kiramt [Tue, 16 Jan 2018 15:45:59 +0000 (15:45 +0000)]
JAL-2759 setup hideBitSet over range for hideInsertions
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, 24 Nov 2017 14:56:35 +0000 (14:56 +0000)]
JAL-2759 update benchmark code
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
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 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 [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 11:17:41 +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...
kiramt [Mon, 13 Nov 2017 15:53:12 +0000 (15:53 +0000)]
JAL-2811 Add layer for cursor in SeqCanvas
Jim Procter [Mon, 13 Nov 2017 15:41:10 +0000 (15:41 +0000)]
JAL-2810 release notes
Jim Procter [Mon, 13 Nov 2017 15:38:34 +0000 (15:38 +0000)]
Merge branch 'imp/JAL-2810_ftsIDtab' into develop
Jim Procter [Mon, 13 Nov 2017 15:32:05 +0000 (15:32 +0000)]
JAL-2698 stub for 2.10.3 new known issues entries
Jim Procter [Mon, 13 Nov 2017 15:31:05 +0000 (15:31 +0000)]
JAL-2702 groovy interpreter update and java 9 jnlp release notes
Jim Procter [Mon, 13 Nov 2017 15:03:27 +0000 (15:03 +0000)]
Merge branch 'bug/JAL-2702_groovyconsoleJava9' into develop
Jim Procter [Mon, 13 Nov 2017 14:33:06 +0000 (14:33 +0000)]
JAL-2702 --illegal-access=warn for JVM launch
gmungoc [Mon, 13 Nov 2017 14:11:08 +0000 (14:11 +0000)]
JAL-2176 removed unused Sequence.index
Jim Procter [Mon, 13 Nov 2017 13:52:48 +0000 (13:52 +0000)]
JAL-2702 update to groovy 2.4.12
Jim Procter [Mon, 13 Nov 2017 13:00:17 +0000 (13:00 +0000)]
JAL-2810 updated help docs for auto search checkbox and retrieve IDs tab
Jim Procter [Mon, 13 Nov 2017 12:44:08 +0000 (12:44 +0000)]
JAL-2810 updated screenshots in documentation
Jim Procter [Mon, 13 Nov 2017 12:43:38 +0000 (12:43 +0000)]
JAL-2810 auto search checkbox state stored as user preference. Enabled by default.
gmungoc [Mon, 13 Nov 2017 12:02:43 +0000 (12:02 +0000)]
JAL-2679 example accession changed to
CAD01290
Jim Procter [Mon, 13 Nov 2017 11:53:27 +0000 (11:53 +0000)]
JAL-2810 mainFramTabs -> tabs
Jim Procter [Mon, 13 Nov 2017 11:53:02 +0000 (11:53 +0000)]
JAL-2810 simpler tooltip (assume user will work out that pressing return will update results)
kiramt [Mon, 13 Nov 2017 09:52:52 +0000 (09:52 +0000)]
JAL-2759 convert findColumnPosition to use cursor
kiramt [Mon, 13 Nov 2017 07:54:56 +0000 (07:54 +0000)]
JAL-2759 Converted getHiddenBoundaryLeft/Right to use cursor
gmungoc [Fri, 10 Nov 2017 15:56:11 +0000 (15:56 +0000)]
JAL-2829 fixes and unit tests
gmungoc [Fri, 10 Nov 2017 15:38:19 +0000 (15:38 +0000)]
JAL-2562 updated findPosition javadoc to match behaviour
gmungoc [Fri, 10 Nov 2017 15:10:50 +0000 (15:10 +0000)]
JAL-2829 unit tests for failing cases
kiramt [Thu, 9 Nov 2017 14:35:12 +0000 (14:35 +0000)]
JAL-2759 make bounds correct for left scrolling with hidden cols
Jim Procter [Wed, 8 Nov 2017 17:02:42 +0000 (17:02 +0000)]
Merge branch 'bug/JAL-2742' into develop
Jim Procter [Wed, 8 Nov 2017 17:02:06 +0000 (17:02 +0000)]
Revert "JAL-2742 release notes - pending confirmation that there was impact to user"
-- no impact so won't include development detail in release notes.
This reverts commit
ba70dbddc08876d8d72bb303823f683b65bf13c7.
Jim Procter [Wed, 8 Nov 2017 16:57:14 +0000 (16:57 +0000)]
JAL-2225 release note
Jim Procter [Wed, 8 Nov 2017 16:52:03 +0000 (16:52 +0000)]
Merge branch 'bug/JAL-2225mapMultipleChains' into develop
kiramt [Wed, 8 Nov 2017 16:06:14 +0000 (16:06 +0000)]
Merge branch 'develop' into feature/JAL-2759
Conflicts:
src/jalview/gui/SeqCanvas.java
src/jalview/renderer/ScaleRenderer.java
test/jalview/datamodel/SequenceTest.java
Jim Procter [Wed, 8 Nov 2017 15:21:13 +0000 (15:21 +0000)]
Merge branch 'develop' into bug/JAL-2225mapMultipleChains
git://source.jalview.org / jalview.git / log