jalview.git
6 years agoMerge branch 'releases/Release_2_10_4_Branch' into develop
Jim Procter [Tue, 20 Feb 2018 13:40:41 +0000 (13:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop

6 years agoJAL-2897 updated unit test for code change features/JAL-1793VCF
gmungoc [Tue, 20 Feb 2018 13:01:36 +0000 (13:01 +0000)]
JAL-2897 updated unit test for code change

6 years agoMerge branch 'develop' into features/JAL-1793VCF
gmungoc [Tue, 20 Feb 2018 12:50:35 +0000 (12:50 +0000)]
Merge branch 'develop' into features/JAL-1793VCF

6 years agoMerge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums' into releases/Release_2_10_4_Branch
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

6 years agoMerge branch 'develop' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 15 Feb 2018 15:52:11 +0000 (15:52 +0000)]
Merge branch 'develop' into releases/Release_2_10_4_Branch

6 years agoJAL-2906 bump release version and cut new release note entry
Jim Procter [Thu, 15 Feb 2018 15:51:48 +0000 (15:51 +0000)]
JAL-2906 bump release version and cut new release note entry

6 years agoJAL-2780 scan all test IDs before testing and reporting test failures - currently... bugs/JAL-2780_JAL-2781_pdbnegativenums
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)

6 years agoJAL-2780 SequenceI.findFeatures takes column numbers in base 1…

Jim Procter [Tue, 13 Feb 2018 16:15:12 +0000 (16:15 +0000)]
JAL-2780 SequenceI.findFeatures takes column numbers in base 1…


6 years agoJAL-2780 JAL-2781 don’t create a mapping if sequence position was not assigned but...
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

6 years agoJAL-2780 JAL-2781 only create a mapping entry or write a character to the ‘mapped...
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

6 years agoJAL-2781 JAL-2780 include sequence start number when computing position in PDB sequen...
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

6 years agoJAL-2781 ensure Trim is disabled before test starts
Jim Procter [Tue, 13 Feb 2018 15:31:35 +0000 (15:31 +0000)]
JAL-2781 ensure Trim is disabled before test starts

6 years agoJAL-2781 refactor ‘trim retrieved sequence’ preference key to string constant for...
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

6 years agoJAL-2781 null local siftsClient variable if exception occurs (probably not needed...
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 ?)

6 years agoJAL-2781 refactor StructureSelectionManager.siftsClient to local variable in computeM...
Jim Procter [Tue, 13 Feb 2018 13:47:37 +0000 (13:47 +0000)]
JAL-2781 refactor StructureSelectionManager.siftsClient to local variable in computeMapping

6 years agoJAL-2781 FIXME: value of sourceType parameter always overwritten
Jim Procter [Tue, 13 Feb 2018 13:46:26 +0000 (13:46 +0000)]
JAL-2781 FIXME: value of sourceType parameter always overwritten

6 years agoJAL-2781 refactor possibly non-functional ‘extract secondary structure’ logic out...
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

6 years agoJAL-2781 tidy up comments on getMapping/computeMapping
Jim Procter [Tue, 13 Feb 2018 13:44:30 +0000 (13:44 +0000)]
JAL-2781 tidy up comments on getMapping/computeMapping

6 years agoJAL-2781 report exactly which residues do not receive RESNUM annotation from associat...
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

6 years agoJAL-2905 added additional jvmarg for testng task conditional on the JVM identifying...
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

6 years agoJAL-2780 JAL-2781 extra column in mapping array
Jim Procter [Mon, 12 Feb 2018 17:13:50 +0000 (17:13 +0000)]
JAL-2780 JAL-2781 extra column in mapping array

6 years agoJAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest for removal of redundant first...
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

6 years agoJAL-2780 JAL-2781 ahem - add a semicolon if there isn’t one
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

6 years agoJAL-2780 use value of ’UNASSIGNED’ constant in assert verifying expected unassigned...
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

6 years agoJAL-2904 replaced assert for (getEnd()-getStart()+1)==getLength() in testPdb/mmCIFSeq...
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.

