wed, 16 Aug 2017 10:21:55 +0000 (11:21 +0100)]
JAL-2556 Resolved group update on colouring and escape
kiramt [Wed, 16 Aug 2017 10:09:39 +0000 (11:09 +0100)]
JAL-2665 Added sequence group update event.
kiramt [Wed, 16 Aug 2017 07:13:04 +0000 (08:13 +0100)]
JAL-2665 Draw selection group - works on scroll but not when static
Jim Procter [Tue, 15 Aug 2017 16:15:25 +0000 (17:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 16:14:32 +0000 (17:14 +0100)]
JAL-2116 fix typo in build.xml for j2se element
Jim Procter [Tue, 15 Aug 2017 15:55:22 +0000 (16:55 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 15:55:06 +0000 (16:55 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 15 Aug 2017 14:02:19 +0000 (15:02 +0100)]
JAL-2418 bump release to Thursday
Jim Procter [Tue, 15 Aug 2017 13:54:20 +0000 (14:54 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
kiramt [Tue, 15 Aug 2017 10:48:33 +0000 (11:48 +0100)]
JAL-2265 turn off NPE
Jim Procter [Mon, 14 Aug 2017 16:25:16 +0000 (17:25 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 16:23:46 +0000 (17:23 +0100)]
JAL-2418 release notes for JAL-2663
Jim Procter [Mon, 14 Aug 2017 16:21:45 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2335_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 16:21:16 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 16:20:28 +0000 (17:20 +0100)]
JAL-2116 add 1.8 1.7 compatible launch string
Jim Procter [Mon, 14 Aug 2017 13:17:35 +0000 (14:17 +0100)]
JAL-2335 choose appropriate alphabet for filtering nonstandard symbols
Jim Procter [Mon, 14 Aug 2017 13:16:27 +0000 (14:16 +0100)]
JAL-2335 source formatting
Jim Procter [Mon, 14 Aug 2017 13:16:17 +0000 (14:16 +0100)]
JAL-2335 filterNonStandardResidues configurable for jabaws clients
Jim Procter [Mon, 14 Aug 2017 09:45:14 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 09:45:05 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:44:25 +0000 (10:44 +0100)]
JAL-2116 switch to java.se.ee https://bugs.openjdk.java.net/browse/JDK-8166438
Jim Procter [Mon, 14 Aug 2017 09:35:00 +0000 (10:35 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:34:44 +0000 (10:34 +0100)]
Merge branch 'patch/JAL-2663_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 09:33:33 +0000 (10:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Sun, 13 Aug 2017 14:34:58 +0000 (15:34 +0100)]
JAL-2663 flag and filter to exclude non-standard amino acids from submission
Jim Procter [Sun, 13 Aug 2017 14:34:20 +0000 (15:34 +0100)]
JAL-2663 source formatting
kiramt [Mon, 14 Aug 2017 08:43:47 +0000 (09:43 +0100)]
JAL-2664 Initial change to drawing hidden regions in overview
Jim Procter [Thu, 10 Aug 2017 20:11:21 +0000 (21:11 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 20:10:23 +0000 (21:10 +0100)]
JAL-2116 try '=' syntax jigsaw-dev.1059479.n5.nabble.com/Java-9-EA-169-Webstart-NoClassDefFoundError-javax-xml-ws-Service-td5716769.html
Jim Procter [Thu, 10 Aug 2017 19:42:30 +0000 (20:42 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 19:38:36 +0000 (20:38 +0100)]
JAL-2116 test java 9 only JNLP launch
Jim Procter [Thu, 10 Aug 2017 15:38:21 +0000 (16:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 15:37:30 +0000 (16:37 +0100)]
JAL-2116 explicit replace j2se element with a java9 specific one since orangevolt-tasks don't support the java-vm-args attribute
gmungoc [Thu, 10 Aug 2017 15:24:53 +0000 (16:24 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Jim Procter [Thu, 10 Aug 2017 14:38:30 +0000 (15:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 14:37:16 +0000 (15:37 +0100)]
JAL-2116 java9 modules dependency for JNLP file
kiramt [Thu, 10 Aug 2017 13:54:37 +0000 (14:54 +0100)]
Merge remote-tracking branch 'origin/develop' into feature/JAL-2587
kiramt [Thu, 10 Aug 2017 13:40:53 +0000 (14:40 +0100)]
JAL-2587 tidy
gmungoc [Thu, 10 Aug 2017 11:56:12 +0000 (12:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 10 Aug 2017 11:29:52 +0000 (12:29 +0100)]
JAL-2660 used saved value of ignoreGapsInConsensus when loading
(/copying) viewport
kiramt [Thu, 10 Aug 2017 11:02:10 +0000 (12:02 +0100)]
JAL-2587 Tinkering with progress panel appearance
kiramt [Thu, 10 Aug 2017 10:20:09 +0000 (11:20 +0100)]
JAL-2587 prevented double overview recalc on opening overview
git://source.jalview.org / jalview.git / log