gmungoc [Mon, 26 Feb 2018 11:10:48 +0000 (11:10 +0000)]
JAL-2599 test coverage and bug fixes for 'minimal file' parsing
gmungoc [Fri, 23 Feb 2018 16:12:16 +0000 (16:12 +0000)]
JAL-2599 corrected case-insensitive symbol indexing
gmungoc [Fri, 23 Feb 2018 15:52:36 +0000 (15:52 +0000)]
JAL-2599 parser and datamodel use primitive double[] not List<Double>
gmungoc [Thu, 22 Feb 2018 16:05:43 +0000 (16:05 +0000)]
JAL-2629 tidy tests, refactor hmmer node mapping slightly
gmungoc [Thu, 22 Feb 2018 13:43:32 +0000 (13:43 +0000)]
JAL-2629 tidy unit tests, constants etc
gmungoc [Wed, 21 Feb 2018 16:18:29 +0000 (16:18 +0000)]
JAL-2629 simplifying method signatures in Hmmer command classes
gmungoc [Tue, 20 Feb 2018 15:36:24 +0000 (15:36 +0000)]
JAL-2629 removed SequenceI.get/setLastPosition and related code
gmungoc [Tue, 20 Feb 2018 14:32:36 +0000 (14:32 +0000)]
Merge branch 'develop' into features/mchmmer
Conflicts:
resources/lang/Messages.properties
src/jalview/api/AlignViewportI.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/schemes/ResidueProperties.java
src/jalview/viewmodel/AlignmentViewport.java
gmungoc [Tue, 20 Feb 2018 13:01:36 +0000 (13:01 +0000)]
JAL-2897 updated unit test for code change
gmungoc [Tue, 20 Feb 2018 12:50:35 +0000 (12:50 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 19 Feb 2018 17:04:07 +0000 (17:04 +0000)]
JAL-2629 refactoring of Hmmer preferences
gmungoc [Mon, 19 Feb 2018 17:03:07 +0000 (17:03 +0000)]
JAL-2629 partial refactoring of Hmmer command classes
gmungoc [Mon, 19 Feb 2018 10:19:19 +0000 (10:19 +0000)]
JAL-2629 formatting only
Jim Procter [Thu, 15 Feb 2018 15:51:48 +0000 (15:51 +0000)]
JAL-2906 bump release version and cut new release note entry
gmungoc [Wed, 7 Feb 2018 15:20:29 +0000 (15:20 +0000)]
JAL-2808 ensure pattern field re-enabled when needed for condition
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
Conflicts:
test/jalview/analysis/AlignmentUtilsTests.java
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
gmungoc [Mon, 5 Feb 2018 09:54:10 +0000 (09:54 +0000)]
Merge branch 'spikes/mungo' into trialMerge
Conflicts:
src/jalview/analysis/AlignmentUtils.java
test/jalview/analysis/AlignmentUtilsTests.java
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 [Fri, 2 Feb 2018 15:55:11 +0000 (15:55 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into features/JAL-1793VCF
gmungoc [Fri, 2 Feb 2018 11:33:39 +0000 (11:33 +0000)]
JAL-984 use cursor for drag regions to adjust annotation height or id width
gmungoc [Fri, 2 Feb 2018 10:14:17 +0000 (10:14 +0000)]
JAL-984 better behaved panel height adjuster
gmungoc [Wed, 31 Jan 2018 11:28:03 +0000 (11:28 +0000)]
JAL-2792 added tooltip to menu items in case of truncation
gmungoc [Tue, 30 Jan 2018 16:26:44 +0000 (16:26 +0000)]
JAL-2069 menu item now "Variable colour..." to hint at more...