6 years agoJAL-2781 use SIFTs mapping rather than maxChain AlignSeq to propagate annotation...
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

6 years agoJAL-2780 JAL-2781 use PDBe numbering to map between sequence extracted from PDB chain...
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

6 years agoJAL-2781 mark aligned positions via StructureMapping’s Mapping object, and transfer...
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

6 years agoJAL-2780 JAL-2781 include a Mapping object in StructureMapping to pass to sequence...
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

6 years agoJAL-2780 JAL-2781 UNASSIGNED positions marked as Integer.Min
Jim Procter [Sun, 11 Feb 2018 10:45:23 +0000 (10:45 +0000)]
JAL-2780 JAL-2781 UNASSIGNED positions marked as Integer.Min

6 years agoJAL-2781 fix test data for full length annotation
Jim Procter [Sun, 11 Feb 2018 10:41:07 +0000 (10:41 +0000)]
JAL-2781 fix test data for full length annotation

6 years agoUse the “PDBe” or “PDB” numbering (starts from 1, corresponds with the PDB SEQRES...
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).

6 years agoJAL-2780 JAL-2781 should always ensure SIFTS mappings are made to dataset sequence...
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.

6 years agoJAL-2780 JAL-2781 run sequentially and ensure windows are closed so structureselectio...
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.

6 years agoJAL-2780 JAL-2891 clear all windows always beforeTest for Jalview2XmlBase
Jim Procter [Wed, 7 Feb 2018 16:56:44 +0000 (16:56 +0000)]
JAL-2780 JAL-2891 clear all windows always beforeTest for Jalview2XmlBase

6 years agoJAL-2902 catch case where viewer is closed (therefore binding is null) before hasMapp...
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.

6 years agoJAL-2902 thread off dialog close op to avoid deadlock on the main swing thread.
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.

6 years agoJAL-2808 ensure pattern field re-enabled when needed for condition
gmungoc [Wed, 7 Feb 2018 15:20:29 +0000 (15:20 +0000)]
JAL-2808 ensure pattern field re-enabled when needed for condition

6 years agoJAL-2780 JAL-2781 first pass at failing test for incorrect colouring of structure...
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

6 years agoJAL-2780 JAL-2781 JAL-2902 refactored helper method in test for programmatically...
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

6 years agoJAL-2902 - isBusy and hasMapping methods so client can wait until a newly opened...
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]

6 years agoJAL-2780 JAL-2781 fix javadoc in line with behaviour for getPDBResNum
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

6 years agoJAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to optionally blocking method for...
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

6 years agoJAL-2780 JAL-2781 don’t assume contiguous mapping to PDB residue numbering when gener...
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).

6 years agoJAL-2780 JAL-2781 (failing) test comparing location of transferred annotation from...
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

6 years agoJAL-2780 JAL-2781 programmatically select structures for retrieval via Structure...
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

6 years agoJAL-2780 JAL-2871 only look up current table view once
Jim Procter [Mon, 5 Feb 2018 16:38:48 +0000 (16:38 +0000)]
JAL-2780 JAL-2871 only look up current table view once

6 years agoJAL-2780 JAL-2781 test AlignmentI.findAnnotations locates sequence associated annotat...
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

6 years agoJAL-2780 JAL-2781 - patch and first test for AlignmentI.findOrCreateAnnotation
Jim Procter [Mon, 5 Feb 2018 16:34:28 +0000 (16:34 +0000)]
JAL-2780 JAL-2781 - patch and first test for AlignmentI.findOrCreateAnnotation

6 years agoJAL-2897 more informative description on synonymous variants
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

6 years agoJAL-2897 more informative description on synonymous variants
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants

6 years agoMerge branch 'spikes/mungo' into trialMerge
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

6 years agoJAL-2897 more informative description on synonymous variants
gmungoc [Mon, 5 Feb 2018 09:32:12 +0000 (09:32 +0000)]
JAL-2897 more informative description on synonymous variants

6 years agoJAL-984 merged to spikes-mungo
gmungoc [Fri, 2 Feb 2018 15:56:43 +0000 (15:56 +0000)]
JAL-984 merged to spikes-mungo

6 years agoMerge branch 'feature/JAL-984splitAdjuster' into features/JAL-1793VCF
gmungoc [Fri, 2 Feb 2018 15:55:11 +0000 (15:55 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into features/JAL-1793VCF

6 years agoJAL-984 use cursor for drag regions to adjust annotation height or id width
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

6 years agoJAL-984 better behaved panel height adjuster
gmungoc [Fri, 2 Feb 2018 10:14:17 +0000 (10:14 +0000)]
JAL-984 better behaved panel height adjuster

6 years agoJAL-2792 added tooltip to menu items in case of truncation
gmungoc [Wed, 31 Jan 2018 11:28:03 +0000 (11:28 +0000)]
JAL-2792 added tooltip to menu items in case of truncation

6 years agoJAL-2069 menu item now "Variable colour..." to hint at more...
gmungoc [Tue, 30 Jan 2018 16:26:44 +0000 (16:26 +0000)]
JAL-2069 menu item now "Variable colour..." to hint at more...

