Jim Procter [Thu, 25 Jun 2015 09:56:03 +0000 (10:56 +0100)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
Jim Procter [Wed, 24 Jun 2015 20:51:35 +0000 (21:51 +0100)]
Merge branch 'features/JAL-1370_patchshowunconserved' into develop
Jim Procter [Wed, 24 Jun 2015 15:36:48 +0000 (16:36 +0100)]
JAL-1790 fix: javac.source=1.7 and javac.target=1.7 variables for all javac tasks in build.xml
Jim Procter [Wed, 24 Jun 2015 15:18:12 +0000 (16:18 +0100)]
JAL-653 JAL-1780 JAL-1892 fix jalviewLite compilation
Jim Procter [Wed, 24 Jun 2015 14:11:45 +0000 (15:11 +0100)]
Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into develop
Jim Procter [Wed, 24 Jun 2015 14:09:06 +0000 (15:09 +0100)]
Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into features/JAL-653_JAL-1766_htslib_refseqsupport
Jim Procter [Wed, 24 Jun 2015 13:26:01 +0000 (14:26 +0100)]
JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG
Jim Procter [Tue, 23 Jun 2015 12:26:11 +0000 (13:26 +0100)]
JAL-1780 JAL-653 jim forgot to put the conditional action in!
Jim Procter [Tue, 23 Jun 2015 09:13:52 +0000 (10:13 +0100)]
Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into features/JAL-653_JAL-1766_htslib_refseqsupport
Jim Procter [Tue, 23 Jun 2015 08:48:13 +0000 (09:48 +0100)]
JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refactored test suite with TestNG
Jim Procter [Mon, 22 Jun 2015 18:43:33 +0000 (19:43 +0100)]
JAL-1270 fix logic in stockholm test allowing annotation.description to be equivalent if both are null, or one or both is an empty string, or a whitespace string
Jim Procter [Mon, 22 Jun 2015 18:21:59 +0000 (19:21 +0100)]
JAL-653 JAL-1780 JAL-1140 added RNAML example alignment file
Jim Procter [Mon, 22 Jun 2015 18:21:07 +0000 (19:21 +0100)]
JAL-653 JAL-1780 dropped unnecessary refs
Jim Procter [Mon, 22 Jun 2015 18:12:07 +0000 (19:12 +0100)]
JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses AlignmentI where possible, and allows configuration via Alignment Panel and ExportSettings interface references
Jim Procter [Mon, 22 Jun 2015 17:26:23 +0000 (18:26 +0100)]
JAL-653 JAL-1780 reorder imports
Jim Procter [Fri, 19 Jun 2015 16:45:50 +0000 (17:45 +0100)]
JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfile adopt same pattern as other parsers
Jim Procter [Fri, 19 Jun 2015 16:44:27 +0000 (17:44 +0100)]
JAL-1780 JAL-653 organise imports
Jim Procter [Fri, 19 Jun 2015 15:14:39 +0000 (16:14 +0100)]
JAL-653 JAL-1780 minimise call rate now av.hasHiddenRows is dynamic
Jim Procter [Fri, 19 Jun 2015 15:13:48 +0000 (16:13 +0100)]
JAL-653 JAL-1780 dropped av.setHasHiddenRows() and made av.hasHiddenRows() dynamic rather than a maintained flag
tcofoegbu [Fri, 19 Jun 2015 15:04:33 +0000 (16:04 +0100)]
JAL-1270 test suits import order refactor
Jim Procter [Fri, 19 Jun 2015 15:02:05 +0000 (16:02 +0100)]
JAL-1780 JAL-653 organise imports
tcofoegbu [Fri, 19 Jun 2015 13:04:02 +0000 (14:04 +0100)]
JAL-1270 JUnit to TestNG refactoring
Jim Procter [Thu, 18 Jun 2015 18:07:17 +0000 (19:07 +0100)]
JAL-653 patch broken test code - test still not passing
Jim Procter [Thu, 18 Jun 2015 18:06:56 +0000 (19:06 +0100)]
JAL-653 JAL-1780 JAL-1543 javadoc and comment about further refactoring
Jim Procter [Thu, 18 Jun 2015 18:00:05 +0000 (19:00 +0100)]
JAL-653 JAL-1780 javadoc for FeatureRenderer prior to splitting into model and renderer concerns
Jim Procter [Thu, 18 Jun 2015 17:54:53 +0000 (18:54 +0100)]
JAL-1780 JAL-653 moved AlignExportSettings reference on AlignViewportI to FileParse, use AlignmentViewPanel for getting FeatureRender
Jim Procter [Wed, 17 Jun 2015 20:54:39 +0000 (21:54 +0100)]
JAL-1784 minimise data duplication, and report out of memory errors and other kinds of parsing problems to the user
Jim Procter [Wed, 17 Jun 2015 20:50:15 +0000 (21:50 +0100)]
JAL-1784 refactor parse method to directly parse FileParser input reader stream.
