Jim Procter [Tue, 5 Sep 2017 12:41:45 +0000 (13:41 +0100)]
Merge branch 'master' into portforward/JAL-2675_2102b1to2103
update and resolve conflicts after 2.10.2b1 release
Conflicts:
src/jalview/gui/SeqCanvas.java
Jim Procter [Tue, 5 Sep 2017 08:13:46 +0000 (09:13 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch'
Jim Procter [Tue, 5 Sep 2017 07:08:22 +0000 (08:08 +0100)]
JAL-2675 update destination jar name of min-jabaws-client to 2.2
Jim Procter [Mon, 4 Sep 2017 22:01:34 +0000 (23:01 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch'
Jim Procter [Mon, 4 Sep 2017 22:01:12 +0000 (23:01 +0100)]
JAL-2675 fix grammar
Jim Procter [Mon, 4 Sep 2017 21:59:19 +0000 (22:59 +0100)]
JAL-2588 update overview image - show the new gap shading
Jim Procter [Mon, 4 Sep 2017 20:39:38 +0000 (21:39 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch'
Jim Procter [Mon, 4 Sep 2017 19:11:44 +0000 (20:11 +0100)]
JAL-2675 what’s new for 2.10.2b1
Jim Procter [Mon, 4 Sep 2017 18:51:31 +0000 (19:51 +0100)]
JAL-2675 source license
Jim Procter [Mon, 4 Sep 2017 17:54:37 +0000 (18:54 +0100)]
Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1
Jim Procter [Mon, 4 Sep 2017 16:23:52 +0000 (17:23 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 16:22:46 +0000 (17:22 +0100)]
JAL-2673 JAL-2675 release notes and release date for 2.10.2b1
Jim Procter [Mon, 4 Sep 2017 16:05:34 +0000 (17:05 +0100)]
Merge branch 'bug/JAL-2673' into documentation/JAL-2675_release2102b1
kiramt [Mon, 4 Sep 2017 15:31:00 +0000 (16:31 +0100)]
JAL-2673 turn off update to running flag from scrollUp/scrollRight
kiramt [Mon, 4 Sep 2017 14:57:49 +0000 (15:57 +0100)]
JAL-2673 Attempt to stop infinite scrolling etc
Jim Procter [Mon, 4 Sep 2017 13:38:15 +0000 (14:38 +0100)]
Merge branch 'patch/JAL-2527_fixappletbuild' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 13:37:56 +0000 (14:37 +0100)]
JAL-2527 move default colours for applet / application out of gui.Preferences so applet build completes
Jim Procter [Mon, 4 Sep 2017 12:32:16 +0000 (13:32 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 12:31:09 +0000 (13:31 +0100)]
JAL-2418 JAL-2116 use 1.7+ and 1.9+ for the version specification - try to suppress the 'this application is asking for a later version of Java than you have installed...' message
Jim Procter [Mon, 4 Sep 2017 12:23:35 +0000 (13:23 +0100)]
Merge branch 'features/JAL-2549_updateJABAWSto220' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 12:23:08 +0000 (13:23 +0100)]
JAL-2549 update release notes
Jim Procter [Mon, 4 Sep 2017 12:20:33 +0000 (13:20 +0100)]
JAL-2549 update JABAWS 2.2 library to client that reports correct version number
Jim Procter [Mon, 4 Sep 2017 12:12:14 +0000 (13:12 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 11:12:08 +0000 (12:12 +0100)]
JAL-2704 release notes
Jim Procter [Mon, 4 Sep 2017 11:10:09 +0000 (12:10 +0100)]
Merge branch 'bug/JAL-2704gapColourFading' into documentation/JAL-2675_release2102b1
Jim Procter [Mon, 4 Sep 2017 09:31:26 +0000 (10:31 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 07:27:15 +0000 (08:27 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
kiramt [Mon, 4 Sep 2017 07:14:38 +0000 (08:14 +0100)]
JAL-2611 reinstated missed commit
Jim Procter [Sun, 3 Sep 2017 17:50:16 +0000 (18:50 +0100)]
JAL-2675 release notes
Jim Procter [Sun, 3 Sep 2017 17:27:09 +0000 (18:27 +0100)]
Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 17:06:24 +0000 (18:06 +0100)]
Merge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 16:35:01 +0000 (17:35 +0100)]
JAL-2672 JAL-2665 release notes. Also note this merge does not resolve JAL-2673
Jim Procter [Sun, 3 Sep 2017 16:12:49 +0000 (17:12 +0100)]
Merge branch 'bug/JAL-2665-2.10.2b' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 14:29:56 +0000 (15:29 +0100)]
JAL-2664 JAL-2527 signs for release
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 12:37:54 +0000 (13:37 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
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
gmungoc [Thu, 31 Aug 2017 07:47:05 +0000 (08:47 +0100)]
JAL-2704 unit test for Above PID gap colour, simplified findColour()
gmungoc [Wed, 30 Aug 2017 16:31:29 +0000 (17:31 +0100)]
JAL-2704 don't shade gap colour for PID/conservation
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 [Tue, 29 Aug 2017 10:59:54 +0000 (11:59 +0100)]
JAL-2665 OOM checks just in case
kiramt [Tue, 29 Aug 2017 08:28:29 +0000 (09:28 +0100)]
JAL-2665 Corrected to draw selections for wrapped printing
kiramt [Mon, 28 Aug 2017 15:38:03 +0000 (16:38 +0100)]
JAL-2527 Started adding overview preferences
kiramt [Mon, 28 Aug 2017 11:15:35 +0000 (12:15 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'
into bug/JAL-2665-2.10.2b
Conflicts:
src/jalview/gui/SeqCanvas.java
kiramt [Mon, 28 Aug 2017 10:56:33 +0000 (11:56 +0100)]
JAL-2665 Changes for review comments; printing with selgroup working
Jim Procter [Sun, 27 Aug 2017 14:50:03 +0000 (15:50 +0100)]
JAL-2691 assert chains are recovered by AAStructureBindingModel
Jim Procter [Sun, 27 Aug 2017 14:49:02 +0000 (15:49 +0100)]
JAL-2691 catchall if passed dataset sequences (tests only)
Jim Procter [Sun, 27 Aug 2017 13:25:01 +0000 (14:25 +0100)]
JAL-2693 TODO comments
Jim Procter [Sun, 27 Aug 2017 13:23:06 +0000 (14:23 +0100)]
JAL-2691 discover any existing chain mappings for a structure view
Jim Procter [Sun, 27 Aug 2017 13:17:30 +0000 (14:17 +0100)]
JAL-2691 cached view combo box value javadoc
kiramt [Fri, 25 Aug 2017 17:36:26 +0000 (18:36 +0100)]
JAL-2587 Removed duplicate events fired to progress bar
kiramt [Fri, 25 Aug 2017 13:13:48 +0000 (14:13 +0100)]
JAL-2587 Removed annoying double repaint on hide insertions
kiramt [Fri, 25 Aug 2017 11:54:05 +0000 (12:54 +0100)]
JAL-2587 Update overview progress bar while drawing rows too
kiramt [Fri, 25 Aug 2017 08:41:25 +0000 (09:41 +0100)]
JAL-2587 Progress bar sizing tweaks
gmungoc [Fri, 25 Aug 2017 08:27:46 +0000 (09:27 +0100)]
JAL-2480 suppress debug timing output that got left in
kiramt [Fri, 25 Aug 2017 07:03:52 +0000 (08:03 +0100)]
JAL-2587 Made progress bar display before overview calc starts
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
git://source.jalview.org / jalview.git / log