gmungoc [Tue, 16 Jan 2018 12:20:18 +0000 (12:20 +0000)]
JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam configurable
gmungoc [Tue, 16 Jan 2018 12:19:24 +0000 (12:19 +0000)]
JAL-1270 JAL-2885 clear properties before load
kiramt [Tue, 16 Jan 2018 12:15:07 +0000 (12:15 +0000)]
JAL-2759 Unit test for PopupMenu hideInsertions code
kiramt [Tue, 16 Jan 2018 09:41:34 +0000 (09:41 +0000)]
JAL-2759 Moved alignment annotation code out of HiddenColumns
kiramt [Tue, 16 Jan 2018 08:10:28 +0000 (08:10 +0000)]
JAL-2759 Replaced StringBuffer with StringBuilder; after review
kiramt [Mon, 15 Jan 2018 16:27:22 +0000 (16:27 +0000)]
JAL-2759 More compact iterator usage; after review
kiramt [Mon, 15 Jan 2018 14:54:35 +0000 (14:54 +0000)]
JAL-2759 First pass instantiate hiddenColumns collection in constructor
kiramt [Mon, 15 Jan 2018 13:40:39 +0000 (13:40 +0000)]
JAL-2759 getVisContigsIterator returns VisibleContigsIterator
kiramt [Mon, 15 Jan 2018 13:38:56 +0000 (13:38 +0000)]
JAL-2759 Rename hideInsertionsFor to hideList, after review
kiramt [Mon, 15 Jan 2018 13:32:35 +0000 (13:32 +0000)]
JAL-2759 Refactor of hideInsertionsFor after review
kiramt [Mon, 15 Jan 2018 11:59:40 +0000 (11:59 +0000)]
JAL-2759 Simplified HiddenColumns constructor after review
kiramt [Mon, 15 Jan 2018 11:59:14 +0000 (11:59 +0000)]
JAL-2759 Changed VisibleColsCollection constructor to take HiddenColumns
kiramt [Mon, 15 Jan 2018 11:46:07 +0000 (11:46 +0000)]
JAL-2759 Minor doc and naming changes
kiramt [Mon, 15 Jan 2018 10:42:48 +0000 (10:42 +0000)]
JAL-2759 Updated absoluteToVisibleColumn doc (prev findColumnPosition)
kiramt [Mon, 15 Jan 2018 10:38:29 +0000 (10:38 +0000)]
JAL-2759 Rename findColumnPosition and adjustForHiddenColumns (yay!)
kiramt [Mon, 15 Jan 2018 10:28:27 +0000 (10:28 +0000)]
JAL-2759 Renamed BoundedHiddenColsIterator to HiddenColsIterator
kiramt [Mon, 15 Jan 2018 10:11:10 +0000 (10:11 +0000)]
JAL-2759 Comments and renaming for has(Many)HiddenColumns after review
kiramt [Mon, 15 Jan 2018 09:57:22 +0000 (09:57 +0000)]
JAL-2759 Tidy up javadoc and naming in HiddenColumnsCursor after review
kiramt [Mon, 15 Jan 2018 09:42:08 +0000 (09:42 +0000)]
JAL-2759 Updated HiddenColumnsTest::testIsVisible following review
kiramt [Mon, 15 Jan 2018 09:38:00 +0000 (09:38 +0000)]
JAL-2759 Update to getHiddenBoundaryRight + unit test after review
kiramt [Mon, 15 Jan 2018 07:51:08 +0000 (07:51 +0000)]
JAL-2759 Updates following review
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 [Tue, 19 Dec 2017 22:39:22 +0000 (11:39 +1300)]
JAL-2880 disabled non-functional test - Jmol parser does not have proper association mechanism to bind PDB data to derived annotation.
Jim Procter [Fri, 1 Dec 2017 16:59:03 +0000 (16:59 +0000)]
Merge branch 'develop' into bugs/JAL-2780_JAL-2781_pdbnegativenums
Jim Procter [Thu, 30 Nov 2017 15:21:02 +0000 (15:21 +0000)]
JAL-2858 tweak OSX specific jar resources in JNLP
Jim Procter [Thu, 30 Nov 2017 12:09:58 +0000 (12:09 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 18:47:03 +0000 (18:47 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 17:19:01 +0000 (17:19 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
kiramt [Fri, 24 Nov 2017 14:56:35 +0000 (14:56 +0000)]
JAL-2759 update benchmark code
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
kiramt [Wed, 22 Nov 2017 16:08:59 +0000 (16:08 +0000)]
JAL-2842 JAL-2759 change to SeqPanel moveCursor
kiramt [Wed, 22 Nov 2017 15:05:01 +0000 (15:05 +0000)]
JAL-2759 code tidy
kiramt [Wed, 22 Nov 2017 14:43:23 +0000 (14:43 +0000)]
JAL-2759 performance improvements to hideColumns
kiramt [Wed, 22 Nov 2017 10:22:20 +0000 (10:22 +0000)]
JAL-2759 performance tweaks
kiramt [Wed, 22 Nov 2017 08:14:21 +0000 (08:14 +0000)]
JAL-2759 HiddenColumns test polishing
kiramt [Tue, 21 Nov 2017 10:44:47 +0000 (10:44 +0000)]
JAL-2759 corrected old getVisibleBlocksIterator calls for new call
kiramt [Tue, 21 Nov 2017 10:28:27 +0000 (10:28 +0000)]
JAL-2759 Remove getVisibleBlocksIterator call
kiramt [Tue, 21 Nov 2017 10:27:55 +0000 (10:27 +0000)]
Merge branch 'develop' into feature/JAL-2759
Conflicts:
benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
src/jalview/gui/AlignViewport.java
kiramt [Tue, 21 Nov 2017 09:57:29 +0000 (09:57 +0000)]
JAL-2759 BoundedStartRegionIterator test
kiramt [Tue, 21 Nov 2017 09:12:35 +0000 (09:12 +0000)]
JAL-2759 unit tests for VisibleContigsIterator
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
kiramt [Mon, 20 Nov 2017 14:25:39 +0000 (14:25 +0000)]
JAL-2759 cursor option for BoundedStartRegionIterator
kiramt [Mon, 20 Nov 2017 11:41:48 +0000 (11:41 +0000)]
JAL-2759 reinstate change from develop (JAL-2636) somehow not merged
kiramt [Mon, 20 Nov 2017 11:31:34 +0000 (11:31 +0000)]
JAL-2759 rationalise visible contigs iteration
kiramt [Mon, 20 Nov 2017 09:33:31 +0000 (09:33 +0000)]
JAL-2759 improvements to speed up synchronisation; caching of size
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
kiramt [Fri, 17 Nov 2017 10:41:02 +0000 (10:41 +0000)]
JAL-2759 Move isVisible to use cursor
kiramt [Fri, 17 Nov 2017 10:36:30 +0000 (10:36 +0000)]
JAL-2759 tidy
kiramt [Fri, 17 Nov 2017 10:31:58 +0000 (10:31 +0000)]
JAL-2759 Update tests
kiramt [Fri, 17 Nov 2017 09:21:10 +0000 (09:21 +0000)]
JAL-2759 Convert reveal to use cursor
kiramt [Fri, 17 Nov 2017 07:34:45 +0000 (07:34 +0000)]
JAL-2759 HiddenColumnsCursor tests
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
git://source.jalview.org / jalview.git / log