gmungoc [Thu, 21 Jan 2016 15:56:06 +0000 (15:56 +0000)]
JAL-1705 removed (only) usage of otherwise unused constant
gmungoc [Thu, 21 Jan 2016 15:55:20 +0000 (15:55 +0000)]
JAL-653 comments/javadoc tidy only
gmungoc [Thu, 21 Jan 2016 15:49:08 +0000 (15:49 +0000)]
JAL-1796 parse ensembl genomic coordinates to set start position
gmungoc [Thu, 21 Jan 2016 15:33:18 +0000 (15:33 +0000)]
JAL-1705 AlignmentUtils method renamed
gmungoc [Thu, 21 Jan 2016 15:31:11 +0000 (15:31 +0000)]
JAL-1705 ENSEMBL added, unused constants removed
gmungoc [Thu, 21 Jan 2016 15:23:20 +0000 (15:23 +0000)]
JAL-1705 features transferred to CDS sequence; makeExon renamed makeCds
gmungoc [Thu, 21 Jan 2016 15:20:43 +0000 (15:20 +0000)]
JAL-1705 redundant comment removed
gmungoc [Thu, 21 Jan 2016 15:18:59 +0000 (15:18 +0000)]
JAL-1705 suppress jvsuffix (for sequence id matching to work)
gmungoc [Thu, 21 Jan 2016 15:18:13 +0000 (15:18 +0000)]
JAL-1705 unused import removed
gmungoc [Thu, 21 Jan 2016 15:17:12 +0000 (15:17 +0000)]
JAL-1705 include dummy sequences in returned alignment
gmungoc [Thu, 21 Jan 2016 14:56:27 +0000 (14:56 +0000)]
JAL-1705 tidy and todo comment, no functional change
gmungoc [Thu, 21 Jan 2016 14:54:41 +0000 (14:54 +0000)]
JAL-1705 tests for amended toString
gmungoc [Thu, 21 Jan 2016 14:44:15 +0000 (14:44 +0000)]
JAL-1705 added isSequenceVariant(), commonly used SO terms as constants
gmungoc [Thu, 21 Jan 2016 14:40:17 +0000 (14:40 +0000)]
JAL-1705 isFromForwardStrand added; toString (for debug) tweaked
gmungoc [Thu, 21 Jan 2016 14:38:21 +0000 (14:38 +0000)]
JAL-1705 canonicalise ENSEMBL name; code tidy
gmungoc [Thu, 21 Jan 2016 14:34:54 +0000 (14:34 +0000)]
JAL-1705 get xrefs only for dna/peptide; code tidy
gmungoc [Thu, 21 Jan 2016 14:30:31 +0000 (14:30 +0000)]
JAL-1705 toString() added (for debugging)
gmungoc [Thu, 21 Jan 2016 14:29:42 +0000 (14:29 +0000)]
JAL-1705 isEmpty() and (debug) toString() methods added
gmungoc [Tue, 12 Jan 2016 08:58:01 +0000 (08:58 +0000)]
JAL-1191 cache isA (great-)grandparents as well for fast isA testing
gmungoc [Fri, 8 Jan 2016 10:03:40 +0000 (10:03 +0000)]
JAL-1705 DbSourceProxy properties converted to methods, tidy/format code
gmungoc [Tue, 5 Jan 2016 13:40:12 +0000 (13:40 +0000)]
JAL-653 updating 'align as' tests to match latest tweaks to algorithm
gmungoc [Tue, 5 Jan 2016 13:09:44 +0000 (13:09 +0000)]
Merge remote-tracking branch 'origin/features/JAL-1705_ensembl' into
features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Tue, 5 Jan 2016 10:15:22 +0000 (10:15 +0000)]
JAL-653 typed map for feature colours in method signature
gmungoc [Tue, 5 Jan 2016 10:12:09 +0000 (10:12 +0000)]
JAL-1191 check for obsolete term when descriptions are duplicated
gmungoc [Wed, 23 Dec 2015 09:48:26 +0000 (09:48 +0000)]
JAL-1191 unzipped OBO file removed
gmungoc [Wed, 23 Dec 2015 09:47:52 +0000 (09:47 +0000)]
JAL-1191 zipped SO OBO file added to /resources, more tests added
gmungoc [Tue, 22 Dec 2015 16:24:02 +0000 (16:24 +0000)]
JAL-1191 more test cases
gmungoc [Tue, 22 Dec 2015 16:01:20 +0000 (16:01 +0000)]
JAL-1191 and provide the SO OBO file in /resources :-)
gmungoc [Tue, 22 Dec 2015 15:49:33 +0000 (15:49 +0000)]
JAL-1191 SequenceOntology wrapping/caching SO.OBO via BioJava library
gmungoc [Tue, 22 Dec 2015 09:28:04 +0000 (09:28 +0000)]
JAL-1191 stub class for a SequenceOntology wrapper
gmungoc [Tue, 22 Dec 2015 09:24:49 +0000 (09:24 +0000)]
JAL-1551 don't autoformat /* comments */
gmungoc [Tue, 22 Dec 2015 09:22:57 +0000 (09:22 +0000)]
JAL-1421 parameterised map constructor used
gmungoc [Tue, 22 Dec 2015 09:21:58 +0000 (09:21 +0000)]
JAL-653 encapsulate Strand, Attributes, Status of SequenceFeature
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 [Tue, 10 Nov 2015 14:46:33 +0000 (14:46 +0000)]
Merge branch 'features/JAL-1705_ensembl' of source.jalview.org/git/jalview into features/JAL-1705_ensembl
gmungoc [Mon, 9 Nov 2015 14:50:16 +0000 (14:50 +0000)]
JAL-1705 type enum can encapsulate the corresponding url parameter value
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 17:51:55 +0000 (18:51 +0100)]
Merge branch 'develop' into features/JAL-1705_ensembl
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
git://source.jalview.org / jalview.git / log