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 [Tue, 30 Jan 2018 15:57:03 +0000 (15:57 +0000)]
JAL-2898 show 'stop_gained' variants on peptide sequences
gmungoc [Tue, 30 Jan 2018 15:34:48 +0000 (15:34 +0000)]
JAL-2897 generate peptide variants for synonymous codon variants
gmungoc [Tue, 30 Jan 2018 15:29:57 +0000 (15:29 +0000)]
JAL-2897 formatting change only prior to functional change
gmungoc [Mon, 29 Jan 2018 09:24:38 +0000 (09:24 +0000)]
JAL-2743 recoded EnsemblLookup without lambda expressions for parsing response
gmungoc [Fri, 26 Jan 2018 14:53:22 +0000 (14:53 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
Jim Procter [Wed, 24 Jan 2018 07:36:56 +0000 (07:36 +0000)]
JAL-2858 update release date and rejig what's new message
Jim Procter [Tue, 23 Jan 2018 13:52:31 +0000 (13:52 +0000)]
JAL-2858 fix what's new
Jim Procter [Tue, 23 Jan 2018 12:03:37 +0000 (12:03 +0000)]
JAL-2858 update latest release notes link in TOC
Jim Procter [Tue, 23 Jan 2018 11:57:05 +0000 (11:57 +0000)]
JAL-2859 release notes
Jim Procter [Tue, 23 Jan 2018 11:54:49 +0000 (11:54 +0000)]
JAL-2858 update release notes
Jim Procter [Mon, 22 Jan 2018 15:26:10 +0000 (15:26 +0000)]
JAL-2858 release notes for 2.10.3b1 (including revision to EnsemblGenomes client as per JAL-2679)
Jim Procter [Mon, 22 Jan 2018 15:25:23 +0000 (15:25 +0000)]
JAL-2858 bump version number for 2.10.3b1
gmungoc [Thu, 18 Jan 2018 16:12:50 +0000 (16:12 +0000)]
JAL-2810 JAL-2886 i18n
gmungoc [Thu, 18 Jan 2018 14:54:49 +0000 (14:54 +0000)]
JAL-2679 update query id to actual case of retrieved gene
gmungoc [Wed, 17 Jan 2018 11:37:09 +0000 (11:37 +0000)]
JAL-2679 case-insensitive comparison of query and retrieved accession
gmungoc [Tue, 16 Jan 2018 16:27:19 +0000 (16:27 +0000)]
JAL-2679 use object_type=Transcript for lookup of Parent for Protein
kiramt [Fri, 12 Jan 2018 11:37:03 +0000 (11:37 +0000)]
JAL-2886 trivial unit test fix
kiramt [Thu, 11 Jan 2018 17:28:29 +0000 (17:28 +0000)]
Merge remote-tracking branch 'origin/task/JAL-2662' into develop
Conflicts:
benchmarking/README
kiramt [Thu, 11 Jan 2018 14:53:00 +0000 (14:53 +0000)]
JAL-2662 Updated README
gmungoc [Wed, 10 Jan 2018 15:20:56 +0000 (15:20 +0000)]
JAL-1793 update spike branch to latest
gmungoc [Wed, 10 Jan 2018 15:17:53 +0000 (15:17 +0000)]
JAL-2791 ignore feature type visibility in getColor()
gmungoc [Tue, 9 Jan 2018 16:53:15 +0000 (16:53 +0000)]
JAL-2843 test roundtrip of feature colours and filters to Jalview project
gmungoc [Tue, 9 Jan 2018 16:28:11 +0000 (16:28 +0000)]
JAL-2843 unit tests for writing filters to Jalview features file
gmungoc [Tue, 9 Jan 2018 15:40:52 +0000 (15:40 +0000)]
JAL-2843 unit tests for Save/Load colours and filters as XML
gmungoc [Tue, 9 Jan 2018 15:39:53 +0000 (15:39 +0000)]
JAL-2808 small tweaks to api / Javadoc
gmungoc [Mon, 8 Jan 2018 14:52:53 +0000 (14:52 +0000)]
JAL-2069 fix setting initial value of slider from threshold
gmungoc [Thu, 14 Dec 2017 16:34:01 +0000 (16:34 +0000)]
JAL-2843 missed Castor class
gmungoc [Thu, 14 Dec 2017 16:33:00 +0000 (16:33 +0000)]
JAL-2843 save/restore colour feature by attribute, and feature filters, to Jalview project
gmungoc [Thu, 14 Dec 2017 15:02:04 +0000 (15:02 +0000)]
JAL-2879 save/restore feature sub-attributes in Jalview project
gmungoc [Thu, 14 Dec 2017 12:46:42 +0000 (12:46 +0000)]
JAL-2843 missed Castor class
gmungoc [Thu, 14 Dec 2017 12:45:32 +0000 (12:45 +0000)]
JAL-2843 and Castor metadata file for latest changes
gmungoc [Thu, 14 Dec 2017 11:25:57 +0000 (11:25 +0000)]
JAL-2843 schema and code changes to save colour by attribute and filters in user colours XML file
gmungoc [Wed, 13 Dec 2017 16:54:31 +0000 (16:54 +0000)]
JAL-2843 add isByAttribute to interface for convenience
gmungoc [Mon, 11 Dec 2017 15:16:05 +0000 (15:16 +0000)]
JAL-2843 add colour by attribute, and no value colour, to features file
gmungoc [Fri, 8 Dec 2017 15:44:34 +0000 (15:44 +0000)]
