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
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
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
kiramt [Wed, 21 Feb 2018 14:15:38 +0000 (14:15 +0000)]
JAL-2909 Partial insertions
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
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 [Wed, 24 Jan 2018 07:36:56 +0000 (07:36 +0000)]
JAL-2858 update release date and rejig what's new message
Jim Procter [Tue, 23 Jan 2018 13:52:31 +0000 (13:52 +0000)]
JAL-2858 fix what's new
Jim Procter [Tue, 23 Jan 2018 12:03:37 +0000 (12:03 +0000)]
JAL-2858 update latest release notes link in TOC
Jim Procter [Tue, 23 Jan 2018 11:57:05 +0000 (11:57 +0000)]
JAL-2859 release notes
Jim Procter [Tue, 23 Jan 2018 11:54:49 +0000 (11:54 +0000)]
JAL-2858 update release notes
Jim Procter [Mon, 22 Jan 2018 15:26:10 +0000 (15:26 +0000)]
JAL-2858 release notes for 2.10.3b1 (including revision to EnsemblGenomes client as per JAL-2679)
Jim Procter [Mon, 22 Jan 2018 15:25:23 +0000 (15:25 +0000)]
JAL-2858 bump version number for 2.10.3b1
gmungoc [Thu, 18 Jan 2018 16:12:50 +0000 (16:12 +0000)]
JAL-2810 JAL-2886 i18n
gmungoc [Thu, 18 Jan 2018 14:54:49 +0000 (14:54 +0000)]
JAL-2679 update query id to actual case of retrieved gene
gmungoc [Wed, 17 Jan 2018 11:37:09 +0000 (11:37 +0000)]
JAL-2679 case-insensitive comparison of query and retrieved accession
gmungoc [Tue, 16 Jan 2018 16:27:19 +0000 (16:27 +0000)]
JAL-2679 use object_type=Transcript for lookup of Parent for Protein
kiramt [Fri, 12 Jan 2018 11:37:03 +0000 (11:37 +0000)]
JAL-2886 trivial unit test fix
kiramt [Thu, 11 Jan 2018 17:28:29 +0000 (17:28 +0000)]
Merge remote-tracking branch 'origin/task/JAL-2662' into develop
Conflicts:
benchmarking/README
kiramt [Thu, 11 Jan 2018 14:53:00 +0000 (14:53 +0000)]
JAL-2662 Updated README
Jim Procter [Thu, 30 Nov 2017 12:04:15 +0000 (12:04 +0000)]
JAL-2849 release notes
Jim Procter [Thu, 30 Nov 2017 11:34:22 +0000 (11:34 +0000)]
Merge branch 'bug/JAL-2849' into develop
Jim Procter [Thu, 30 Nov 2017 11:34:02 +0000 (11:34 +0000)]
JAL-2849 JAL-2863 file format preferences TODO
Jim Procter [Thu, 30 Nov 2017 11:28:36 +0000 (11:28 +0000)]
JAL-2849 fix
Jim Procter [Tue, 28 Nov 2017 15:18:14 +0000 (15:18 +0000)]
Merge branch 'bug/JAL-2859_uniprottowrongpdbid' into develop
Jim Procter [Tue, 28 Nov 2017 15:06:57 +0000 (15:06 +0000)]
JAL-2740 release notes
Jim Procter [Tue, 28 Nov 2017 14:55:23 +0000 (14:55 +0000)]
Merge branch 'bug/JAL-2740' into develop
Jim Procter [Tue, 28 Nov 2017 14:53:51 +0000 (14:53 +0000)]
JAL-2827 release notes
Jim Procter [Tue, 28 Nov 2017 14:45:15 +0000 (14:45 +0000)]
Merge branch 'bug/JAL-2827' into develop
Jim Procter [Tue, 28 Nov 2017 14:42:00 +0000 (14:42 +0000)]
JAL-2842 release notes
Jim Procter [Tue, 28 Nov 2017 14:24:05 +0000 (14:24 +0000)]
Merge branch 'bug/JAL-2842' into develop
