kiramt [Thu, 1 Feb 2018 08:59:07 +0000 (08:59 +0000)]
JAL-2759 use right iterator for getVisibleColsIterator
kiramt [Wed, 31 Jan 2018 16:38:57 +0000 (16:38 +0000)]
JAL-2759 Rationalise VisibleColsIterator and HiddenColsIterator
kiramt [Wed, 31 Jan 2018 13:37:10 +0000 (13:37 +0000)]
JAL-2759 Generalised HiddenColsIterator naming
kiramt [Wed, 31 Jan 2018 09:21:20 +0000 (09:21 +0000)]
JAL-2759 test renaming
kiramt [Wed, 31 Jan 2018 08:17:08 +0000 (08:17 +0000)]
JAL-2759 minor refactor to hiding bitsets
kiramt [Tue, 30 Jan 2018 15:56:59 +0000 (15:56 +0000)]
JAL-2759 Add missing hiddenColumns empty check
kiramt [Tue, 30 Jan 2018 15:43:08 +0000 (15:43 +0000)]
JAL-2759 updateForDeletedRegion no longer needed
kiramt [Tue, 30 Jan 2018 14:45:24 +0000 (14:45 +0000)]
JAL-2759 Rationalising hidden cols cursor, and sorting out coverage
kiramt [Tue, 30 Jan 2018 10:58:50 +0000 (10:58 +0000)]
JAL-2759 comment
kiramt [Tue, 30 Jan 2018 10:56:15 +0000 (10:56 +0000)]
JAL-2759 Additional tests and tweaks to numColumns update
kiramt [Tue, 30 Jan 2018 10:24:37 +0000 (10:24 +0000)]
JAL-2759 Keep numColumns up to date
kiramt [Mon, 29 Jan 2018 14:46:00 +0000 (14:46 +0000)]
JAL-2759 remove unneeded cast
kiramt [Mon, 29 Jan 2018 14:37:54 +0000 (14:37 +0000)]
Merge branch 'feature/JAL-2759' of https://source.jalview.org/git/jalview.git into feature/JAL-2759
kiramt [Mon, 29 Jan 2018 14:37:30 +0000 (14:37 +0000)]
JAL-2759 Combine findRegionForColumn code in HiddenColumnsCursor
gmungoc [Mon, 29 Jan 2018 14:04:43 +0000 (14:04 +0000)]
Merge branch 'feature/JAL-2759' of https://source.jalview.org/git/jalview.git into feature/JAL-2759
gmungoc [Mon, 29 Jan 2018 14:04:34 +0000 (14:04 +0000)]
JAL-1270 testPadGaps() added
kiramt [Mon, 29 Jan 2018 12:00:35 +0000 (12:00 +0000)]
JAL-2759 numColumns reset
kiramt [Mon, 29 Jan 2018 11:46:44 +0000 (11:46 +0000)]
JAL-2759 remove redundant hiddenColumns.clear()
kiramt [Mon, 29 Jan 2018 10:35:47 +0000 (10:35 +0000)]
JAL-2759 Tidy
kiramt [Mon, 29 Jan 2018 10:21:58 +0000 (10:21 +0000)]
JAL-2759 make a new cursor instead of resetting, updated after review
kiramt [Mon, 29 Jan 2018 09:35:15 +0000 (09:35 +0000)]
JAL-2759 Fix unintended type change
kiramt [Mon, 22 Jan 2018 14:44:09 +0000 (14:44 +0000)]
JAL-2579 Moved locateVisibleStartOfSequence to Sequence (refactored)
kiramt [Mon, 22 Jan 2018 10:06:25 +0000 (10:06 +0000)]
JAL-2759 Various minor HiddenColumns updates after review
kiramt [Fri, 19 Jan 2018 16:25:16 +0000 (16:25 +0000)]
JAL-2759 Changes to getVisibleSequenceStrings after review
kiramt [Fri, 19 Jan 2018 12:36:12 +0000 (12:36 +0000)]
JAL-2759 Moved propagateInsertions out of HiddenColumns
kiramt [Fri, 19 Jan 2018 07:51:31 +0000 (07:51 +0000)]
JAL-2759 Update to getVisibleStartAndEndIndex after review
kiramt [Thu, 18 Jan 2018 16:30:45 +0000 (16:30 +0000)]
JAL-2759 change subtractVisibleColumns and removal of reverse iterator
kiramt [Thu, 18 Jan 2018 14:12:08 +0000 (14:12 +0000)]
JAL-2759 Updated test
kiramt [Thu, 18 Jan 2018 09:07:41 +0000 (09:07 +0000)]
JAL-2759 unit tests (incomplete)
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
git://source.jalview.org / jalview.git / log