6 years agoJAL-1793 update spike build to latest incl stop and synonymous variants on peptides
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

6 years agoJAL-2898 show 'stop_gained' variants on peptide sequences
gmungoc [Tue, 30 Jan 2018 15:57:03 +0000 (15:57 +0000)]
JAL-2898 show 'stop_gained' variants on peptide sequences

6 years agoJAL-2897 generate peptide variants for synonymous codon variants
gmungoc [Tue, 30 Jan 2018 15:34:48 +0000 (15:34 +0000)]
JAL-2897 generate peptide variants for synonymous codon variants

6 years agoJAL-2897 formatting change only prior to functional change
gmungoc [Tue, 30 Jan 2018 15:29:57 +0000 (15:29 +0000)]
JAL-2897 formatting change only prior to functional change

6 years agoJAL-2743 recoded EnsemblLookup without lambda expressions for parsing response
gmungoc [Mon, 29 Jan 2018 09:24:38 +0000 (09:24 +0000)]
JAL-2743 recoded EnsemblLookup without lambda expressions for parsing response

6 years agoMerge branch 'releases/Release_2_10_3_Branch' into bugs/JAL-2780_JAL-2781_pdbnegativenums
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

6 years agoMerge branch 'develop' into features/JAL-1793VCF
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

6 years agoMerge branch 'develop' into releases/Release_2_10_3_Branch releases/Release_2_10_3_Branch Release_2_10_3b1
Jim Procter [Wed, 24 Jan 2018 07:37:42 +0000 (07:37 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch

6 years agoJAL-2858 update release date and rejig what's new message
Jim Procter [Wed, 24 Jan 2018 07:36:56 +0000 (07:36 +0000)]
JAL-2858 update release date and rejig what's new message

6 years agoMerge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Tue, 23 Jan 2018 14:11:15 +0000 (14:11 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch

6 years agoJAL-2858 fix what's new
Jim Procter [Tue, 23 Jan 2018 13:52:31 +0000 (13:52 +0000)]
JAL-2858 fix what's new

6 years agoMerge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Tue, 23 Jan 2018 12:04:09 +0000 (12:04 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch

6 years agoJAL-2858 update latest release notes link in TOC
Jim Procter [Tue, 23 Jan 2018 12:03:37 +0000 (12:03 +0000)]
JAL-2858 update latest release notes link in TOC

6 years agoJAL-2859 release notes
Jim Procter [Tue, 23 Jan 2018 11:57:05 +0000 (11:57 +0000)]
JAL-2859 release notes

6 years agoJAL-2858 update release notes
Jim Procter [Tue, 23 Jan 2018 11:54:49 +0000 (11:54 +0000)]
JAL-2858 update release notes

6 years agoMerge branch 'develop' into releases/Release_2_10_3_Branch
Jim Procter [Mon, 22 Jan 2018 15:27:07 +0000 (15:27 +0000)]
Merge branch 'develop' into releases/Release_2_10_3_Branch

6 years agoJAL-2858 release notes for 2.10.3b1 (including revision to EnsemblGenomes client...
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)

6 years agoJAL-2858 bump version number for 2.10.3b1
Jim Procter [Mon, 22 Jan 2018 15:25:23 +0000 (15:25 +0000)]
JAL-2858 bump version number for 2.10.3b1

6 years agoJAL-2810 JAL-2886 i18n
gmungoc [Thu, 18 Jan 2018 16:12:50 +0000 (16:12 +0000)]
JAL-2810 JAL-2886 i18n

6 years agoJAL-2679 update query id to actual case of retrieved gene
gmungoc [Thu, 18 Jan 2018 14:54:49 +0000 (14:54 +0000)]
JAL-2679 update query id to actual case of retrieved gene

6 years agoJAL-2679 case-insensitive comparison of query and retrieved accession
gmungoc [Wed, 17 Jan 2018 11:37:09 +0000 (11:37 +0000)]
JAL-2679 case-insensitive comparison of query and retrieved accession