Jim Procter [Mon, 27 Nov 2017 22:09:45 +0000 (22:09 +0000)]
JAL-2859 disambiguate with PDB ID if no file path
Jim Procter [Mon, 27 Nov 2017 22:07:07 +0000 (22:07 +0000)]
JAL-2859 failing test demonstrating sequences with pdb without a local file map all get mapped together
Jim Procter [Mon, 27 Nov 2017 18:46:19 +0000 (18:46 +0000)]
JAL-2851 JAL-2858 release notes for 2.10.3b1
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
kiramt [Thu, 23 Nov 2017 11:52:01 +0000 (11:52 +0000)]
Merge branch 'develop' into bug/JAL-2851
kiramt [Thu, 23 Nov 2017 11:50:39 +0000 (11:50 +0000)]
JAL-2851 Fix merge error breaking vertical scrolling
Jim Procter [Mon, 20 Nov 2017 16:17:26 +0000 (16:17 +0000)]
JAL-2698 only allow InstallAnywhere launches with version 1.8.* of java - java 9 JVM args not yet working for 2.10.3
Jim Procter [Mon, 20 Nov 2017 14:44:16 +0000 (14:44 +0000)]
JAL-2698 patch path for InstallAnywhere build. Webstart and source builds unchanged
Jim Procter [Fri, 17 Nov 2017 21:29:19 +0000 (21:29 +0000)]
JAL-2698 tidy release notes and whats new
Jim Procter [Fri, 17 Nov 2017 15:13:58 +0000 (15:13 +0000)]
JAL-2698 source code licencing
Jim Procter [Fri, 17 Nov 2017 14:56:24 +0000 (14:56 +0000)]
JAL-2698 tidy up release notes
Jim Procter [Fri, 17 Nov 2017 14:40:37 +0000 (14:40 +0000)]
JAL-2698 Cached PDB Entries -> Cached Structures in UI and help doc
Jim Procter [Fri, 17 Nov 2017 13:52:03 +0000 (13:52 +0000)]
JAL-2466 revised help text for sort by PID
Jim Procter [Fri, 17 Nov 2017 13:51:25 +0000 (13:51 +0000)]
JAL-2698 what’s new and release notes
Jim Procter [Fri, 17 Nov 2017 13:24:33 +0000 (13:24 +0000)]
JAL-2822 known defect for 2.10.3
Jim Procter [Fri, 17 Nov 2017 13:16:10 +0000 (13:16 +0000)]
Merge branch 'bug/JAL-2784' into develop
Jim Procter [Fri, 17 Nov 2017 13:15:20 +0000 (13:15 +0000)]
JAL-2841 JAL-2791 new known defect
Jim Procter [Fri, 17 Nov 2017 13:08:56 +0000 (13:08 +0000)]
JAL-2541 known defect
Jim Procter [Fri, 17 Nov 2017 13:03:05 +0000 (13:03 +0000)]
JAL-2684 clarify release notes
Jim Procter [Fri, 17 Nov 2017 12:31:58 +0000 (12:31 +0000)]
Merge branch 'bug/JAL-2821' into develop
Jim Procter [Fri, 17 Nov 2017 12:26:42 +0000 (12:26 +0000)]
JAL-2840 release notes
Jim Procter [Fri, 17 Nov 2017 12:21:17 +0000 (12:21 +0000)]
Merge branch 'bug/JAL-2837' into develop
kiramt [Fri, 17 Nov 2017 12:14:59 +0000 (12:14 +0000)]
Merge branch 'develop' into bug/JAL-2837
Conflicts:
src/jalview/gui/SeqPanel.java
Jim Procter [Fri, 17 Nov 2017 12:14:21 +0000 (12:14 +0000)]
Merge branch 'doc/JAL-2494_JAL-2828_mergefindAnnotation' into develop
kiramt [Fri, 17 Nov 2017 12:09:20 +0000 (12:09 +0000)]
Merge branch 'develop' into bug/JAL-2837
Jim Procter [Fri, 17 Nov 2017 11:56:59 +0000 (11:56 +0000)]
JAL-2811 release note
Jim Procter [Fri, 17 Nov 2017 11:47:51 +0000 (11:47 +0000)]
JAL-2541 not in 2.10.3, JAL-2831 signed off.
