gmungoc [Tue, 22 Dec 2015 09:21:22 +0000 (09:21 +0000)]
JAL-653 realise virtual mappings and align when adding sequences
gmungoc [Tue, 22 Dec 2015 09:15:40 +0000 (09:15 +0000)]
JAL-391 new Calculate options to Reverse, Reverse Complement nucleotide
gmungoc [Tue, 22 Dec 2015 09:14:08 +0000 (09:14 +0000)]
JAL-653 AlignedCodonFrame collections changed from Set to List
gmungoc [Tue, 22 Dec 2015 09:11:48 +0000 (09:11 +0000)]
JAL-653 set showSequenceFeatures=true on loading a FeaturesSourceI
gmungoc [Tue, 22 Dec 2015 09:10:07 +0000 (09:10 +0000)]
JAL-653 GFF new/refactored helper classes
gmungoc [Tue, 22 Dec 2015 09:03:03 +0000 (09:03 +0000)]
JAL-653 AlignedCodonFrame internal refactor, merge ranges with
MapList.addMapList
gmungoc [Tue, 22 Dec 2015 08:58:50 +0000 (08:58 +0000)]
JAL-653 hold AlignedCodonFrame collections as list rather than set
gmungoc [Thu, 3 Dec 2015 16:27:57 +0000 (16:27 +0000)]
JAL-653 code tidy / tests for 'realise gff mappings'
gmungoc [Thu, 3 Dec 2015 16:26:51 +0000 (16:26 +0000)]
JAL-653 handle reverse strand mapping in SearchResults matches
gmungoc [Thu, 3 Dec 2015 16:26:08 +0000 (16:26 +0000)]
JAL-653 mappings always reside on the dataset alignment if there is one
gmungoc [Thu, 3 Dec 2015 14:46:53 +0000 (14:46 +0000)]
JAL-653 handle reverse strand mappings also
gmungoc [Mon, 30 Nov 2015 10:05:57 +0000 (10:05 +0000)]
JAL-1421 generics loop syntax; 'bug?' comment added
gmungoc [Mon, 30 Nov 2015 10:04:40 +0000 (10:04 +0000)]
JAL-653 test for 'resolving GFF mappings to sequences' (wip)
gmungoc [Mon, 30 Nov 2015 10:03:15 +0000 (10:03 +0000)]
JAL-653 small comment change only
gmungoc [Mon, 30 Nov 2015 09:51:08 +0000 (09:51 +0000)]
JAL-652 refactored to remove one method
gmungoc [Mon, 30 Nov 2015 09:33:36 +0000 (09:33 +0000)]
JAL-653 (experimental) 'realise' dummy sequences in add alignment
gmungoc [Mon, 30 Nov 2015 09:31:51 +0000 (09:31 +0000)]
JAL-1980 check for null alignment; JAL-1551 @Override's added
gmungoc [Mon, 30 Nov 2015 09:30:20 +0000 (09:30 +0000)]
JAL-653 (experimental) methods to resolve dummy to real sequence
gmungoc [Mon, 30 Nov 2015 09:28:43 +0000 (09:28 +0000)]
JAL-1270 constructor test added
gmungoc [Mon, 30 Nov 2015 09:27:47 +0000 (09:27 +0000)]
JAL-653 getStrand javadoc/refactor/test
gmungoc [Mon, 30 Nov 2015 09:19:11 +0000 (09:19 +0000)]
JAL-1421 use generics JAL-1551 @Override annotations added
gmungoc [Mon, 30 Nov 2015 09:16:49 +0000 (09:16 +0000)]
JAL-1270 constructor tests added, compiler warnings removed
gmungoc [Mon, 30 Nov 2015 09:14:34 +0000 (09:14 +0000)]
JAL-652 further refactoring / tests
gmungoc [Mon, 30 Nov 2015 09:11:48 +0000 (09:11 +0000)]
JAL-652 correct case for test file name
gmungoc [Mon, 30 Nov 2015 09:10:47 +0000 (09:10 +0000)]
