Jim Procter [Sun, 3 Sep 2017 13:04:52 +0000 (14:04 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into portforward/JAL-2675_2102b1to2103
Jim Procter [Sun, 3 Sep 2017 12:35:45 +0000 (13:35 +0100)]
JAL-2588 overview tab docs, whats new and release notes
Jim Procter [Sun, 3 Sep 2017 12:18:18 +0000 (13:18 +0100)]
JAL-2675 typo
Jim Procter [Sun, 3 Sep 2017 11:26:58 +0000 (12:26 +0100)]
Merge branch 'feature/JAL-2527' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 10:55:42 +0000 (11:55 +0100)]
JAL-2681 release notes
Jim Procter [Sun, 3 Sep 2017 10:38:15 +0000 (11:38 +0100)]
Merge branch 'features/JAL-2681_duplicatecrossrefs' into documentation/JAL-2675_release2102b1
kiramt [Fri, 1 Sep 2017 06:37:10 +0000 (07:37 +0100)]
JAL-2527 Additional test
kiramt [Fri, 1 Sep 2017 06:22:55 +0000 (07:22 +0100)]
JAL-2527 Unit test for group colouring
kiramt [Thu, 31 Aug 2017 13:27:50 +0000 (14:27 +0100)]
JAL-2527 Unit test
kiramt [Thu, 31 Aug 2017 11:06:41 +0000 (12:06 +0100)]
JAL-2527 Fix typo
kiramt [Thu, 31 Aug 2017 11:04:39 +0000 (12:04 +0100)]
JAL-2527 Updated Spanish, adjusted UI so Spanish fits
kiramt [Thu, 31 Aug 2017 10:46:14 +0000 (11:46 +0100)]
JAL-2527 Updates following code review
kiramt [Wed, 30 Aug 2017 12:28:40 +0000 (13:28 +0100)]
JAL-2527 Code comments, tidy
kiramt [Wed, 30 Aug 2017 12:22:47 +0000 (13:22 +0100)]
JAL-2527 Added default setting/resetting and first pass at Spanish
kiramt [Wed, 30 Aug 2017 09:59:38 +0000 (10:59 +0100)]
JAL-2527 Wired up cached values to overview
kiramt [Wed, 30 Aug 2017 08:30:11 +0000 (09:30 +0100)]
Merge remote-tracking branch 'origin/feature/2588' into feature/JAL-2527
Conflicts:
src/jalview/renderer/OverviewRenderer.java
kiramt [Wed, 30 Aug 2017 07:11:40 +0000 (08:11 +0100)]
Merge branch 'feature/JAL-2664' into feature/JAL-2527
kiramt [Tue, 29 Aug 2017 15:27:40 +0000 (16:27 +0100)]
JAL-2664 Updates following review
Jim Procter [Tue, 29 Aug 2017 14:44:55 +0000 (15:44 +0100)]
Merge branch 'patch/JAL-2698_blockingAutoAssociateDiaog' into develop
kiramt [Tue, 29 Aug 2017 13:55:53 +0000 (14:55 +0100)]
JAL-2527 Added overview prefs - don't get picked up by overview yet
Jim Procter [Tue, 29 Aug 2017 13:35:37 +0000 (14:35 +0100)]
JAL-2698 spawn a thread to test for and raise auto associate dialogs for PDB file drops on the alignment view
kiramt [Mon, 28 Aug 2017 15:38:03 +0000 (16:38 +0100)]
JAL-2527 Started adding overview preferences
gmungoc [Fri, 25 Aug 2017 08:27:46 +0000 (09:27 +0100)]
JAL-2480 suppress debug timing output that got left in
gmungoc [Wed, 23 Aug 2017 13:42:32 +0000 (14:42 +0100)]
JAL-2435 last lost commit e926a5d redone
gmungoc [Wed, 23 Aug 2017 13:42:32 +0000 (14:42 +0100)]
JAL-2435 last lost commit e926a5d redone
gmungoc [Wed, 23 Aug 2017 10:48:20 +0000 (11:48 +0100)]
JAL-2481 a smidgin more test coverage of findFeatures
Jim Procter [Tue, 22 Aug 2017 21:42:11 +0000 (22:42 +0100)]
JAL-1551 formatting
Jim Procter [Tue, 22 Aug 2017 21:13:07 +0000 (22:13 +0100)]
JAL-2681 cross-ref selection for targeted debugging
Jim Procter [Tue, 22 Aug 2017 21:12:07 +0000 (22:12 +0100)]
JAL-2681 source formatting
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
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 11:37:50 +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
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 21:37:37 +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
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
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
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
git://source.jalview.org / jalview.git / log