kiramt [Tue, 6 Feb 2018 13:28:54 +0000 (13:28 +0000)]
Merge branch 'develop' into feature/JAL-2759
Conflicts:
benchmarking/README
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
kiramt [Mon, 5 Feb 2018 14:41:46 +0000 (14:41 +0000)]
JAL-2759 Fix errant RangeElementsIterator (unit tests were failing)
kiramt [Mon, 5 Feb 2018 13:49:19 +0000 (13:49 +0000)]
JAL-2759 Rename getBoundedStartIterator
kiramt [Mon, 5 Feb 2018 13:46:09 +0000 (13:46 +0000)]
JAL-2759 Changes to StartRegionIterator after review
kiramt [Thu, 1 Feb 2018 09:15:35 +0000 (09:15 +0000)]
JAL-2759 Added in JAL-2851 fix
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
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
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
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
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)
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 [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, 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 [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
git://source.jalview.org / jalview.git / log