gmungoc [Thu, 22 Feb 2018 13:43:32 +0000 (13:43 +0000)]
JAL-2629 tidy unit tests, constants etc
Jim Procter [Wed, 21 Feb 2018 17:40:04 +0000 (17:40 +0000)]
JAL-2906 release notes for 2.10.4
Jim Procter [Wed, 21 Feb 2018 17:19:01 +0000 (17:19 +0000)]
Merge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Feb 2018 16:28:31 +0000 (16:28 +0000)]
JAL-2778 reinstate transparent windows to avoid ugly borders on OSX
gmungoc [Wed, 21 Feb 2018 16:18:29 +0000 (16:18 +0000)]
JAL-2629 simplifying method signatures in Hmmer command classes
kiramt [Wed, 21 Feb 2018 09:28:40 +0000 (09:28 +0000)]
JAL-2778 Adjust cursor changes in overview panel
kiramt [Wed, 21 Feb 2018 08:00:35 +0000 (08:00 +0000)]
JAL-2778 Revert back to old synchronisation
gmungoc [Tue, 20 Feb 2018 15:36:24 +0000 (15:36 +0000)]
JAL-2629 removed SequenceI.get/setLastPosition and related code
gmungoc [Tue, 20 Feb 2018 14:32:36 +0000 (14:32 +0000)]
Merge branch 'develop' into features/mchmmer
Conflicts:
resources/lang/Messages.properties
src/jalview/api/AlignViewportI.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/schemes/ResidueProperties.java
src/jalview/viewmodel/AlignmentViewport.java
Jim Procter [Tue, 20 Feb 2018 13:40:41 +0000 (13:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
gmungoc [Tue, 20 Feb 2018 13:01:36 +0000 (13:01 +0000)]
JAL-2897 updated unit test for code change
gmungoc [Tue, 20 Feb 2018 12:50:35 +0000 (12:50 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
Jim Procter [Tue, 20 Feb 2018 09:02:56 +0000 (09:02 +0000)]
Merge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums' into releases/Release_2_10_4_Branch
gmungoc [Mon, 19 Feb 2018 17:04:07 +0000 (17:04 +0000)]
JAL-2629 refactoring of Hmmer preferences
gmungoc [Mon, 19 Feb 2018 17:03:07 +0000 (17:03 +0000)]
JAL-2629 partial refactoring of Hmmer command classes
gmungoc [Mon, 19 Feb 2018 10:19:19 +0000 (10:19 +0000)]
JAL-2629 formatting only
Jim Procter [Thu, 15 Feb 2018 15:52:11 +0000 (15:52 +0000)]
Merge branch 'develop' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 15 Feb 2018 15:51:48 +0000 (15:51 +0000)]
JAL-2906 bump release version and cut new release note entry
Jim Procter [Tue, 13 Feb 2018 16:16:04 +0000 (16:16 +0000)]
JAL-2780 scan all test IDs before testing and reporting test failures - currently failing for 4im2 and Resnum==0 (seq pos 0)
Jim Procter [Tue, 13 Feb 2018 16:15:12 +0000 (16:15 +0000)]
JAL-2780 SequenceI.findFeatures takes column numbers in base 1…
Jim Procter [Tue, 13 Feb 2018 15:35:41 +0000 (15:35 +0000)]
JAL-2780 JAL-2781 don’t create a mapping if sequence position was not assigned but still keep track of ‘unobserved’ counts for bookkeeping
Jim Procter [Tue, 13 Feb 2018 15:34:22 +0000 (15:34 +0000)]
JAL-2780 JAL-2781 only create a mapping entry or write a character to the ‘mapped sequence’ for observed residues regardless of to/from coordinate frames
Jim Procter [Tue, 13 Feb 2018 15:33:16 +0000 (15:33 +0000)]
JAL-2781 JAL-2780 include sequence start number when computing position in PDB sequence when mapping from PDB to PDB
Jim Procter [Tue, 13 Feb 2018 15:31:35 +0000 (15:31 +0000)]
JAL-2781 ensure Trim is disabled before test starts
Jim Procter [Tue, 13 Feb 2018 15:28:21 +0000 (15:28 +0000)]
JAL-2781 refactor ‘trim retrieved sequence’ preference key to string constant for reuse in tests
Jim Procter [Tue, 13 Feb 2018 13:48:23 +0000 (13:48 +0000)]
JAL-2781 null local siftsClient variable if exception occurs (probably not needed but clearer this way ?)
Jim Procter [Tue, 13 Feb 2018 13:47:37 +0000 (13:47 +0000)]
JAL-2781 refactor StructureSelectionManager.siftsClient to local variable in computeMapping
Jim Procter [Tue, 13 Feb 2018 13:46:26 +0000 (13:46 +0000)]
JAL-2781 FIXME: value of sourceType parameter always overwritten
Jim Procter [Tue, 13 Feb 2018 13:45:28 +0000 (13:45 +0000)]
JAL-2781 refactor possibly non-functional ‘extract secondary structure’ logic out of computeMapping
Jim Procter [Tue, 13 Feb 2018 13:44:30 +0000 (13:44 +0000)]
JAL-2781 tidy up comments on getMapping/computeMapping
Jim Procter [Tue, 13 Feb 2018 12:50:40 +0000 (12:50 +0000)]
JAL-2781 report exactly which residues do not receive RESNUM annotation from associated structure data
Jim Procter [Tue, 13 Feb 2018 12:49:25 +0000 (12:49 +0000)]
JAL-2905 added additional jvmarg for testng task conditional on the JVM identifying as java.version==9
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
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.
gmungoc [Wed, 7 Feb 2018 15:20:29 +0000 (15:20 +0000)]
JAL-2808 ensure pattern field re-enabled when needed for condition
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
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 14:23:21 +0000 (14:23 +0000)]
JAL-2899 asynchronous Jmol colour updates
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
gmungoc [Thu, 1 Feb 2018 15:16:12 +0000 (15:16 +0000)]
JAL-2899 update structure and overview on slider drag release
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