Jim Procter [Wed, 21 Mar 2018 16:43:47 +0000 (16:43 +0000)]
Merge branch 'feature/JAL-2909bamfiles_features' into features/JAL-2909_bamImport2_11
Jim Procter [Wed, 21 Mar 2018 16:35:39 +0000 (16:35 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Jim Procter [Wed, 21 Mar 2018 16:32:59 +0000 (16:32 +0000)]
Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Mar 2018 16:32:34 +0000 (16:32 +0000)]
JAL-2754 clean up proguard path spec and config variables
gmungoc [Fri, 27 Oct 2017 11:20:28 +0000 (12:20 +0100)]
JAL-2754 renamed proguard.jar to include version number
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 09:52:05 +0000 (10:52 +0100)]
JAL-2754 update to specify Java 1.8(+)
gmungoc [Fri, 6 Oct 2017 08:39:02 +0000 (09:39 +0100)]
JAL-2754 update to Java 1.8
Jim Procter [Tue, 20 Mar 2018 16:34:10 +0000 (16:34 +0000)]
JAL-2909 separate reverse and forward strand reads. fix subtle bug in handling inserts. gross hack & WIP to try to get reference sequences added to alignment (doesn’t work - see FIXME)
Jim Procter [Tue, 20 Mar 2018 16:29:25 +0000 (16:29 +0000)]
JAL-2909 recognise .bam extension in URL and allow location spec as suffix - e.g. file:///…mybam.bam#2:121212-150000
gmungoc [Fri, 16 Mar 2018 15:15:49 +0000 (15:15 +0000)]
JAL-2679 getGeneId() now uses the same pattern as getGeneLoci, getSpecies
gmungoc [Fri, 16 Mar 2018 15:03:11 +0000 (15:03 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop
Conflicts:
src/jalview/ext/ensembl/EnsemblLookup.java
gmungoc [Fri, 16 Mar 2018 14:47:12 +0000 (14:47 +0000)]
JAL-2922 update FeatureRenderer and repaint feature settings after Invert Selection
gmungoc [Fri, 16 Mar 2018 09:59:01 +0000 (09:59 +0000)]
Merge branch 'bug/JAL-2865removeGC' into develop
gmungoc [Thu, 15 Mar 2018 16:24:06 +0000 (16:24 +0000)]
JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
gmungoc [Wed, 14 Mar 2018 16:36:29 +0000 (16:36 +0000)]
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db source'
gmungoc [Wed, 14 Mar 2018 14:41:14 +0000 (14:41 +0000)]
JAL-2679 reinstating changes lost in VCF merge
Conflicts:
src/jalview/ext/ensembl/EnsemblLookup.java
gmungoc [Wed, 14 Mar 2018 14:41:14 +0000 (14:41 +0000)]
JAL-2679 reinstating changes lost in VCF merge
Jim Procter [Wed, 14 Mar 2018 08:53:17 +0000 (08:53 +0000)]
JAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4 release notes
gmungoc [Tue, 13 Mar 2018 16:22:55 +0000 (16:22 +0000)]
JAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH)
gmungoc [Thu, 8 Mar 2018 14:06:44 +0000 (14:06 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges/JAL-2906_update2_11_from_2_10_4
gmungoc [Thu, 8 Mar 2018 14:05:51 +0000 (14:05 +0000)]
JAL-2885 tests updated for code changes
gmungoc [Thu, 8 Mar 2018 11:29:11 +0000 (11:29 +0000)]
JAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation
Jim Procter [Wed, 7 Mar 2018 14:40:59 +0000 (14:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
check carefully that JAL-2885 (configurable Ensembl/Genomes Endpoints) functionality is still present
gmungoc [Wed, 7 Mar 2018 12:05:23 +0000 (12:05 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 12:04:58 +0000 (12:04 +0000)]
JAL-2922 [2] not [1] for Boolean column of table
gmungoc [Wed, 7 Mar 2018 11:53:57 +0000 (11:53 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:53:26 +0000 (11:53 +0000)]
