Jim Procter [Wed, 7 Feb 2018 12:57:24 +0000 (12:57 +0000)]
JAL-2780 JAL-2781 fix javadoc in line with behaviour for getPDBResNum
Jim Procter [Wed, 7 Feb 2018 12:55:30 +0000 (12:55 +0000)]
JAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to optionally blocking method for retrieval/opening view for selected structures and getter for retrieving the handle for the last opened viewer
Jim Procter [Wed, 7 Feb 2018 12:50:36 +0000 (12:50 +0000)]
JAL-2780 JAL-2781 don’t assume contiguous mapping to PDB residue numbering when generating Jmol colour commands (unmapped PDB residue data shouldn’t receive colour if mapped positions either side receive the same colour).
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
Jim Procter [Mon, 5 Feb 2018 16:43:26 +0000 (16:43 +0000)]
JAL-2780 JAL-2781 (failing) test comparing location of transferred annotation from PDB file via SIFTs to full length uniprot sequence vs transfer from same structure/SIFTS file to a subsequence through the StructureChooser
Jim Procter [Mon, 5 Feb 2018 16:39:20 +0000 (16:39 +0000)]
JAL-2780 JAL-2781 programmatically select structures for retrieval via Structure Chooser GUI
Jim Procter [Mon, 5 Feb 2018 16:38:48 +0000 (16:38 +0000)]
JAL-2780 JAL-2871 only look up current table view once
Jim Procter [Mon, 5 Feb 2018 16:36:33 +0000 (16:36 +0000)]
JAL-2780 JAL-2781 test AlignmentI.findAnnotations locates sequence associated annotation by id and sequence reference
Jim Procter [Mon, 5 Feb 2018 16:34:28 +0000 (16:34 +0000)]
JAL-2780 JAL-2781 - patch and first test for AlignmentI.findOrCreateAnnotation
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 [Mon, 5 Feb 2018 13:41:52 +0000 (13:41 +0000)]
JAL-2788 possible adjustments to sequence accesses
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
Conflicts:
test/jalview/analysis/AlignmentUtilsTests.java
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
gmungoc [Mon, 5 Feb 2018 09:54:10 +0000 (09:54 +0000)]
Merge branch 'spikes/mungo' into trialMerge
Conflicts:
src/jalview/analysis/AlignmentUtils.java
test/jalview/analysis/AlignmentUtilsTests.java
kiramt [Mon, 5 Feb 2018 09:52:38 +0000 (09:52 +0000)]
JAL-2778 Sequence width benchmark
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants
gmungoc [Fri, 2 Feb 2018 15:56:43 +0000 (15:56 +0000)]
JAL-984 merged to spikes-mungo
gmungoc [Fri, 2 Feb 2018 15:55:11 +0000 (15:55 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into features/JAL-1793VCF
gmungoc [Fri, 2 Feb 2018 11:33:39 +0000 (11:33 +0000)]
JAL-984 use cursor for drag regions to adjust annotation height or id width
gmungoc [Fri, 2 Feb 2018 10:14:17 +0000 (10:14 +0000)]
JAL-984 better behaved panel height adjuster
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
gmungoc [Wed, 31 Jan 2018 11:28:03 +0000 (11:28 +0000)]
JAL-2792 added tooltip to menu items in case of truncation
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
gmungoc [Tue, 30 Jan 2018 16:26:44 +0000 (16:26 +0000)]
JAL-2069 menu item now "Variable colour..." to hint at more...
gmungoc [Tue, 30 Jan 2018 16:07:17 +0000 (16:07 +0000)]
JAL-1793 update spike build to latest incl stop and synonymous variants on peptides
gmungoc [Tue, 30 Jan 2018 15:57:03 +0000 (15:57 +0000)]
JAL-2898 show 'stop_gained' variants on peptide sequences
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
gmungoc [Tue, 30 Jan 2018 15:34:48 +0000 (15:34 +0000)]
JAL-2897 generate peptide variants for synonymous codon variants
gmungoc [Tue, 30 Jan 2018 15:29:57 +0000 (15:29 +0000)]
JAL-2897 formatting change only prior to functional change
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
gmungoc [Mon, 29 Jan 2018 09:24:38 +0000 (09:24 +0000)]
JAL-2743 recoded EnsemblLookup without lambda expressions for parsing response
Jim Procter [Fri, 26 Jan 2018 18:30:48 +0000 (18:30 +0000)]
Merge branch 'releases/Release_2_10_3_Branch' into bugs/JAL-2780_JAL-2781_pdbnegativenums
kiramt [Fri, 26 Jan 2018 16:32:50 +0000 (16:32 +0000)]
JAL-2778 try another way to draw sequences with reduced synchronisation
gmungoc [Fri, 26 Jan 2018 14:53:22 +0000 (14:53 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
kiramt [Fri, 26 Jan 2018 10:27:46 +0000 (10:27 +0000)]
JAL-2778 tightened up use of resetAlignmentDims
kiramt [Thu, 25 Jan 2018 17:09:16 +0000 (17:09 +0000)]
JAL-2778 Tidy
kiramt [Thu, 25 Jan 2018 14:06:52 +0000 (14:06 +0000)]
JAL-2778 added JAL-2851 fix to avoid confusion
kiramt [Thu, 25 Jan 2018 13:49:36 +0000 (13:49 +0000)]
JAL-2778 Reinstate id width adjuster
Jim Procter [Wed, 24 Jan 2018 07:37:42 +0000 (07:37 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 14:11:15 +0000 (14:11 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 12:04:09 +0000 (12:04 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 15:27:07 +0000 (15:27 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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
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
git://source.jalview.org / jalview.git / log