JAL-653 MapList constructor merges any contiguous ranges
gmungoc [Mon, 23 Nov 2015 10:16:13 +0000 (10:16 +0000)]
JAL-653 Gff tests moved back in to FeaturesFileTest
gmungoc [Sun, 22 Nov 2015 18:24:26 +0000 (18:24 +0000)]
JAL-653 test for 'groups file' and mixed Jalview/GFF
gmungoc [Sat, 21 Nov 2015 19:33:37 +0000 (19:33 +0000)]
JAL-1968 remove feature links
gmungoc [Sat, 21 Nov 2015 19:24:24 +0000 (19:24 +0000)]
JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3
(partially); feature links option removed
gmungoc [Tue, 17 Nov 2015 10:29:06 +0000 (10:29 +0000)]
JAL-1961 update link to GFF2 spec
Jim Procter [Tue, 10 Nov 2015 15:00:47 +0000 (15:00 +0000)]
JAL-653 added missing pragma string to processing filter
Jim Procter [Thu, 15 Oct 2015 18:35:13 +0000 (19:35 +0100)]
JAL-653 JAL-1766 merge 290b1 - fix erroneous conflicts on test asserts
Jim Procter [Thu, 15 Oct 2015 18:28:27 +0000 (19:28 +0100)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
Jim Procter [Thu, 15 Oct 2015 16:35:18 +0000 (17:35 +0100)]
JAL-1791 remove blanket sign of examples/*.jar
Jim Procter [Thu, 15 Oct 2015 16:27:30 +0000 (17:27 +0100)]
JAL-1791 id rather than name attrib
Jim Procter [Thu, 15 Oct 2015 15:59:31 +0000 (16:59 +0100)]
JAL-1791 sign the applet with/out timestamps
Jim Procter [Thu, 15 Oct 2015 15:28:58 +0000 (16:28 +0100)]
JAL-1791 add explicit proxy for benefit of jalview's build server when timestamping signed jars
Jim Procter [Thu, 15 Oct 2015 13:52:24 +0000 (14:52 +0100)]
JAL-1791 fix ant target dependencies
Jim Procter [Thu, 15 Oct 2015 13:45:06 +0000 (14:45 +0100)]
JAL-1791 make timestamping optional using -Dtimestamp
Jim Procter [Thu, 15 Oct 2015 13:20:38 +0000 (14:20 +0100)]
JAL-1791 add jalview.tsaurl for specifying timestamp server when signing jars
Jim Procter [Thu, 15 Oct 2015 13:20:38 +0000 (14:20 +0100)]
JAL-1791 add jalview.tsaurl for specifying timestamp server when signing jars
Jim Procter [Thu, 15 Oct 2015 13:00:15 +0000 (14:00 +0100)]
Merge branch 'bug/JAL-1923_290b2_group_annots' into develop
Jim Procter [Thu, 15 Oct 2015 12:59:34 +0000 (13:59 +0100)]
JAL-1923 formatting
Jim Procter [Thu, 15 Oct 2015 12:59:22 +0000 (13:59 +0100)]
JAL-1923 add groups to codon-complement and notify annotation update for all linked views
Jim Procter [Thu, 15 Oct 2015 12:58:22 +0000 (13:58 +0100)]
JAL-1923 fix: don’t add group twice
Jim Procter [Thu, 8 Oct 2015 14:47:39 +0000 (15:47 +0100)]
JAL-1684 updated fragment alignment for example and added aligned protein and cDNA
Jim Procter [Thu, 8 Oct 2015 11:11:51 +0000 (12:11 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 8 Oct 2015 11:05:01 +0000 (12:05 +0100)]
JAL-1894 add licensing
tcofoegbu [Thu, 8 Oct 2015 11:02:04 +0000 (12:02 +0100)]
JAL-1912 JAL-1896 release notes updated
