gmungoc [Mon, 13 Aug 2018 10:29:15 +0000 (11:29 +0100)]
patch broken help link
gmungoc [Mon, 13 Aug 2018 10:14:08 +0000 (11:14 +0100)]
scrubbing HMM classes on spike-mungo
gmungoc [Mon, 13 Aug 2018 10:10:16 +0000 (11:10 +0100)]
update spikes/mungo from JAL-3076 patch branch
gmungoc [Wed, 30 May 2018 11:23:18 +0000 (12:23 +0100)]
Update spike branch to latest (HMMSearch file chooser arg)
gmungoc [Wed, 23 May 2018 14:05:50 +0000 (15:05 +0100)]
Update spike branch to latest
gmungoc [Mon, 14 May 2018 13:20:19 +0000 (14:20 +0100)]
Update spike branch to latest
gmungoc [Fri, 11 May 2018 15:36:03 +0000 (16:36 +0100)]
JAL-2629 push latest to spike branch
gmungoc [Fri, 11 May 2018 11:29:53 +0000 (12:29 +0100)]
JAL-2629 update spike branch to latest
gmungoc [Mon, 23 Apr 2018 08:43:16 +0000 (09:43 +0100)]
JAL-2957 don't validate input on arrow keys
gmungoc [Mon, 23 Apr 2018 08:41:59 +0000 (09:41 +0100)]
JAL-591 ensure slider hidden if text input field only
gmungoc [Fri, 20 Apr 2018 21:01:08 +0000 (22:01 +0100)]
JAL-2629 update spikes/mungo to latest
gmungoc [Fri, 30 Mar 2018 14:56:41 +0000 (15:56 +0100)]
Updated with latest from mchmmer branch
gmungoc [Fri, 9 Feb 2018 15:35:34 +0000 (15:35 +0000)]
JAL-1793 update spike to latest
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
gmungoc [Fri, 2 Feb 2018 15:56:43 +0000 (15:56 +0000)]
JAL-984 merged to spikes-mungo
gmungoc [Tue, 30 Jan 2018 16:07:17 +0000 (16:07 +0000)]
JAL-1793 update spike build to latest incl stop and synonymous variants on peptides
gmungoc [Wed, 10 Jan 2018 15:20:56 +0000 (15:20 +0000)]
JAL-1793 update spike branch to latest
gmungoc [Mon, 4 Dec 2017 15:56:16 +0000 (15:56 +0000)]
JAL-2808 JAL-2850 update spike build to latest
gmungoc [Mon, 4 Dec 2017 15:21:25 +0000 (15:21 +0000)]
JAL-2850 JAL-1766 option to load contig sequence referenced by VCF
gmungoc [Mon, 4 Dec 2017 11:31:41 +0000 (11:31 +0000)]
JAL-2845 locate reverse strand insertion as complement insertion at a preceding position
gmungoc [Mon, 4 Dec 2017 09:21:09 +0000 (09:21 +0000)]
JAL-2835 small refactor to only extract transcript consequence once
gmungoc [Fri, 1 Dec 2017 17:03:17 +0000 (17:03 +0000)]
JAL-2835 spike updated to latest (use specific SO term for feature)
gmungoc [Fri, 24 Nov 2017 14:50:45 +0000 (14:50 +0000)]
JAL-2808 update spike to latest
gmungoc [Thu, 23 Nov 2017 16:21:26 +0000 (16:21 +0000)]
JAL-2808 update spike to latest (filter range tooltip, Present condition)
gmungoc [Thu, 23 Nov 2017 12:52:45 +0000 (12:52 +0000)]
JAL-2808 update spike to latest (filter range, Present option)
gmungoc [Wed, 22 Nov 2017 15:36:06 +0000 (15:36 +0000)]
JAL-2069 spike updated with latest (FeatureTypeSettings)
gmungoc [Wed, 15 Nov 2017 10:51:51 +0000 (10:51 +0000)]
JAL-2835 spike updated with latest
gmungoc [Wed, 8 Nov 2017 11:34:40 +0000 (11:34 +0000)]
JAL-2069 updated spike to latest
gmungoc [Tue, 7 Nov 2017 16:40:57 +0000 (16:40 +0000)]
JAL-2069 update spike to latest (no value colour options)
gmungoc [Tue, 7 Nov 2017 13:14:45 +0000 (13:14 +0000)]
JAL-2069 update spike with latest
gmungoc [Tue, 7 Nov 2017 11:50:54 +0000 (11:50 +0000)]
JAL-2069 update spike branch with latest
gmungoc [Thu, 2 Nov 2017 15:53:06 +0000 (15:53 +0000)]
JAL-2808 spike updated with latest
gmungoc [Fri, 27 Oct 2017 11:27:04 +0000 (12:27 +0100)]
JAL-2754 rename proguard.jar on spike branch
gmungoc [Fri, 27 Oct 2017 11:21:21 +0000 (12:21 +0100)]
JAL-2754 spike branch updated to latest
gmungoc [Fri, 27 Oct 2017 11:03:22 +0000 (12:03 +0100)]
JAL-2754 5.3.3 update of proguard.jar
gmungoc [Fri, 27 Oct 2017 09:54:03 +0000 (10:54 +0100)]
JAL-1793 spike branch updated to latest
gmungoc [Tue, 24 Oct 2017 12:50:46 +0000 (13:50 +0100)]
JAL-2738 update spike branch with latest
gmungoc [Fri, 20 Oct 2017 13:26:36 +0000 (14:26 +0100)]
Push 1793 latest to spike branch
gmungoc [Thu, 5 Oct 2017 14:36:38 +0000 (15:36 +0100)]
JAL-2738 update spikes/mungo
gmungoc [Wed, 4 Oct 2017 15:02:59 +0000 (16:02 +0100)]
Merge branch 'features/JAL-1793VCF' into spikes/mungo
Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/gui/PopupMenu.java
src/jalview/io/vcf/VCFLoader.java
gmungoc [Wed, 4 Oct 2017 14:19:02 +0000 (15:19 +0100)]
JAL-2738 fix bug of premature exit from adding attributes
gmungoc [Wed, 4 Oct 2017 10:31:12 +0000 (11:31 +0100)]
JAL-2738 match consequence "Allele" to VCF allele; add non-SNP variants
on nucleotide
gmungoc [Wed, 4 Oct 2017 10:29:03 +0000 (11:29 +0100)]
JAL-2744 handle null features list
gmungoc [Tue, 3 Oct 2017 10:25:45 +0000 (11:25 +0100)]
JAL-2738 copy to spikes/mungo
gmungoc [Tue, 3 Oct 2017 10:21:52 +0000 (11:21 +0100)]
JAL-2738 update test for threaded VCFLoader
gmungoc [Tue, 3 Oct 2017 10:21:11 +0000 (11:21 +0100)]
JAL-2738 code formatting
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
git://source.jalview.org / jalview.git / log