gmungoc [Mon, 25 Sep 2017 15:37:55 +0000 (16:37 +0100)]
JAL-2738 getGeneLoci promoted to SequenceI
gmungoc [Mon, 25 Sep 2017 13:46:27 +0000 (14:46 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 25 Sep 2017 13:44:56 +0000 (14:44 +0100)]
JAL-2525 return no features if none matches ontology term!
gmungoc [Mon, 25 Sep 2017 13:42:40 +0000 (14:42 +0100)]
JAL-2738 query unindexed file, unit test for VCFLoader
gmungoc [Mon, 25 Sep 2017 09:07:32 +0000 (10:07 +0100)]
JAL-2738 one constant in codebase for "alleles" attribute of
GFF/SequenceFeature
gmungoc [Mon, 25 Sep 2017 09:02:03 +0000 (10:02 +0100)]
JAL-2738 extract SNP variants from SNP or MIXED variant records
gmungoc [Fri, 22 Sep 2017 15:15:23 +0000 (16:15 +0100)]
JAL-2738 extract utility method to MappingUtils
gmungoc [Fri, 22 Sep 2017 14:03:07 +0000 (15:03 +0100)]
JAL-2738 correct handling of reverse strand genes
gmungoc [Fri, 22 Sep 2017 10:58:48 +0000 (11:58 +0100)]
JAL-2738 lookup GRCh38/37 gene mapping
gmungoc [Thu, 21 Sep 2017 15:28:09 +0000 (16:28 +0100)]
JAL-2738 compute VCF on peptide, extract AF (allele frequency) score
gmungoc [Thu, 21 Sep 2017 15:27:01 +0000 (16:27 +0100)]
JAL-2738 add chromosome coordinate mappings to transcripts
gmungoc [Thu, 21 Sep 2017 13:14:41 +0000 (14:14 +0100)]
JAL-2738 PoC of Load VCF file on to gene sequence
gmungoc [Thu, 21 Sep 2017 13:13:28 +0000 (14:13 +0100)]
JAL-2738 GeneLoci holds mapping of sequence to chromosome
kiramt [Wed, 20 Sep 2017 10:28:01 +0000 (11:28 +0100)]
JAL-2662 Adjustments to hidden columns benchmark
gmungoc [Tue, 19 Sep 2017 14:34:39 +0000 (15:34 +0100)]
JAL-1793 wrapper for plain or indexed VCF + simple tests
kiramt [Tue, 19 Sep 2017 14:26:56 +0000 (15:26 +0100)]
JAL-2662 Updated README
kiramt [Tue, 19 Sep 2017 14:23:59 +0000 (15:23 +0100)]
JAL-2737 Checkstyle error fixes
kiramt [Tue, 19 Sep 2017 14:10:19 +0000 (15:10 +0100)]
JAL-2622 Tidied up gitignore, added to README
kiramt [Tue, 19 Sep 2017 14:05:01 +0000 (15:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Tue, 19 Sep 2017 14:03:14 +0000 (15:03 +0100)]
Merge remote-tracking branch 'origin/task/JAL-2662' into develop
gmungoc [Tue, 19 Sep 2017 13:52:58 +0000 (14:52 +0100)]
JAL-1793 simple tests of reading raw and indexed VCF files with htsjdk
gmungoc [Mon, 18 Sep 2017 09:44:25 +0000 (10:44 +0100)]
Merge remote-tracking branch 'origin/patch/JAL-2732' into develop
gmungoc [Mon, 18 Sep 2017 08:26:43 +0000 (09:26 +0100)]
JAL-2728 fine tuned initial split of split frame view
Jim Procter [Fri, 15 Sep 2017 15:37:47 +0000 (16:37 +0100)]
Merge branch 'documentation/JAL-2698_release2103' into develop
Jim Procter [Fri, 15 Sep 2017 15:37:31 +0000 (16:37 +0100)]
JAL-2698 new releases.html entry, whatsNew.html and first signoff : JAL-2728
Jim Procter [Fri, 15 Sep 2017 15:21:22 +0000 (16:21 +0100)]
Merge branch 'bug/JAL-2728splitFrameDivision' into develop
Jim Procter [Fri, 15 Sep 2017 15:05:12 +0000 (16:05 +0100)]
JAL-1625 ensure we don’t regress on JAL-20 - we always use the DefaultDesktopManager on Windows
Jim Procter [Fri, 15 Sep 2017 15:04:06 +0000 (16:04 +0100)]
JAL-1625 javadoc
Jim Procter [Fri, 15 Sep 2017 14:45:46 +0000 (15:45 +0100)]
JAL-2733 redraw after changing the memory status display setting
Jim Procter [Fri, 15 Sep 2017 14:43:46 +0000 (15:43 +0100)]
JAL-1625 JAL-1900 preserve the original DesktopManager instance provided by platform rather than create our own, so iconify works correctly (should mean we also get iconify working in Linux too)
Jim Procter [Fri, 15 Sep 2017 14:42:50 +0000 (15:42 +0100)]
JAL-1900 JAL-1625 back out OSX specific double buffer disabling (seems to do nothing)
Jim Procter [Fri, 15 Sep 2017 14:23:58 +0000 (15:23 +0100)]
JAL-1551 standard code formatting
Jim Procter [Fri, 15 Sep 2017 14:23:15 +0000 (15:23 +0100)]
JAL-2732 force a redraw after resize/drag to clear any outlines
gmungoc [Fri, 15 Sep 2017 14:03:34 +0000 (15:03 +0100)]
JAL-2728 use right denominator for min/max ratio calculations
gmungoc [Fri, 15 Sep 2017 13:49:05 +0000 (14:49 +0100)]
JAL-2728 limit divider to ensure seqs visible (wip!)
