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 14:53:41 +0000 (15:53 +0100)]
JAL-1783 add java 1.7 and 1.8 class numbers
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
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)
gmungoc [Mon, 8 Jun 2015 12:29:00 +0000 (13:29 +0100)]
JAL-1421 undid premature 'improvement' of method parameter to interface
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
gmungoc [Fri, 5 Jun 2015 12:54:18 +0000 (13:54 +0100)]
JAL-1749 correcting snafu in last commit
Jim Procter [Thu, 19 Feb 2015 15:23:47 +0000 (15:23 +0000)]
JAL-653 refactor sequence interface to separate concrete sequence data methods from sequence metadata methods & containers
Jim Procter [Thu, 19 Feb 2015 15:22:36 +0000 (15:22 +0000)]
JAL-845 jim @mungo: should this be in a package local to jalview.analysis.Dna ?
Jim Procter [Thu, 19 Feb 2015 15:21:30 +0000 (15:21 +0000)]
JAL-1551 formatting
Jim Procter [Thu, 19 Feb 2015 15:20:51 +0000 (15:20 +0000)]
JAL-653 set the warningMessage for the file source to allow the GUI to report problems if necessary.
Jim Procter [Thu, 19 Feb 2015 15:20:14 +0000 (15:20 +0000)]
JAL-653 GFF attributes parsing mechanism, with first attempt at processing exonerate's 'similarity' features as cDNA/protein mappings
Jim Procter [Thu, 19 Feb 2015 15:12:04 +0000 (15:12 +0000)]
JAL-653 trim initial tab in sequence feature ATTRIBUTES
Jim Procter [Thu, 19 Feb 2015 15:11:12 +0000 (15:11 +0000)]
JAL-653 allow dummy sequences to be created if a sequence ID is not found in the dataset
Jim Procter [Thu, 19 Feb 2015 15:07:55 +0000 (15:07 +0000)]
JAL-1551 formatting
Jim Procter [Thu, 19 Feb 2015 15:01:35 +0000 (15:01 +0000)]
JAL-653 convenience method to resolve strand attribute for feature
Jim Procter [Thu, 19 Feb 2015 15:00:03 +0000 (15:00 +0000)]
JAL-1115 JAL-653 partial introduction of List interface for sequence matcher
Jim Procter [Thu, 19 Feb 2015 14:57:01 +0000 (14:57 +0000)]
JAL-653 JAL-966 TODO and avoid NPE when desktop instance unavailable
Jim Procter [Thu, 19 Feb 2015 14:55:44 +0000 (14:55 +0000)]
JAL-653 codon frames go on the dataset
Jim Procter [Thu, 19 Feb 2015 14:55:10 +0000 (14:55 +0000)]
JAL-653 refactored exonerate full output to separate text file, leaving gffv2 fragment for first testcase
Jim Procter [Wed, 18 Feb 2015 12:18:46 +0000 (12:18 +0000)]
JAL-653 JAL-845 test to check exonerate cDNA-Protein mappings import as GFF3
Jim Procter [Wed, 18 Feb 2015 11:14:26 +0000 (11:14 +0000)]
JAL-1482 JAL-653 refactor feature file import code to alignview controller
Jim Procter [Wed, 18 Feb 2015 11:08:00 +0000 (11:08 +0000)]
JAL-1482 refactor setTableData to more sensible name for feature settings api
Jim Procter [Tue, 17 Feb 2015 18:40:35 +0000 (18:40 +0000)]
JAL-1551 formatting
gmungoc [Thu, 4 Jun 2015 15:29:40 +0000 (16:29 +0100)]
Clear status bar message when initialisation complete
gmungoc [Thu, 4 Jun 2015 15:09:30 +0000 (16:09 +0100)]
JAL-1750 small tidy of AlignSeq.printMapping (+Junit)
gmungoc [Thu, 4 Jun 2015 14:40:27 +0000 (15:40 +0100)]
JAL-1544 spelling in javadoc only
gmungoc [Thu, 4 Jun 2015 14:39:29 +0000 (15:39 +0100)]
JAL-1622 code tidy (+Junit) of collateForPdb()
gmungoc [Thu, 4 Jun 2015 14:07:41 +0000 (15:07 +0100)]
JAL-1747 close all windows on Quit (+small bug fix)
gmungoc [Thu, 4 Jun 2015 13:43:53 +0000 (14:43 +0100)]
toString method added to aid viewing in the debugger
gmungoc [Thu, 4 Jun 2015 13:43:12 +0000 (14:43 +0100)]
JAL-1270 testToString added
gmungoc [Thu, 4 Jun 2015 13:37:13 +0000 (14:37 +0100)]
JAL-1750 View Mapping scoped to that viewer's mappings only
gmungoc [Thu, 4 Jun 2015 13:08:04 +0000 (14:08 +0100)]
JAL-1743 new Chimera menu option to 'fit to window'
gmungoc [Thu, 4 Jun 2015 13:01:27 +0000 (14:01 +0100)]
JAL-1743 View Chain sub-menu now being populated
gmungoc [Thu, 4 Jun 2015 12:53:21 +0000 (13:53 +0100)]
JAL-1753 statusPanel added (for ProgressBar); 'Fit to Window' menu
option added
gmungoc [Thu, 4 Jun 2015 12:40:55 +0000 (13:40 +0100)]
JAL-1753 ChimeraViewFrame hosts its own ProgressBar
gmungoc [Thu, 4 Jun 2015 11:05:55 +0000 (12:05 +0100)]
JAL-1742 don't offer to align another chain to the same structure
gmungoc [Thu, 4 Jun 2015 10:51:47 +0000 (11:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jun 2015 10:51:28 +0000 (11:51 +0100)]
JAL-1757 match only first altloc CA in PDB structure for superposition
tcofoegbu [Thu, 4 Jun 2015 10:45:31 +0000 (11:45 +0100)]
JAL-1641 added some JSON libraries to appletlib
tcofoegbu [Thu, 4 Jun 2015 10:20:42 +0000 (11:20 +0100)]
clean up
tcofoegbu [Thu, 4 Jun 2015 10:12:03 +0000 (11:12 +0100)]
JAL-1756 fix failed test as a result of runing the BioJS updater from a new thread
gmungoc [Thu, 4 Jun 2015 10:07:28 +0000 (11:07 +0100)]
JAL-1421 generic collections in MCView package (+unit tests)
tcofoegbu [Thu, 4 Jun 2015 09:52:06 +0000 (10:52 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Thu, 4 Jun 2015 09:42:08 +0000 (10:42 +0100)]
JAL-1756 bug-fix
git://source.jalview.org / jalview.git / log