JAL-2843 example filters added
gmungoc [Fri, 8 Dec 2017 15:21:04 +0000 (15:21 +0000)]
JAL-2843 read/write feature filters from/to Jalview features file
gmungoc [Fri, 8 Dec 2017 15:20:23 +0000 (15:20 +0000)]
JAL-2843 refactor / tidy for feature filter input/output
gmungoc [Fri, 8 Dec 2017 15:17:25 +0000 (15:17 +0000)]
JAL-2843 methods relocated
gmungoc [Fri, 8 Dec 2017 15:13:41 +0000 (15:13 +0000)]
JAL-2843 toStableString, fromString for Jalview features file format
gmungoc [Fri, 8 Dec 2017 15:10:59 +0000 (15:10 +0000)]
JAL-2843 FeatureRenderer.getFeatureFilters returns the map, not a copy
gmungoc [Tue, 5 Dec 2017 09:25:37 +0000 (09:25 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
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 15:53:44 +0000 (15:53 +0000)]
Merge branch 'spikes/mungo' into features/JAL-1793VCF
Conflicts:
src/jalview/ext/htsjdk/HtsContigDb.java
src/jalview/io/vcf/VCFLoader.java
test/jalview/ext/htsjdk/TestHtsContigDb.java
test/jalview/io/vcf/VCFLoaderTest.java
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, 1 Dec 2017 17:01:36 +0000 (17:01 +0000)]
JAL-2835 refactored to extract specific consequence term per transcript and allele
gmungoc [Fri, 1 Dec 2017 15:52:58 +0000 (15:52 +0000)]
JAL-2792 sort feature attributes for output, not for storage
gmungoc [Fri, 1 Dec 2017 15:51:29 +0000 (15:51 +0000)]
JAL-2835 additional sub-terms of sequence_variant added
gmungoc [Thu, 30 Nov 2017 15:20:19 +0000 (15:20 +0000)]
JAL-2850 improved use of htsjdk api to read contig info
gmungoc [Thu, 30 Nov 2017 15:19:40 +0000 (15:19 +0000)]
JAL-1766 additional tests for stub htsjdk wrapper
Jim Procter [Thu, 30 Nov 2017 12:04:15 +0000 (12:04 +0000)]
JAL-2849 release notes
Jim Procter [Thu, 30 Nov 2017 11:34:22 +0000 (11:34 +0000)]
Merge branch 'bug/JAL-2849' into develop
Jim Procter [Thu, 30 Nov 2017 11:34:02 +0000 (11:34 +0000)]
JAL-2849 JAL-2863 file format preferences TODO
Jim Procter [Thu, 30 Nov 2017 11:28:36 +0000 (11:28 +0000)]
JAL-2849 fix
Jim Procter [Tue, 28 Nov 2017 15:18:14 +0000 (15:18 +0000)]
Merge branch 'bug/JAL-2859_uniprottowrongpdbid' into develop
Jim Procter [Tue, 28 Nov 2017 15:06:57 +0000 (15:06 +0000)]
JAL-2740 release notes
Jim Procter [Tue, 28 Nov 2017 14:55:23 +0000 (14:55 +0000)]
Merge branch 'bug/JAL-2740' into develop
Jim Procter [Tue, 28 Nov 2017 14:53:51 +0000 (14:53 +0000)]
JAL-2827 release notes
Jim Procter [Tue, 28 Nov 2017 14:45:15 +0000 (14:45 +0000)]
Merge branch 'bug/JAL-2827' into develop
Jim Procter [Tue, 28 Nov 2017 14:42:00 +0000 (14:42 +0000)]
JAL-2842 release notes
Jim Procter [Tue, 28 Nov 2017 14:24:05 +0000 (14:24 +0000)]
Merge branch 'bug/JAL-2842' into develop
gmungoc [Tue, 28 Nov 2017 10:25:22 +0000 (10:25 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Tue, 28 Nov 2017 09:07:51 +0000 (09:07 +0000)]
JAL-2850 MapList.isToForwardStrand added
Jim Procter [Mon, 27 Nov 2017 22:09:45 +0000 (22:09 +0000)]
JAL-2859 disambiguate with PDB ID if no file path
Jim Procter [Mon, 27 Nov 2017 22:07:07 +0000 (22:07 +0000)]
JAL-2859 failing test demonstrating sequences with pdb without a local file map all get mapped together
Jim Procter [Mon, 27 Nov 2017 18:46:19 +0000 (18:46 +0000)]
JAL-2851 JAL-2858 release notes for 2.10.3b1
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
gmungoc [Mon, 27 Nov 2017 15:21:33 +0000 (15:21 +0000)]
JAL-2850 VCFLoader refactored to load VCF to contig sequences
gmungoc [Fri, 24 Nov 2017 14:50:45 +0000 (14:50 +0000)]
JAL-2808 update spike to latest
gmungoc [Fri, 24 Nov 2017 14:46:42 +0000 (14:46 +0000)]
JAL-2808 refactoring to better handler filter by Score or Label etc
gmungoc [Fri, 24 Nov 2017 14:42:08 +0000 (14:42 +0000)]
JAL-2808 relocate constants for compiler, add COLUMN_COUNT constant
gmungoc [Fri, 24 Nov 2017 14:40:21 +0000 (14:40 +0000)]
JAL-2808 refine FeatureMatcher interface and matcher toString methods
git://source.jalview.org / jalview.git / log