gmungoc [Fri, 15 Sep 2017 10:00:46 +0000 (11:00 +0100)]
JAL-741 add tooltip to feature group checkbox
gmungoc [Tue, 12 Sep 2017 13:54:15 +0000 (14:54 +0100)]
Merge branch 'bug/JAL-2721fastPaintNPE' into develop
Jim Procter [Thu, 7 Sep 2017 13:18:36 +0000 (14:18 +0100)]
Merge branch 'bug/JAL-2511idAlignment' into develop
Jim Procter [Thu, 7 Sep 2017 13:17:07 +0000 (14:17 +0100)]
JAL-2511 release notes for 2.10.2b1
gmungoc [Thu, 7 Sep 2017 10:06:34 +0000 (11:06 +0100)]
JAL-2511 invalidate scale panel holder on font change to update layout
Jim Procter [Thu, 7 Sep 2017 06:36:22 +0000 (07:36 +0100)]
JAL-2675 update release date to 7th Sept
Jim Procter [Wed, 6 Sep 2017 21:03:40 +0000 (22:03 +0100)]
JAL-2587 makes sure idWidthAdjuster is resized when container panel’s preference changes
gmungoc [Wed, 6 Sep 2017 15:03:47 +0000 (16:03 +0100)]
JAL-2721 no fastPaint if img has been nulled by fontChanged!
Jim Procter [Wed, 6 Sep 2017 11:01:48 +0000 (12:01 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' into portforward/JAL-2675_2102b1to2103
Jim Procter [Wed, 6 Sep 2017 10:58:49 +0000 (11:58 +0100)]
JAL-2675 update release date to 6th September 2017
Jim Procter [Wed, 6 Sep 2017 10:57:17 +0000 (11:57 +0100)]
Merge JAL-2724 branch 'bug/JAL_2724_annotationcolourongroups' into releases/Release_2_10_2b1_Branch
Jim Procter [Wed, 6 Sep 2017 10:56:08 +0000 (11:56 +0100)]
JAL-2724 release notes for 2.10.2b1
Jim Procter [Wed, 6 Sep 2017 10:55:57 +0000 (11:55 +0100)]
JAL-2724 patch to fix ClassCastException - method should be refactored and tests written as part of JAL-2725
gmungoc [Wed, 6 Sep 2017 10:43:37 +0000 (11:43 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2722' into portforward/JAL-2675_2102b1to2103
kiramt [Wed, 30 Aug 2017 06:35:51 +0000 (07:35 +0100)]
JAL-2587 Removed dissolve
Conflicts:
src/jalview/gui/OverviewCanvas.java
gmungoc [Tue, 5 Sep 2017 14:40:41 +0000 (15:40 +0100)]
JAL-2665 check for null selection group image
Jim Procter [Tue, 5 Sep 2017 17:26:37 +0000 (18:26 +0100)]
Merge branch 'bug/JAL-2722' into releases/Release_2_10_2b1_Branch
gmungoc [Tue, 5 Sep 2017 14:40:41 +0000 (15:40 +0100)]
JAL-2665 check for null selection group image
kiramt [Tue, 5 Sep 2017 13:30:08 +0000 (14:30 +0100)]
JAL-2722 unit test
kiramt [Tue, 5 Sep 2017 13:04:17 +0000 (14:04 +0100)]
JAL-2722 Reinstate allGroups value setting in getResidueColour
Jim Procter [Tue, 5 Sep 2017 12:58:04 +0000 (13:58 +0100)]
Merge branch 'bug/JAL-2665-2.10.3' into portforward/JAL-2675_2102b1to2103
Conflicts:
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/SeqCanvas.java
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
git://source.jalview.org / jalview.git / log