JAL-2922 i18n and bespoke handler for Invert Selection
gmungoc [Wed, 7 Mar 2018 11:30:09 +0000 (11:30 +0000)]
Merge branch 'bug/JAL-2924nullTooltip' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:27:57 +0000 (11:27 +0000)]
JAL-2926 fix copy group consensus (and paste sequence with space in name)
gmungoc [Wed, 7 Mar 2018 11:27:20 +0000 (11:27 +0000)]
JAL-2925 handle empty annotation when copying group consensus
gmungoc [Wed, 7 Mar 2018 11:04:42 +0000 (11:04 +0000)]
JAL-2913 use FIGURE_USERIDWIDTH for fixed id width property
Jim Procter [Sat, 3 Mar 2018 11:17:34 +0000 (11:17 +0000)]
JAL-2909 soft clip and handclap features (should use SO terms for ‘Clipped’)
Jim Procter [Fri, 2 Mar 2018 10:35:28 +0000 (10:35 +0000)]
JAL-2909 add sequence feature for quality
Jim Procter [Fri, 2 Mar 2018 10:34:27 +0000 (10:34 +0000)]
JAL-2909 add sequence feature for insertions
kiramt [Thu, 1 Mar 2018 13:28:43 +0000 (13:28 +0000)]
JAL-2909 Updated tests
kiramt [Thu, 1 Mar 2018 11:50:26 +0000 (11:50 +0000)]
JAL-2909 fixed another insertions bug
kiramt [Wed, 28 Feb 2018 19:43:55 +0000 (19:43 +0000)]
JAL-2909 Fixed a bug in the insertions code
gmungoc [Wed, 28 Feb 2018 17:54:15 +0000 (17:54 +0000)]
JAL-2924 no tooltip over null annotation positions
kiramt [Wed, 28 Feb 2018 16:39:49 +0000 (16:39 +0000)]
JAL-2909 Gaps at start of reads only from start of alignment window
kiramt [Wed, 28 Feb 2018 15:47:06 +0000 (15:47 +0000)]
JAL-2909 Wire up coordinates dialog with bam file reader
Jim Procter [Wed, 28 Feb 2018 10:32:14 +0000 (10:32 +0000)]
Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2_10_4_Branch
Jim Procter [Tue, 27 Feb 2018 16:18:59 +0000 (16:18 +0000)]
JAL-2759 release notes for 2.10.4
Jim Procter [Tue, 27 Feb 2018 11:16:41 +0000 (11:16 +0000)]
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
Jim Procter [Tue, 27 Feb 2018 11:07:48 +0000 (11:07 +0000)]
fix for JAL-2922 - update states all at once and then refresh
kiramt [Tue, 27 Feb 2018 09:16:13 +0000 (09:16 +0000)]
JAL-2909 Tidy up bam file cigar code
kiramt [Mon, 26 Feb 2018 10:43:10 +0000 (10:43 +0000)]
JAL-2909 Bam file parsing with insertions, first pass
kiramt [Mon, 26 Feb 2018 10:41:51 +0000 (10:41 +0000)]
JAL-2909 Changes to htsjdk import control
kiramt [Mon, 26 Feb 2018 10:41:27 +0000 (10:41 +0000)]
JAL-2909 Cigar parsing tests
Jim Procter [Mon, 26 Feb 2018 10:13:30 +0000 (10:13 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 26 Feb 2018 10:12:45 +0000 (10:12 +0000)]
JAL-984 remove all references to idwidth.gif - in build.xml too :)
Jim Procter [Fri, 23 Feb 2018 16:54:28 +0000 (16:54 +0000)]
JAL-2885 release notes
Jim Procter [Fri, 23 Feb 2018 16:01:42 +0000 (16:01 +0000)]
Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 23 Feb 2018 11:40:15 +0000 (11:40 +0000)]
JAL-2885 xfam https
Jim Procter [Fri, 23 Feb 2018 11:39:34 +0000 (11:39 +0000)]
JAL-2885 XFAM_DOMAIN->XFAM_BASEURL
Jim Procter [Fri, 23 Feb 2018 11:35:43 +0000 (11:35 +0000)]
JAL-2885 Ensembl* -> https
Jim Procter [Fri, 23 Feb 2018 11:33:41 +0000 (11:33 +0000)]
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
Jim Procter [Fri, 23 Feb 2018 11:24:03 +0000 (11:24 +0000)]
JAL-2885 renamed base URL getter from getDomain..
Jim Procter [Thu, 22 Feb 2018 15:15:35 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 15:14:46 +0000 (15:14 +0000)]
JAL-984 ID width adjuster needs to be white !
