Jim Procter [Mon, 12 Feb 2018 16:43:30 +0000 (16:43 +0000)]
JAL-2780 use value of ’UNASSIGNED’ constant in assert verifying expected unassigned positions
Jim Procter [Mon, 12 Feb 2018 16:29:49 +0000 (16:29 +0000)]
JAL-2904 replaced assert for (getEnd()-getStart()+1)==getLength() in testPdb/mmCIFSeqRetrieve with test for RESNUM features at each position extracted from the PDB chain.
Jim Procter [Sun, 11 Feb 2018 11:04:57 +0000 (11:04 +0000)]
JAL-2781 use SIFTs mapping rather than maxChain AlignSeq to propagate annotation and sequence features to sequence being associated
Jim Procter [Sun, 11 Feb 2018 11:03:27 +0000 (11:03 +0000)]
JAL-2780 JAL-2781 use PDBe numbering to map between sequence extracted from PDB chain and Uniprot mapping
Jim Procter [Sun, 11 Feb 2018 10:54:00 +0000 (10:54 +0000)]
JAL-2781 mark aligned positions via StructureMapping’s Mapping object, and transfer residue positions via the Atom.resNum position rather than Residue.number
Jim Procter [Sun, 11 Feb 2018 10:49:50 +0000 (10:49 +0000)]
JAL-2780 JAL-2781 include a Mapping object in StructureMapping to pass to sequence annotation and feature transfer
Jim Procter [Sun, 11 Feb 2018 10:45:23 +0000 (10:45 +0000)]
JAL-2780 JAL-2781 UNASSIGNED positions marked as Integer.Min
Jim Procter [Sun, 11 Feb 2018 10:41:07 +0000 (10:41 +0000)]
JAL-2781 fix test data for full length annotation
gmungoc [Fri, 9 Feb 2018 12:14:38 +0000 (12:14 +0000)]
JAL-2789 avoid using transcript (with no UTR) as CDS sequence
gmungoc [Fri, 9 Feb 2018 12:07:56 +0000 (12:07 +0000)]
JAL-2789 code format changes only (before functional fixes)
gmungoc [Fri, 9 Feb 2018 12:03:57 +0000 (12:03 +0000)]
JAL-2666 fix failure to scroll split alignment of height 1
Jim Procter [Fri, 9 Feb 2018 09:46:25 +0000 (09:46 +0000)]
Use the “PDBe” or “PDB” numbering (starts from 1, corresponds with the PDB SEQRES record) to map to the dataset sequence if its primary coord system is PDB. (fixes StructureSelectionManagerTest.testMapping_EqualsSeqFeatures with 4im2_missing.pdb).
Jim Procter [Fri, 9 Feb 2018 09:42:25 +0000 (09:42 +0000)]
JAL-2780 JAL-2781 should always ensure SIFTS mappings are made to dataset sequence rather than the alignment sequence.
gmungoc [Thu, 8 Feb 2018 16:16:41 +0000 (16:16 +0000)]
JAL-2666 basic initial fix for split screen scroll bug
Jim Procter [Wed, 7 Feb 2018 16:58:09 +0000 (16:58 +0000)]
JAL-2780 JAL-2781 run sequentially and ensure windows are closed so structureselectionmanager is tidied up after each test.
Jim Procter [Wed, 7 Feb 2018 16:56:44 +0000 (16:56 +0000)]
JAL-2780 JAL-2891 clear all windows always beforeTest for Jalview2XmlBase
Jim Procter [Wed, 7 Feb 2018 16:48:22 +0000 (16:48 +0000)]
JAL-2902 catch case where viewer is closed (therefore binding is null) before hasMapping is called. technically, hasMapping should return false… but not if it is being used to poll.
Jim Procter [Wed, 7 Feb 2018 16:47:26 +0000 (16:47 +0000)]
JAL-2902 thread off dialog close op to avoid deadlock on the main swing thread.
Jim Procter [Wed, 7 Feb 2018 13:10:18 +0000 (13:10 +0000)]
JAL-2780 JAL-2781 first pass at failing test for incorrect colouring of structure after import and display of fragment of PDB 4IM2
Jim Procter [Wed, 7 Feb 2018 13:08:22 +0000 (13:08 +0000)]
JAL-2780 JAL-2781 JAL-2902 refactored helper method in test for programmatically viewing structure via structure chooser
Jim Procter [Wed, 7 Feb 2018 13:04:07 +0000 (13:04 +0000)]
JAL-2902 - isBusy and hasMapping methods so client can wait until a newly opened structure view has finished mapping sequences to structure data and sending initial colour commands to the structure view.
[ needed for JAL-2780 JAL-2781 tests]
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
kiramt [Mon, 5 Feb 2018 09:52:38 +0000 (09:52 +0000)]
JAL-2778 Sequence width benchmark
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
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 [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
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
git://source.jalview.org / jalview.git / log