kiramt [Mon, 29 Jan 2018 11:46:44 +0000 (11:46 +0000)]
JAL-2759 remove redundant hiddenColumns.clear()
kiramt [Mon, 29 Jan 2018 10:35:47 +0000 (10:35 +0000)]
JAL-2759 Tidy
kiramt [Mon, 29 Jan 2018 10:21:58 +0000 (10:21 +0000)]
JAL-2759 make a new cursor instead of resetting, updated after review
kiramt [Mon, 29 Jan 2018 09:35:15 +0000 (09:35 +0000)]
JAL-2759 Fix unintended type change
gmungoc [Mon, 29 Jan 2018 09:24:38 +0000 (09:24 +0000)]
JAL-2743 recoded EnsemblLookup without lambda expressions for parsing response
Jim Procter [Fri, 26 Jan 2018 18:30:48 +0000 (18:30 +0000)]
Merge branch 'releases/Release_2_10_3_Branch' into bugs/JAL-2780_JAL-2781_pdbnegativenums
kiramt [Fri, 26 Jan 2018 16:32:50 +0000 (16:32 +0000)]
JAL-2778 try another way to draw sequences with reduced synchronisation
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
kiramt [Fri, 26 Jan 2018 10:27:46 +0000 (10:27 +0000)]
JAL-2778 tightened up use of resetAlignmentDims
kiramt [Thu, 25 Jan 2018 17:09:16 +0000 (17:09 +0000)]
JAL-2778 Tidy
kiramt [Thu, 25 Jan 2018 14:06:52 +0000 (14:06 +0000)]
JAL-2778 added JAL-2851 fix to avoid confusion
kiramt [Thu, 25 Jan 2018 13:49:36 +0000 (13:49 +0000)]
JAL-2778 Reinstate id width adjuster
Jim Procter [Wed, 24 Jan 2018 07:37:42 +0000 (07:37 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 14:11:15 +0000 (14:11 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 12:04:09 +0000 (12:04 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 15:27:07 +0000 (15:27 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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
kiramt [Mon, 22 Jan 2018 14:44:09 +0000 (14:44 +0000)]
JAL-2579 Moved locateVisibleStartOfSequence to Sequence (refactored)
kiramt [Mon, 22 Jan 2018 10:06:25 +0000 (10:06 +0000)]
JAL-2759 Various minor HiddenColumns updates after review
kiramt [Fri, 19 Jan 2018 16:25:16 +0000 (16:25 +0000)]
JAL-2759 Changes to getVisibleSequenceStrings after review
kiramt [Fri, 19 Jan 2018 12:36:12 +0000 (12:36 +0000)]
JAL-2759 Moved propagateInsertions out of HiddenColumns
kiramt [Fri, 19 Jan 2018 07:51:31 +0000 (07:51 +0000)]
JAL-2759 Update to getVisibleStartAndEndIndex after review
kiramt [Thu, 18 Jan 2018 16:30:45 +0000 (16:30 +0000)]
JAL-2759 change subtractVisibleColumns and removal of reverse iterator
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
kiramt [Thu, 18 Jan 2018 14:12:08 +0000 (14:12 +0000)]
JAL-2759 Updated test
kiramt [Thu, 18 Jan 2018 09:07:41 +0000 (09:07 +0000)]
JAL-2759 unit tests (incomplete)
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 [Tue, 16 Jan 2018 15:45:59 +0000 (15:45 +0000)]
JAL-2759 setup hideBitSet over range for hideInsertions
gmungoc [Tue, 16 Jan 2018 12:20:18 +0000 (12:20 +0000)]
JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam configurable
gmungoc [Tue, 16 Jan 2018 12:19:24 +0000 (12:19 +0000)]
JAL-1270 JAL-2885 clear properties before load
kiramt [Tue, 16 Jan 2018 12:15:07 +0000 (12:15 +0000)]
JAL-2759 Unit test for PopupMenu hideInsertions code
kiramt [Tue, 16 Jan 2018 09:41:34 +0000 (09:41 +0000)]
JAL-2759 Moved alignment annotation code out of HiddenColumns