Jim Procter [Thu, 22 Feb 2018 15:05:36 +0000 (15:05 +0000)]
JAL-2666 release notes
Jim Procter [Thu, 22 Feb 2018 14:48:58 +0000 (14:48 +0000)]
Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:34:44 +0000 (14:34 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:34:23 +0000 (14:34 +0000)]
JAL-984 remove all references to idwidth.gif and use int constants in place of width/height of image when switching between margin adjustment active/inactive mouse cursor
Jim Procter [Thu, 22 Feb 2018 14:16:26 +0000 (14:16 +0000)]
JAL-2906 typo fixes
Jim Procter [Thu, 22 Feb 2018 14:15:19 +0000 (14:15 +0000)]
JAL-984 release notes
Jim Procter [Thu, 22 Feb 2018 14:08:47 +0000 (14:08 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:08:15 +0000 (14:08 +0000)]
JAL-294 remove unneeded paint() method
Jim Procter [Thu, 22 Feb 2018 14:07:58 +0000 (14:07 +0000)]
JAL-984 remove commented/unnecessary if clause
Jim Procter [Wed, 21 Feb 2018 17:40:04 +0000 (17:40 +0000)]
JAL-2906 release notes for 2.10.4
Jim Procter [Wed, 21 Feb 2018 17:19:01 +0000 (17:19 +0000)]
Merge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Feb 2018 16:28:31 +0000 (16:28 +0000)]
JAL-2778 reinstate transparent windows to avoid ugly borders on OSX
kiramt [Wed, 21 Feb 2018 14:15:38 +0000 (14:15 +0000)]
JAL-2909 Partial insertions
kiramt [Wed, 21 Feb 2018 09:28:40 +0000 (09:28 +0000)]
JAL-2778 Adjust cursor changes in overview panel
kiramt [Wed, 21 Feb 2018 08:00:35 +0000 (08:00 +0000)]
JAL-2778 Revert back to old synchronisation
kiramt [Tue, 20 Feb 2018 16:37:44 +0000 (16:37 +0000)]
JAL-2909 Modified classpath
kiramt [Tue, 20 Feb 2018 16:37:01 +0000 (16:37 +0000)]
JAL-2909 Insertions almost
Jim Procter [Tue, 20 Feb 2018 13:40:41 +0000 (13:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
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
Jim Procter [Tue, 20 Feb 2018 09:02:56 +0000 (09:02 +0000)]
Merge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums' into releases/Release_2_10_4_Branch
kiramt [Fri, 16 Feb 2018 13:15:40 +0000 (13:15 +0000)]
JAL-2909 Read in a bam file - but strand/location unaware
kiramt [Fri, 16 Feb 2018 10:16:28 +0000 (10:16 +0000)]
JAL-2909 Removed buggy CIGAR parsing code which was not used
Jim Procter [Thu, 15 Feb 2018 15:52:11 +0000 (15:52 +0000)]
Merge branch 'develop' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 15 Feb 2018 15:51:48 +0000 (15:51 +0000)]
JAL-2906 bump release version and cut new release note entry
Jim Procter [Tue, 13 Feb 2018 16:16:04 +0000 (16:16 +0000)]
JAL-2780 scan all test IDs before testing and reporting test failures - currently failing for 4im2 and Resnum==0 (seq pos 0)
Jim Procter [Tue, 13 Feb 2018 16:15:12 +0000 (16:15 +0000)]
JAL-2780 SequenceI.findFeatures takes column numbers in base 1…
Jim Procter [Tue, 13 Feb 2018 15:35:41 +0000 (15:35 +0000)]
JAL-2780 JAL-2781 don’t create a mapping if sequence position was not assigned but still keep track of ‘unobserved’ counts for bookkeeping
Jim Procter [Tue, 13 Feb 2018 15:34:22 +0000 (15:34 +0000)]
JAL-2780 JAL-2781 only create a mapping entry or write a character to the ‘mapped sequence’ for observed residues regardless of to/from coordinate frames
Jim Procter [Tue, 13 Feb 2018 15:33:16 +0000 (15:33 +0000)]
JAL-2781 JAL-2780 include sequence start number when computing position in PDB sequence when mapping from PDB to PDB
Jim Procter [Tue, 13 Feb 2018 15:31:35 +0000 (15:31 +0000)]
JAL-2781 ensure Trim is disabled before test starts
Jim Procter [Tue, 13 Feb 2018 15:28:21 +0000 (15:28 +0000)]
JAL-2781 refactor ‘trim retrieved sequence’ preference key to string constant for reuse in tests
Jim Procter [Tue, 13 Feb 2018 13:48:23 +0000 (13:48 +0000)]
JAL-2781 null local siftsClient variable if exception occurs (probably not needed but clearer this way ?)
Jim Procter [Tue, 13 Feb 2018 13:47:37 +0000 (13:47 +0000)]
JAL-2781 refactor StructureSelectionManager.siftsClient to local variable in computeMapping
Jim Procter [Tue, 13 Feb 2018 13:46:26 +0000 (13:46 +0000)]
JAL-2781 FIXME: value of sourceType parameter always overwritten
Jim Procter [Tue, 13 Feb 2018 13:45:28 +0000 (13:45 +0000)]
JAL-2781 refactor possibly non-functional ‘extract secondary structure’ logic out of computeMapping
Jim Procter [Tue, 13 Feb 2018 13:44:30 +0000 (13:44 +0000)]
JAL-2781 tidy up comments on getMapping/computeMapping
Jim Procter [Tue, 13 Feb 2018 12:50:40 +0000 (12:50 +0000)]
JAL-2781 report exactly which residues do not receive RESNUM annotation from associated structure data
Jim Procter [Tue, 13 Feb 2018 12:49:25 +0000 (12:49 +0000)]
JAL-2905 added additional jvmarg for testng task conditional on the JVM identifying as java.version==9
Jim Procter [Mon, 12 Feb 2018 17:13:50 +0000 (17:13 +0000)]
JAL-2780 JAL-2781 extra column in mapping array
git://source.jalview.org / jalview.git / log