jalview.git
6 years agoJAL-2679 reinstating changes lost in VCF merge
gmungoc [Wed, 14 Mar 2018 14:41:14 +0000 (14:41 +0000)]
JAL-2679 reinstating changes lost in VCF merge

6 years agoMerge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges... merges/JAL-2906_update2_11_from_2_10_4
gmungoc [Thu, 8 Mar 2018 14:06:44 +0000 (14:06 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges/JAL-2906_update2_11_from_2_10_4

6 years agoJAL-2885 tests updated for code changes
gmungoc [Thu, 8 Mar 2018 14:05:51 +0000 (14:05 +0000)]
JAL-2885 tests updated for code changes

6 years agoJAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation
gmungoc [Thu, 8 Mar 2018 11:29:11 +0000 (11:29 +0000)]
JAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation

6 years agoMerge branch 'releases/Release_2_10_4_Branch' into develop
Jim Procter [Wed, 7 Mar 2018 14:40:59 +0000 (14:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
check carefully that JAL-2885 (configurable Ensembl/Genomes Endpoints) functionality is still present

6 years agoMerge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 12:05:23 +0000 (12:05 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch

6 years agoJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922
gmungoc [Wed, 7 Mar 2018 12:04:58 +0000 (12:04 +0000)]
JAL-2922 [2] not [1] for Boolean column of table

6 years agoMerge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:53:57 +0000 (11:53 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch

6 years agoJAL-2922 i18n and bespoke handler for Invert Selection
gmungoc [Wed, 7 Mar 2018 11:53:26 +0000 (11:53 +0000)]
JAL-2922 i18n and bespoke handler for Invert Selection

6 years agoMerge branch 'bug/JAL-2924nullTooltip' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:30:09 +0000 (11:30 +0000)]
Merge branch 'bug/JAL-2924nullTooltip' into releases/Release_2_10_4_Branch

6 years agoJAL-2926 fix copy group consensus (and paste sequence with space in name)
gmungoc [Wed, 7 Mar 2018 11:27:57 +0000 (11:27 +0000)]
JAL-2926 fix copy group consensus (and paste sequence with space in name)

6 years agoJAL-2925 handle empty annotation when copying group consensus
gmungoc [Wed, 7 Mar 2018 11:27:20 +0000 (11:27 +0000)]
JAL-2925 handle empty annotation when copying group consensus

6 years agoJAL-2913 use FIGURE_USERIDWIDTH for fixed id width property
gmungoc [Wed, 7 Mar 2018 11:04:42 +0000 (11:04 +0000)]
JAL-2913 use FIGURE_USERIDWIDTH for fixed id width property

6 years agoJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip
gmungoc [Wed, 28 Feb 2018 17:54:15 +0000 (17:54 +0000)]
JAL-2924 no tooltip over null annotation positions

6 years agoMerge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2...
Jim Procter [Wed, 28 Feb 2018 10:32:14 +0000 (10:32 +0000)]
Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2_10_4_Branch

6 years agoJAL-2759 release notes for 2.10.4
Jim Procter [Tue, 27 Feb 2018 16:18:59 +0000 (16:18 +0000)]
JAL-2759 release notes for 2.10.4

6 years agoMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
Jim Procter [Tue, 27 Feb 2018 11:16:41 +0000 (11:16 +0000)]
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104

6 years agofix for JAL-2922 - update states all at once and then refresh
Jim Procter [Tue, 27 Feb 2018 11:07:48 +0000 (11:07 +0000)]
fix for JAL-2922 - update states all at once and then refresh

6 years agoMerge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 26 Feb 2018 10:13:30 +0000 (10:13 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

6 years agoJAL-984 remove all references to idwidth.gif - in build.xml too :) feature/JAL-984splitAdjuster
Jim Procter [Mon, 26 Feb 2018 10:12:45 +0000 (10:12 +0000)]
JAL-984 remove all references to idwidth.gif - in build.xml too :)

6 years agoJAL-2885 release notes
Jim Procter [Fri, 23 Feb 2018 16:54:28 +0000 (16:54 +0000)]
JAL-2885 release notes

6 years agoMerge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 23 Feb 2018 16:01:42 +0000 (16:01 +0000)]
Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

6 years agoJAL-2885 xfam https features/JAL-2885UniprotHttps
Jim Procter [Fri, 23 Feb 2018 11:40:15 +0000 (11:40 +0000)]
JAL-2885 xfam https

6 years agoJAL-2885 XFAM_DOMAIN->XFAM_BASEURL
Jim Procter [Fri, 23 Feb 2018 11:39:34 +0000 (11:39 +0000)]
JAL-2885 XFAM_DOMAIN->XFAM_BASEURL

6 years agoJAL-2885 Ensembl* -> https
Jim Procter [Fri, 23 Feb 2018 11:35:43 +0000 (11:35 +0000)]
JAL-2885 Ensembl* -> https

6 years agoJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
Jim Procter [Fri, 23 Feb 2018 11:33:41 +0000 (11:33 +0000)]
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL

6 years agoJAL-2885 renamed base URL getter from getDomain..
Jim Procter [Fri, 23 Feb 2018 11:24:03 +0000 (11:24 +0000)]
JAL-2885 renamed base URL getter from getDomain..

