Jim Procter [Mon, 12 Feb 2018 17:13:50 +0000 (17:13 +0000)]
JAL-2780 JAL-2781 extra column in mapping array
Jim Procter [Mon, 12 Feb 2018 17:13:12 +0000 (17:13 +0000)]
JAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest for removal of redundant first semicolon in commandset
Jim Procter [Mon, 12 Feb 2018 17:12:19 +0000 (17:12 +0000)]
JAL-2780 JAL-2781 ahem - add a semicolon if there isn’t one
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
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.
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).
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
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
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
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
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 [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 [Tue, 19 Dec 2017 22:39:22 +0000 (11:39 +1300)]
JAL-2880 disabled non-functional test - Jmol parser does not have proper association mechanism to bind PDB data to derived annotation.
Jim Procter [Fri, 1 Dec 2017 16:59:03 +0000 (16:59 +0000)]
Merge branch 'develop' into bugs/JAL-2780_JAL-2781_pdbnegativenums
Jim Procter [Thu, 30 Nov 2017 15:21:02 +0000 (15:21 +0000)]
JAL-2858 tweak OSX specific jar resources in JNLP
Jim Procter [Thu, 30 Nov 2017 12:09:58 +0000 (12:09 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 18:47:03 +0000 (18:47 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
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 17:19:01 +0000 (17:19 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
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
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
Jim Procter [Fri, 17 Nov 2017 21:29:19 +0000 (21:29 +0000)]
JAL-2698 tidy release notes and whats new
Jim Procter [Fri, 17 Nov 2017 15:13:58 +0000 (15:13 +0000)]
JAL-2698 source code licencing
Jim Procter [Fri, 17 Nov 2017 14:56:24 +0000 (14:56 +0000)]
JAL-2698 tidy up release notes
Jim Procter [Fri, 17 Nov 2017 14:40:37 +0000 (14:40 +0000)]
JAL-2698 Cached PDB Entries -> Cached Structures in UI and help doc
Jim Procter [Fri, 17 Nov 2017 13:52:03 +0000 (13:52 +0000)]
JAL-2466 revised help text for sort by PID
Jim Procter [Fri, 17 Nov 2017 13:51:25 +0000 (13:51 +0000)]
JAL-2698 what’s new and release notes
Jim Procter [Fri, 17 Nov 2017 13:24:33 +0000 (13:24 +0000)]
JAL-2822 known defect for 2.10.3
Jim Procter [Fri, 17 Nov 2017 13:16:10 +0000 (13:16 +0000)]
Merge branch 'bug/JAL-2784' into develop
Jim Procter [Fri, 17 Nov 2017 13:15:20 +0000 (13:15 +0000)]
JAL-2841 JAL-2791 new known defect
Jim Procter [Fri, 17 Nov 2017 13:08:56 +0000 (13:08 +0000)]
JAL-2541 known defect
Jim Procter [Fri, 17 Nov 2017 13:03:05 +0000 (13:03 +0000)]
JAL-2684 clarify release notes
Jim Procter [Fri, 17 Nov 2017 12:31:58 +0000 (12:31 +0000)]
Merge branch 'bug/JAL-2821' into develop
Jim Procter [Fri, 17 Nov 2017 12:26:42 +0000 (12:26 +0000)]
JAL-2840 release notes
Jim Procter [Fri, 17 Nov 2017 12:21:17 +0000 (12:21 +0000)]
Merge branch 'bug/JAL-2837' into develop
kiramt [Fri, 17 Nov 2017 12:14:59 +0000 (12:14 +0000)]
Merge branch 'develop' into bug/JAL-2837
Conflicts:
src/jalview/gui/SeqPanel.java
Jim Procter [Fri, 17 Nov 2017 12:14:21 +0000 (12:14 +0000)]
Merge branch 'doc/JAL-2494_JAL-2828_mergefindAnnotation' into develop
kiramt [Fri, 17 Nov 2017 12:09:20 +0000 (12:09 +0000)]
Merge branch 'develop' into bug/JAL-2837
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
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 [Thu, 16 Nov 2017 09:12:06 +0000 (09:12 +0000)]
JAL-2842 remove infinite loop in cursor move
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
git://source.jalview.org / jalview.git / log