Jim Procter [Thu, 8 Oct 2015 10:58:43 +0000 (11:58 +0100)]
JAL-1894 update what's new
Jim Procter [Thu, 8 Oct 2015 10:52:15 +0000 (11:52 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 8 Oct 2015 10:45:07 +0000 (11:45 +0100)]
JAL-1912 JAL-1896 release notes updated
gmungoc [Thu, 8 Oct 2015 10:40:08 +0000 (11:40 +0100)]
JAL-1544 typo fix
Jim Procter [Thu, 8 Oct 2015 10:33:48 +0000 (11:33 +0100)]
JAL-1894 formatting
Jim Procter [Thu, 8 Oct 2015 10:31:24 +0000 (11:31 +0100)]
JAL-1894 organise imports
tcofoegbu [Thu, 8 Oct 2015 10:09:41 +0000 (11:09 +0100)]
merge
Jim Procter [Wed, 7 Oct 2015 21:35:09 +0000 (22:35 +0100)]
JAL-1894 source formatting
Jim Procter [Wed, 7 Oct 2015 21:29:55 +0000 (22:29 +0100)]
JAL-1894 organise imports
Jim Procter [Wed, 7 Oct 2015 21:21:52 +0000 (22:21 +0100)]
JAL-1894 update release date
tcofoegbu [Wed, 7 Oct 2015 16:39:59 +0000 (17:39 +0100)]
JAL-1912 added documentation
Jim Procter [Wed, 7 Oct 2015 11:52:23 +0000 (12:52 +0100)]
JAL-1912 formatting
Jim Procter [Wed, 7 Oct 2015 11:51:59 +0000 (12:51 +0100)]
JAL-1912 javadoc for adjustForAlignment stating current behaviour
Jim Procter [Wed, 7 Oct 2015 11:51:27 +0000 (12:51 +0100)]
JAL-1912 efficiency: look up sequenceMapping once per position and only when sequenceMapping!=null
Jim Procter [Wed, 7 Oct 2015 10:57:37 +0000 (11:57 +0100)]
Merge branch 'features/JAL-1912_biojson-per-sequence-annotation' of source.jalview.org/git/jalview into features/JAL-1912_biojson-per-sequence-annotation
tcofoegbu [Mon, 5 Oct 2015 17:08:09 +0000 (18:08 +0100)]
JAL-1912 house keeping
tcofoegbu [Mon, 5 Oct 2015 16:33:01 +0000 (17:33 +0100)]
JAL-1912 added null check for SequenceMapping variable at the point of reference
gmungoc [Mon, 5 Oct 2015 14:23:31 +0000 (15:23 +0100)]
JAL-1812 set/return currentAlFrame for Groovy in headless mode
Jim Procter [Mon, 5 Oct 2015 12:43:27 +0000 (13:43 +0100)]
Merge branch 'develop' into features/JAL-1912_biojson-per-sequence-annotation
Jim Procter [Mon, 5 Oct 2015 12:01:25 +0000 (13:01 +0100)]
JAL-1894 note about menu option bugfix JAL-1865 JAL-1864 JAL-1152
Jim Procter [Mon, 5 Oct 2015 11:38:39 +0000 (12:38 +0100)]
JAL-1894 update release notes for JAL-1815 JAL-1860
gmungoc [Mon, 5 Oct 2015 11:00:23 +0000 (12:00 +0100)]
JAL-1684 JAL-1452 new applet parameters defaultColourNuc
defaultColourProt, used in split frame applet example
tcofoegbu [Mon, 5 Oct 2015 10:44:07 +0000 (11:44 +0100)]
merge
tcofoegbu [Mon, 5 Oct 2015 10:42:56 +0000 (11:42 +0100)]
JAL-1908 bugfix
Jim Procter [Mon, 5 Oct 2015 10:12:51 +0000 (11:12 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Mon, 5 Oct 2015 10:12:46 +0000 (11:12 +0100)]
JAL-1684 trimmed proteins to just those sequences that are mapped to cDNA fragment
tcofoegbu [Mon, 5 Oct 2015 09:57:28 +0000 (10:57 +0100)]