kiramt [Tue, 16 Jan 2018 08:10:28 +0000 (08:10 +0000)]
JAL-2759 Replaced StringBuffer with StringBuilder; after review
kiramt [Mon, 15 Jan 2018 16:27:22 +0000 (16:27 +0000)]
JAL-2759 More compact iterator usage; after review
kiramt [Mon, 15 Jan 2018 14:54:35 +0000 (14:54 +0000)]
JAL-2759 First pass instantiate hiddenColumns collection in constructor
kiramt [Mon, 15 Jan 2018 13:40:39 +0000 (13:40 +0000)]
JAL-2759 getVisContigsIterator returns VisibleContigsIterator
kiramt [Mon, 15 Jan 2018 13:38:56 +0000 (13:38 +0000)]
JAL-2759 Rename hideInsertionsFor to hideList, after review
kiramt [Mon, 15 Jan 2018 13:32:35 +0000 (13:32 +0000)]
JAL-2759 Refactor of hideInsertionsFor after review
kiramt [Mon, 15 Jan 2018 11:59:40 +0000 (11:59 +0000)]
JAL-2759 Simplified HiddenColumns constructor after review
kiramt [Mon, 15 Jan 2018 11:59:14 +0000 (11:59 +0000)]
JAL-2759 Changed VisibleColsCollection constructor to take HiddenColumns
kiramt [Mon, 15 Jan 2018 11:46:07 +0000 (11:46 +0000)]
JAL-2759 Minor doc and naming changes
kiramt [Mon, 15 Jan 2018 10:42:48 +0000 (10:42 +0000)]
JAL-2759 Updated absoluteToVisibleColumn doc (prev findColumnPosition)
kiramt [Mon, 15 Jan 2018 10:38:29 +0000 (10:38 +0000)]
JAL-2759 Rename findColumnPosition and adjustForHiddenColumns (yay!)
kiramt [Mon, 15 Jan 2018 10:28:27 +0000 (10:28 +0000)]
JAL-2759 Renamed BoundedHiddenColsIterator to HiddenColsIterator
kiramt [Mon, 15 Jan 2018 10:11:10 +0000 (10:11 +0000)]
JAL-2759 Comments and renaming for has(Many)HiddenColumns after review
kiramt [Mon, 15 Jan 2018 09:57:22 +0000 (09:57 +0000)]
JAL-2759 Tidy up javadoc and naming in HiddenColumnsCursor after review
kiramt [Mon, 15 Jan 2018 09:42:08 +0000 (09:42 +0000)]
JAL-2759 Updated HiddenColumnsTest::testIsVisible following review
kiramt [Mon, 15 Jan 2018 09:38:00 +0000 (09:38 +0000)]
JAL-2759 Update to getHiddenBoundaryRight + unit test after review
kiramt [Mon, 15 Jan 2018 07:51:08 +0000 (07:51 +0000)]
JAL-2759 Updates following review
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 15:30:27 +0000 (15:30 +0000)]
JAL-2865 unhelpful System.gc() calls removed
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()
kiramt [Wed, 10 Jan 2018 09:21:54 +0000 (09:21 +0000)]
JAL-797: Added keybindings so that ctrl- or cmd-W close internal frames
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
Jim Procter [Tue, 19 Dec 2017 22:39:22 +0000 (11:39 +1300)]
JAL-2880 disabled non-functional test - Jmol parser does not have proper association mechanism to bind PDB data to derived annotation.
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
Jim Procter [Fri, 1 Dec 2017 16:59:03 +0000 (16:59 +0000)]
Merge branch 'develop' into bugs/JAL-2780_JAL-2781_pdbnegativenums
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
Jim Procter [Thu, 30 Nov 2017 15:21:02 +0000 (15:21 +0000)]
JAL-2858 tweak OSX specific jar resources in JNLP
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 12:09:58 +0000 (12:09 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Thu, 30 Nov 2017 12:04:15 +0000 (12:04 +0000)]
JAL-2849 release notes
git://source.jalview.org / jalview.git / log