6 years agoMerge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 15:15:35 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

6 years agoJAL-984 ID width adjuster needs to be white !
Jim Procter [Thu, 22 Feb 2018 15:14:46 +0000 (15:14 +0000)]
JAL-984 ID width adjuster needs to be white !

6 years agoJAL-2666 release notes
Jim Procter [Thu, 22 Feb 2018 15:05:36 +0000 (15:05 +0000)]
JAL-2666 release notes

6 years agoMerge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:48:58 +0000 (14:48 +0000)]
Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch

6 years agoMerge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:34:44 +0000 (14:34 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

6 years agoJAL-984 remove all references to idwidth.gif and use int constants in place of width...
Jim Procter [Thu, 22 Feb 2018 14:34:23 +0000 (14:34 +0000)]
JAL-984 remove all references to idwidth.gif and use int constants in place of width/height of image when switching between margin adjustment active/inactive mouse cursor

6 years agoJAL-2906 typo fixes
Jim Procter [Thu, 22 Feb 2018 14:16:26 +0000 (14:16 +0000)]
JAL-2906 typo fixes

6 years agoJAL-984 release notes
Jim Procter [Thu, 22 Feb 2018 14:15:19 +0000 (14:15 +0000)]
JAL-984 release notes

6 years agoMerge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:08:47 +0000 (14:08 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

6 years agoJAL-294 remove unneeded paint() method
Jim Procter [Thu, 22 Feb 2018 14:08:15 +0000 (14:08 +0000)]
JAL-294 remove unneeded paint() method

6 years agoJAL-984 remove commented/unnecessary if clause
Jim Procter [Thu, 22 Feb 2018 14:07:58 +0000 (14:07 +0000)]
JAL-984 remove commented/unnecessary if clause

6 years agoJAL-2906 release notes for 2.10.4
Jim Procter [Wed, 21 Feb 2018 17:40:04 +0000 (17:40 +0000)]
JAL-2906 release notes for 2.10.4

6 years agoMerge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch
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

6 years agoJAL-2778 reinstate transparent windows to avoid ugly borders on OSX bug/JAL-2778again
Jim Procter [Wed, 21 Feb 2018 16:28:31 +0000 (16:28 +0000)]
JAL-2778 reinstate transparent windows to avoid ugly borders on OSX

6 years agoJAL-2778 Adjust cursor changes in overview panel
kiramt [Wed, 21 Feb 2018 09:28:40 +0000 (09:28 +0000)]
JAL-2778 Adjust cursor changes in overview panel

6 years agoJAL-2778 Revert back to old synchronisation
kiramt [Wed, 21 Feb 2018 08:00:35 +0000 (08:00 +0000)]
JAL-2778 Revert back to old synchronisation

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 agoJAL-2789 avoid using transcript (with no UTR) as CDS sequence bug/JAL-2666
gmungoc [Fri, 9 Feb 2018 12:14:38 +0000 (12:14 +0000)]
JAL-2789 avoid using transcript (with no UTR) as CDS sequence

6 years agoJAL-2789 code format changes only (before functional fixes)
gmungoc [Fri, 9 Feb 2018 12:07:56 +0000 (12:07 +0000)]
JAL-2789 code format changes only (before functional fixes)

6 years agoJAL-2666 fix failure to scroll split alignment of height 1
gmungoc [Fri, 9 Feb 2018 12:03:57 +0000 (12:03 +0000)]
JAL-2666 fix failure to scroll split alignment of height 1

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-2666 basic initial fix for split screen scroll bug
gmungoc [Thu, 8 Feb 2018 16:16:41 +0000 (16:16 +0000)]
JAL-2666 basic initial fix for split screen scroll bug

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 agoMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
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

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-2759 Fix errant RangeElementsIterator (unit tests were failing)
kiramt [Mon, 5 Feb 2018 14:41:46 +0000 (14:41 +0000)]
JAL-2759 Fix errant RangeElementsIterator (unit tests were failing)

6 years agoJAL-2759 Rename getBoundedStartIterator
kiramt [Mon, 5 Feb 2018 13:49:19 +0000 (13:49 +0000)]
JAL-2759 Rename getBoundedStartIterator

6 years agoJAL-2759 Changes to StartRegionIterator after review
kiramt [Mon, 5 Feb 2018 13:46:09 +0000 (13:46 +0000)]
JAL-2759 Changes to StartRegionIterator after review