Jim Procter [Fri, 17 Nov 2017 11:47:25 +0000 (11:47 +0000)]
JAL-2698 11th hour release today
Jim Procter [Fri, 17 Nov 2017 11:28:43 +0000 (11:28 +0000)]
Merge branch 'bug/JAL-2831' into develop
Jim Procter [Thu, 16 Nov 2017 16:50:03 +0000 (16:50 +0000)]
JAL-2541 JAL-2829 JAL-2830 JAL-2822 catch all release note entry for sequence feature relocation
Jim Procter [Thu, 16 Nov 2017 16:45:35 +0000 (16:45 +0000)]
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into develop
kiramt [Thu, 16 Nov 2017 11:57:15 +0000 (11:57 +0000)]
JAL-2831 Removed unwanted hidden sequences checks
kiramt [Thu, 16 Nov 2017 09:12:06 +0000 (09:12 +0000)]
JAL-2842 remove infinite loop in cursor move
kiramt [Wed, 15 Nov 2017 16:22:21 +0000 (16:22 +0000)]
JAL-2831 Don't show cursor if position in hidden region
kiramt [Wed, 15 Nov 2017 16:05:18 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Wed, 15 Nov 2017 13:23:00 +0000 (13:23 +0000)]
JAL-2811 Updated following review
kiramt [Wed, 15 Nov 2017 11:44:44 +0000 (11:44 +0000)]
JAL-2840 fix wrapped scrolling when using cursor at a hidden region
kiramt [Wed, 15 Nov 2017 11:17:41 +0000 (11:17 +0000)]
JAL-2834 JAL-2836 temporarily disabled wrapped mode fastpaint
kiramt [Wed, 15 Nov 2017 08:47:47 +0000 (08:47 +0000)]
JAL-2831 ported to applet
kiramt [Tue, 14 Nov 2017 19:36:53 +0000 (19:36 +0000)]
JAL-2831 tidies and tests
kiramt [Tue, 14 Nov 2017 16:03:47 +0000 (16:03 +0000)]
JAL-2831 tidy
kiramt [Tue, 14 Nov 2017 14:59:52 +0000 (14:59 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 14:56:37 +0000 (14:56 +0000)]
JAL-2811 Changed to overlay on via graphics context, not separate image
kiramt [Tue, 14 Nov 2017 14:10:30 +0000 (14:10 +0000)]
JAL-2811 Missed commit
kiramt [Tue, 14 Nov 2017 13:43:40 +0000 (13:43 +0000)]
JAL-2811 Made it work for hidden columns/seqs too
kiramt [Tue, 14 Nov 2017 12:11:21 +0000 (12:11 +0000)]
JAL-2831 Attempt at cursor fix for wrapped mode
Jim Procter [Tue, 14 Nov 2017 12:11:04 +0000 (12:11 +0000)]
JAL-2758 update uniprot retrieval test
kiramt [Tue, 14 Nov 2017 11:12:55 +0000 (11:12 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 10:33:33 +0000 (10:33 +0000)]
JAL-2831 deal with hidden cols and seqs in new cursor code
kiramt [Tue, 14 Nov 2017 10:15:46 +0000 (10:15 +0000)]
JAL-2831 Added move viewport event and set up cursor code to use it
kiramt [Tue, 14 Nov 2017 09:30:31 +0000 (09:30 +0000)]
Merge branch 'imp/JAL-2774' into bug/JAL-2831
Jim Procter [Mon, 13 Nov 2017 20:25:06 +0000 (20:25 +0000)]
JAL-2758 release notes
Jim Procter [Mon, 13 Nov 2017 20:22:01 +0000 (20:22 +0000)]
JAL-2698 formatting
kiramt [Mon, 13 Nov 2017 19:40:06 +0000 (19:40 +0000)]
JAL-2811 Tidy
Jim Procter [Mon, 13 Nov 2017 18:59:59 +0000 (18:59 +0000)]
Merge branch 'features/JAL-2758_shorteruniprot' into develop
Jim Procter [Mon, 13 Nov 2017 18:57:10 +0000 (18:57 +0000)]
JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name
Jim Procter [Mon, 13 Nov 2017 18:56:22 +0000 (18:56 +0000)]
JAL-2758 typo
kiramt [Mon, 13 Nov 2017 16:42:20 +0000 (16:42 +0000)]
JAl-2811 Working for wrapped panels too
gmungoc [Mon, 13 Nov 2017 16:23:12 +0000 (16:23 +0000)]
JAL-2662 tweak README, format code
Jim Procter [Mon, 13 Nov 2017 16:05:37 +0000 (16:05 +0000)]
JAL-2698 what's new...
git://source.jalview.org / jalview.git / log