Jim Procter [Wed, 17 Jun 2015 15:42:09 +0000 (16:42 +0100)]
Merge branch 'features/JAL-653_gffalignments' into trial/JAL-1780_JAL-653
Jim Procter [Wed, 17 Jun 2015 15:39:40 +0000 (16:39 +0100)]
Merge branch 'features/JAL-653_gffalignments' into features/JAL-653_JAL-1766_htslib_refseqsupport
Jim Procter [Wed, 17 Jun 2015 15:35:29 +0000 (16:35 +0100)]
Merge branch 'develop' into features/JAL-653_gffalignments
update for incoming changes and finessing against JAL-1641
Jim Procter [Wed, 17 Jun 2015 14:58:48 +0000 (15:58 +0100)]
Merge branch 'develop' into features/JAL-1780_export-settings_flatfile
Jim Procter [Wed, 17 Jun 2015 14:53:41 +0000 (15:53 +0100)]
JAL-1783 add java 1.7 and 1.8 class numbers
Jim Procter [Wed, 17 Jun 2015 10:40:07 +0000 (11:40 +0100)]
Merge branch 'develop' into features/JAL-1780_export-settings_flatfile
tcofoegbu [Wed, 17 Jun 2015 10:22:22 +0000 (11:22 +0100)]
JAL-1780 more support for export setting for flatfile output
tcofoegbu [Wed, 17 Jun 2015 10:16:58 +0000 (11:16 +0100)]
JAL-1780 Export settings for flatfile output
gmungoc [Wed, 17 Jun 2015 08:30:03 +0000 (09:30 +0100)]
JAL-1588 restore ChimeraViewFrame geometry as well
gmungoc [Wed, 17 Jun 2015 07:50:13 +0000 (08:50 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 17 Jun 2015 07:49:34 +0000 (08:49 +0100)]
JAL-1778 reinstated this.ssm to handle 'close all windows' robustly
Jim Procter [Mon, 15 Jun 2015 17:58:55 +0000 (18:58 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 17:52:02 +0000 (18:52 +0100)]
JAL-1665 patch for regression: failing jalview.ws.jabaws.DisorderAnnotExportImport due to different sequence features in original and reimported alignment (originally, sequence features were not available on local sequenceI)
Jim Procter [Mon, 15 Jun 2015 17:39:28 +0000 (18:39 +0100)]
JAL-1775 patch for regression from Anne Menard’s pseudo knot support JAL-1598
Jim Procter [Mon, 15 Jun 2015 16:07:45 +0000 (17:07 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 16:06:51 +0000 (17:06 +0100)]
JAL-1775 patch regression bug when displayChar is null and secondaryStructure contains secondary structure info
Jim Procter [Mon, 15 Jun 2015 15:09:37 +0000 (16:09 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 15:08:47 +0000 (16:08 +0100)]
fix for JAL-1775 (and reorganise imports)
Jim Procter [Mon, 15 Jun 2015 14:24:38 +0000 (15:24 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 13:03:22 +0000 (14:03 +0100)]
JAL-1775 test demonstrating bug
Jim Procter [Mon, 15 Jun 2015 13:03:07 +0000 (14:03 +0100)]
JAL-1775 FileLoader javadoc
Jim Procter [Mon, 15 Jun 2015 13:02:37 +0000 (14:02 +0100)]
Jim Procter [Mon, 15 Jun 2015 12:37:44 +0000 (13:37 +0100)]
Merge branch 'develop' into bug/JAL-1775
gmungoc [Mon, 15 Jun 2015 11:19:54 +0000 (12:19 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 15 Jun 2015 11:18:55 +0000 (12:18 +0100)]
JAL-1778 deregister as a listener when panel closed
Jim Procter [Mon, 15 Jun 2015 10:42:52 +0000 (11:42 +0100)]
JAL-1775 fix broken test due to missing file (RF0031_unfolded).