merge
tcofoegbu [Mon, 5 Oct 2015 09:56:45 +0000 (10:56 +0100)]
JAL-1726 updated test error msg
tcofoegbu [Mon, 5 Oct 2015 09:54:54 +0000 (10:54 +0100)]
JAL-1912 updated AnnotationDisplaySettingPojo
gmungoc [Fri, 2 Oct 2015 15:18:07 +0000 (16:18 +0100)]
JAL-1815 restore split frame geometry including horizontal scroll
correctly
Jim Procter [Fri, 2 Oct 2015 11:37:48 +0000 (12:37 +0100)]
JAL-1900 JAL-1625 disable iconify button for internal frames on Macs
Jim Procter [Thu, 1 Oct 2015 16:13:46 +0000 (17:13 +0100)]
JAL-1894 release notes update and 6th October release date for 2.9.0b1
tcofoegbu [Thu, 1 Oct 2015 14:53:10 +0000 (15:53 +0100)]
JAL-1912 Double.NaN breaks JSON serialization - added check to prevent this
tcofoegbu [Thu, 1 Oct 2015 13:50:52 +0000 (14:50 +0100)]
JAL-1912 refactor annotation refsequence assignemnt mechanism
tcofoegbu [Wed, 30 Sep 2015 15:44:58 +0000 (16:44 +0100)]
house keeping
tcofoegbu [Wed, 30 Sep 2015 15:07:47 +0000 (16:07 +0100)]
JAL-1860 house keeping
tcofoegbu [Wed, 30 Sep 2015 14:00:19 +0000 (15:00 +0100)]
JAL-1852 made disabling querying of unpublished PDB entries configurable
tcofoegbu [Wed, 30 Sep 2015 13:28:41 +0000 (14:28 +0100)]
JAL-1912 added support of tcoffee annotation and other per sequence annotation for BioJSON
tcofoegbu [Wed, 30 Sep 2015 13:23:35 +0000 (14:23 +0100)]
merge
tcofoegbu [Wed, 30 Sep 2015 13:20:22 +0000 (14:20 +0100)]
JAL-1852 disable querying of unpublished PDB entries by default
Jim Procter [Wed, 30 Sep 2015 13:18:16 +0000 (14:18 +0100)]
fix for JAL-1883
tcofoegbu [Tue, 29 Sep 2015 10:46:54 +0000 (11:46 +0100)]
JAL-1896 fixed NPE for RNA Helice without equivalent annotation
tcofoegbu [Mon, 28 Sep 2015 10:14:30 +0000 (11:14 +0100)]
merge
tcofoegbu [Mon, 28 Sep 2015 10:14:04 +0000 (11:14 +0100)]
JAL-1896 revised implementation to construct a ColourSchemeI instance after creating an alignment object rather than from within bioJSON parser
gmungoc [Mon, 28 Sep 2015 09:10:13 +0000 (10:10 +0100)]
JAL-1909 repaint complementary alignment panel after up/down reordering
gmungoc [Fri, 25 Sep 2015 13:02:05 +0000 (14:02 +0100)]
JAL-1859 try hoverDelay of 0.1s in Jmol for more responsive hover
tcofoegbu [Fri, 25 Sep 2015 11:31:56 +0000 (12:31 +0100)]
merge
tcofoegbu [Fri, 25 Sep 2015 11:29:24 +0000 (12:29 +0100)]
JAL-1907 bugfix for NPE while parsing a features file
gmungoc [Fri, 25 Sep 2015 10:46:11 +0000 (11:46 +0100)]
JAL-1815 restore split frame geometry correctly including position
tcofoegbu [Fri, 25 Sep 2015 10:11:52 +0000 (11:11 +0100)]
merge
tcofoegbu [Fri, 25 Sep 2015 10:11:34 +0000 (11:11 +0100)]
JAL-1860 disabled default enter behaviour on pdb search summary table, and added implementation for backtab
git://source.jalview.org / jalview.git / log