gmungoc [Mon, 2 Oct 2017 17:52:23 +0000 (18:52 +0100)]
JAL-2738 code tidy up, null checks &c
gmungoc [Mon, 2 Oct 2017 14:45:33 +0000 (15:45 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 2 Oct 2017 14:41:02 +0000 (15:41 +0100)]
JAL-2525 lookup transcript features by Ontology
gmungoc [Mon, 2 Oct 2017 14:37:01 +0000 (15:37 +0100)]
JAL-2738 filter VEP consequence data to that for current transcript
Jim Procter [Fri, 29 Sep 2017 16:00:57 +0000 (17:00 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 15:48:58 +0000 (16:48 +0100)]
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher
Jim Procter [Fri, 29 Sep 2017 15:48:21 +0000 (16:48 +0100)]
JAL-2745 patch tests for https
Jim Procter [Fri, 29 Sep 2017 15:47:59 +0000 (16:47 +0100)]
JAL-2748 formatting
Jim Procter [Fri, 29 Sep 2017 15:47:48 +0000 (16:47 +0100)]
JAL-2745 JAL-2748 direct download of XML from uniprot.org
gmungoc [Fri, 29 Sep 2017 15:11:11 +0000 (16:11 +0100)]
JAL-2738 one sequence feature per (SNP) VCF allele
gmungoc [Fri, 29 Sep 2017 15:10:18 +0000 (16:10 +0100)]
JAL-2744 indent CSQ lines to catch the eye
Jim Procter [Fri, 29 Sep 2017 10:51:41 +0000 (11:51 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 10:49:49 +0000 (11:49 +0100)]
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
EBI ftp confirmed to remain accesible via HTTP
This reverts commit
c7f663521cb82b94d832015010fa488d3dc7ff58.
Jim Procter [Fri, 29 Sep 2017 07:20:59 +0000 (08:20 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 07:18:53 +0000 (08:18 +0100)]
JAL-2745 update default EBI-eye search URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:18:30 +0000 (08:18 +0100)]
JAL-2745 update SIFTS FTP URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:03:39 +0000 (08:03 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 06:58:32 +0000 (07:58 +0100)]
JAL-2745 stderr rather than stdout for unexpected HTTP response
gmungoc [Thu, 28 Sep 2017 15:51:30 +0000 (16:51 +0100)]
JAL-2745 update www.ebi.ac.uk to https
gmungoc [Thu, 28 Sep 2017 13:25:12 +0000 (14:25 +0100)]
JAL-2738 separate thread to load VCF; update FeatureSettings when done
gmungoc [Thu, 28 Sep 2017 12:34:10 +0000 (13:34 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Thu, 28 Sep 2017 12:12:28 +0000 (13:12 +0100)]
JAL-2036 set menus after fully loading AlignFrame
gmungoc [Thu, 28 Sep 2017 10:21:59 +0000 (11:21 +0100)]
JAL-1796 GeneLociI as distinguished DBRefEntry
gmungoc [Thu, 28 Sep 2017 08:52:45 +0000 (09:52 +0100)]
JAL-2744 simple Feature Details report from Popup menu
gmungoc [Thu, 28 Sep 2017 08:37:46 +0000 (09:37 +0100)]
JAL-2744 refactor PopupMenu constructor to enable adding feature details
gmungoc [Tue, 26 Sep 2017 12:15:30 +0000 (13:15 +0100)]
JAL-2738 transfer VCF variant features to CDS sequences
gmungoc [Tue, 26 Sep 2017 12:14:59 +0000 (13:14 +0100)]
JAL-2738 JAL-2154 add DBRef from transcript to synthesized CDS and vice
versa
gmungoc [Tue, 26 Sep 2017 09:17:30 +0000 (10:17 +0100)]
JAL-2738 unit test for reverse strand gene
gmungoc [Tue, 26 Sep 2017 09:16:47 +0000 (10:16 +0100)]
JAL-2738 promote setGeneLoci to SequenceI!
gmungoc [Mon, 25 Sep 2017 15:38:51 +0000 (16:38 +0100)]
JAL-2738 use complement base for a VCF variant on reverse strand gene
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
git://source.jalview.org / jalview.git / log