tcofoegbu [Mon, 15 Jun 2015 10:39:23 +0000 (11:39 +0100)]
JAL-1641 clean up
tcofoegbu [Mon, 15 Jun 2015 10:29:46 +0000 (11:29 +0100)]
JAL-1641 docs for ComplexAlignFile interface
tcofoegbu [Mon, 15 Jun 2015 09:31:04 +0000 (10:31 +0100)]
clean up
tcofoegbu [Fri, 12 Jun 2015 16:52:28 +0000 (17:52 +0100)]
merge
tcofoegbu [Fri, 12 Jun 2015 16:50:02 +0000 (17:50 +0100)]
JAL-1627 removed extra spaces at end of tooltip
tcofoegbu [Fri, 12 Jun 2015 16:43:51 +0000 (17:43 +0100)]
JAL-1641 refactor
Jim Procter [Fri, 12 Jun 2015 15:14:42 +0000 (16:14 +0100)]
JAL-1766 update HTSJDK to Version 1.133
Jim Procter [Thu, 11 Jun 2015 10:52:49 +0000 (11:52 +0100)]
JAL-653 tidy comments
tcofoegbu [Wed, 10 Jun 2015 15:50:03 +0000 (16:50 +0100)]
updated build.xml
gmungoc [Wed, 10 Jun 2015 14:23:52 +0000 (15:23 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 10 Jun 2015 14:23:33 +0000 (15:23 +0100)]
Merge remote-tracking branch
'origin/schema/JAL-1764_structureViewAttribute' into develop
JAL-1764 save structure viewer type in project file
tcofoegbu [Wed, 10 Jun 2015 14:20:04 +0000 (15:20 +0100)]
merge
tcofoegbu [Wed, 10 Jun 2015 14:19:01 +0000 (15:19 +0100)]
JAL-1641 updated applet version
gmungoc [Wed, 10 Jun 2015 10:25:08 +0000 (11:25 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 10 Jun 2015 10:23:17 +0000 (11:23 +0100)]
JAL-1764 save Chimera/Jmol state as separate entries in project Jar
Jim Procter [Wed, 10 Jun 2015 10:19:17 +0000 (11:19 +0100)]
JAL-1764 add structure view type attribute to project schema
tcofoegbu [Tue, 9 Jun 2015 15:03:54 +0000 (16:03 +0100)]
merge commit
tcofoegbu [Tue, 9 Jun 2015 15:01:48 +0000 (16:01 +0100)]
JAL-1488 bug-fix for incorrect start/end position in flatfiles exported from alignments with hidden columns
gmungoc [Mon, 8 Jun 2015 14:05:35 +0000 (15:05 +0100)]
JAl-1421 fix method reflection argument (properly this time)
Jim Procter [Mon, 8 Jun 2015 12:43:17 +0000 (13:43 +0100)]
JAL-1766 basic test to retrieve named sequences from indexed fasta files via HTS library
gmungoc [Mon, 8 Jun 2015 12:29:00 +0000 (13:29 +0100)]
JAL-1421 undid premature 'improvement' of method parameter to interface
Jim Procter [Mon, 8 Jun 2015 10:50:09 +0000 (11:50 +0100)]
JAL-1766 test and buggy implementation of fasta index builder for a FASTA contig database
Jim Procter [Mon, 8 Jun 2015 10:47:44 +0000 (11:47 +0100)]
JAL-1766 added a snapshot build of the htsjdk
Jim Procter [Sun, 7 Jun 2015 18:06:27 +0000 (19:06 +0100)]
JAL-429 remove pointless code from phylip parser
Jim Procter [Sun, 7 Jun 2015 18:04:31 +0000 (19:04 +0100)]
JAL-653 test for GFF file recognition and alignment import