6 years agoJAL-2679 use object_type=Transcript for lookup of Parent for Protein
gmungoc [Tue, 16 Jan 2018 16:27:19 +0000 (16:27 +0000)]
JAL-2679 use object_type=Transcript for lookup of Parent for Protein

6 years agoJAL-2886 trivial unit test fix
kiramt [Fri, 12 Jan 2018 11:37:03 +0000 (11:37 +0000)]
JAL-2886 trivial unit test fix

6 years agoMerge remote-tracking branch 'origin/task/JAL-2662' into develop
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

6 years agoJAL-2662 Updated README task/JAL-2662
kiramt [Thu, 11 Jan 2018 14:53:00 +0000 (14:53 +0000)]
JAL-2662 Updated README

6 years agoJAL-1793 update spike branch to latest
gmungoc [Wed, 10 Jan 2018 15:20:56 +0000 (15:20 +0000)]
JAL-1793 update spike branch to latest

6 years agoJAL-2791 ignore feature type visibility in getColor()
gmungoc [Wed, 10 Jan 2018 15:17:53 +0000 (15:17 +0000)]
JAL-2791 ignore feature type visibility in getColor()

6 years agoJAL-2843 test roundtrip of feature colours and filters to Jalview project
gmungoc [Tue, 9 Jan 2018 16:53:15 +0000 (16:53 +0000)]
JAL-2843 test roundtrip of feature colours and filters to Jalview project

6 years agoJAL-2843 unit tests for writing filters to Jalview features file
gmungoc [Tue, 9 Jan 2018 16:28:11 +0000 (16:28 +0000)]
JAL-2843 unit tests for writing filters to Jalview features file

6 years agoJAL-2843 unit tests for Save/Load colours and filters as XML
gmungoc [Tue, 9 Jan 2018 15:40:52 +0000 (15:40 +0000)]
JAL-2843 unit tests for Save/Load colours and filters as XML

6 years agoJAL-2808 small tweaks to api / Javadoc
gmungoc [Tue, 9 Jan 2018 15:39:53 +0000 (15:39 +0000)]
JAL-2808 small tweaks to api / Javadoc

6 years agoJAL-2069 fix setting initial value of slider from threshold
gmungoc [Mon, 8 Jan 2018 14:52:53 +0000 (14:52 +0000)]
JAL-2069 fix setting initial value of slider from threshold

6 years agoJAL-2880 disabled non-functional test - Jmol parser does not have proper association...
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.

6 years agoJAL-2843 missed Castor class
gmungoc [Thu, 14 Dec 2017 16:34:01 +0000 (16:34 +0000)]
JAL-2843 missed Castor class

6 years agoJAL-2843 save/restore colour feature by attribute, and feature filters, to Jalview...
gmungoc [Thu, 14 Dec 2017 16:33:00 +0000 (16:33 +0000)]
JAL-2843 save/restore colour feature by attribute, and feature filters, to Jalview project

6 years agoJAL-2879 save/restore feature sub-attributes in Jalview project
gmungoc [Thu, 14 Dec 2017 15:02:04 +0000 (15:02 +0000)]
JAL-2879 save/restore feature sub-attributes in Jalview project

6 years agoJAL-2843 missed Castor class
gmungoc [Thu, 14 Dec 2017 12:46:42 +0000 (12:46 +0000)]
JAL-2843 missed Castor class

6 years agoJAL-2843 and Castor metadata file for latest changes
gmungoc [Thu, 14 Dec 2017 12:45:32 +0000 (12:45 +0000)]
JAL-2843 and Castor metadata file for latest changes

6 years agoJAL-2843 schema and code changes to save colour by attribute and filters in user...
gmungoc [Thu, 14 Dec 2017 11:25:57 +0000 (11:25 +0000)]
JAL-2843 schema and code changes to save colour by attribute and filters in user colours XML file

6 years agoJAL-2843 add isByAttribute to interface for convenience
gmungoc [Wed, 13 Dec 2017 16:54:31 +0000 (16:54 +0000)]
JAL-2843 add isByAttribute to interface for convenience

6 years agoJAL-2843 add colour by attribute, and no value colour, to features file
gmungoc [Mon, 11 Dec 2017 15:16:05 +0000 (15:16 +0000)]
JAL-2843 add colour by attribute, and no value colour, to features file