Jim Procter [Sun, 7 Jun 2015 18:03:45 +0000 (19:03 +0100)]
JAL-653 GFF recognition for identifyFile and format adapters
Jim Procter [Sun, 7 Jun 2015 18:01:45 +0000 (19:01 +0100)]
JAL-653 basic GFF3 alignment import wrapper class
Jim Procter [Sat, 6 Jun 2015 17:00:53 +0000 (18:00 +0100)]
JAL-653 make sure dummy sequences created during GFF parsing are actually resolved and annotated
Jim Procter [Sat, 6 Jun 2015 16:59:39 +0000 (17:59 +0100)]
JAL-653 first stab at parsing GFF3 pragmas to support ##fasta
Jim Procter [Sat, 6 Jun 2015 16:58:18 +0000 (17:58 +0100)]
JAL-653 gff version number field
Jim Procter [Sat, 6 Jun 2015 16:57:53 +0000 (17:57 +0100)]
JAL-653 test and testdata for importing GFF3 file with ##fasta pragma
Jim Procter [Sat, 6 Jun 2015 16:56:22 +0000 (17:56 +0100)]
JAL-653 missing imports after rebase
Jim Procter [Sat, 6 Jun 2015 16:54:34 +0000 (17:54 +0100)]
JAL-653 test for SequenceDummy methods
Jim Procter [Sat, 6 Jun 2015 16:46:27 +0000 (17:46 +0100)]
JAL-653 allow a dummy sequence to take on attributes from a fully instantiated sequence via Sequence copy constructor
tcofoegbu [Fri, 5 Jun 2015 16:12:41 +0000 (17:12 +0100)]
Merge branch 'bug/JAL-1760_restore-hidden-seqs' into develop
tcofoegbu [Fri, 5 Jun 2015 16:08:15 +0000 (17:08 +0100)]
JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability to retrieve hidden Seqs
Jim Procter [Fri, 5 Jun 2015 15:28:56 +0000 (16:28 +0100)]
Merge branch 'develop' into features/JAL-653_gffalignments
Jim Procter [Fri, 5 Jun 2015 15:27:36 +0000 (16:27 +0100)]
JAL-653 abstract sequence model to support file backed alignment/data views
gmungoc [Fri, 5 Jun 2015 15:26:15 +0000 (16:26 +0100)]
JAL-1752 structure highlight scoped to only its mapped sequences
gmungoc [Fri, 5 Jun 2015 14:51:07 +0000 (15:51 +0100)]
JAL-1588 error dialog if Chimera project opened on a m/c w/o Chimera
gmungoc [Fri, 5 Jun 2015 14:15:01 +0000 (15:15 +0100)]
JAL-1622 fix bug computing superposition + associated refactorings
gmungoc [Fri, 5 Jun 2015 14:09:25 +0000 (15:09 +0100)]
JAL-1746 return empty string rather than null in getStateInfo
gmungoc [Fri, 5 Jun 2015 13:59:21 +0000 (14:59 +0100)]
JAL-1622 Chimera command timeout increased to 5 secs (+minor changes)
gmungoc [Fri, 5 Jun 2015 13:52:10 +0000 (14:52 +0100)]
JAL-1622 duplicate assignment removed (no functional change)
gmungoc [Fri, 5 Jun 2015 13:49:22 +0000 (14:49 +0100)]
JAL-1753 JAL-1596 asynchronous command to Chimera (with progress update)
gmungoc [Fri, 5 Jun 2015 13:43:00 +0000 (14:43 +0100)]
JAL-1622 code tidy only, no functional change
git://source.jalview.org / jalview.git / log