jalview.git
8 years agoJAL-2110 wip CrossRefs rewrite of CrossRef
gmungoc [Wed, 25 May 2016 08:25:19 +0000 (09:25 +0100)]
JAL-2110 wip CrossRefs rewrite of CrossRef

8 years agoMerge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef
gmungoc [Mon, 23 May 2016 12:22:40 +0000 (13:22 +0100)]
Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef

8 years agoJAL-2114 explicit invalid test cases added
gmungoc [Fri, 20 May 2016 20:00:28 +0000 (21:00 +0100)]
JAL-2114 explicit invalid test cases added

8 years agoJAL-2114 accept "<123..178" or "123..>178" format
gmungoc [Fri, 20 May 2016 17:30:55 +0000 (18:30 +0100)]
JAL-2114 accept "<123..178" or "123..>178" format

8 years agoJAL-2115 updated web link for MAFFT (and one typo)
gmungoc [Fri, 20 May 2016 17:18:57 +0000 (18:18 +0100)]
JAL-2115 updated web link for MAFFT (and one typo)

8 years agoJAL-2110 unit tests for and minor refactoring of CrossRef
gmungoc [Fri, 20 May 2016 12:36:08 +0000 (13:36 +0100)]
JAL-2110 unit tests for and minor refactoring of CrossRef

8 years agoJAL-2049 unit test updated for HGVS syntax, feature group = "Jalview"
gmungoc [Fri, 20 May 2016 07:51:47 +0000 (08:51 +0100)]
JAL-2049 unit test updated for HGVS syntax, feature group = "Jalview"

8 years agoJAL-2114 added single-locus case and more error tests
gmungoc [Thu, 19 May 2016 16:14:09 +0000 (17:14 +0100)]
JAL-2114 added single-locus case and more error tests

8 years agoJAL-2114 parser + tests for GenBank location descriptors
gmungoc [Thu, 19 May 2016 16:01:14 +0000 (17:01 +0100)]
JAL-2114 parser + tests for GenBank location descriptors

8 years agomerge
tcofoegbu [Wed, 18 May 2016 15:50:26 +0000 (16:50 +0100)]
merge

8 years agoJAL-1563 User documentation for Uniprot FTS
tcofoegbu [Wed, 18 May 2016 15:49:58 +0000 (16:49 +0100)]
JAL-1563 User documentation for Uniprot FTS

8 years agoJAL-1563 smarter support for advanced querying of Uniprot FTS
tcofoegbu [Wed, 18 May 2016 15:48:39 +0000 (16:48 +0100)]
JAL-1563 smarter support for advanced querying of Uniprot FTS

8 years agoJAL-2049 set sequence feature group to "Jalview" for computed protein
gmungoc [Wed, 18 May 2016 12:18:09 +0000 (13:18 +0100)]
JAL-2049 set sequence feature group to "Jalview" for computed protein
variants

8 years agoJAL-2049 use HGVS notation for variant on protein residue
gmungoc [Wed, 18 May 2016 12:09:50 +0000 (13:09 +0100)]
JAL-2049 use HGVS notation for variant on protein residue

8 years agoJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
tcofoegbu [Tue, 17 May 2016 11:31:25 +0000 (12:31 +0100)]
JAL-2106 JAL-1926 updated source doc for set/getSourceDBRef

8 years agomerge
tcofoegbu [Tue, 17 May 2016 11:11:39 +0000 (12:11 +0100)]
merge

8 years agoJAL-1270 Fixed anntatedPDBFileInputTest and updated implementation for testDeriveSequ...
tcofoegbu [Tue, 17 May 2016 11:11:06 +0000 (12:11 +0100)]
JAL-1270 Fixed anntatedPDBFileInputTest and updated implementation for testDeriveSequence_existingDataset method in SequenceTest

8 years agoJAL-2105 capture Ensembl data version, check REST version (per domain)
gmungoc [Fri, 13 May 2016 09:17:57 +0000 (10:17 +0100)]
JAL-2105 capture Ensembl data version, check REST version (per domain)

8 years agoJAL-2104 format tooltips to wrap correctly
gmungoc [Thu, 12 May 2016 08:45:17 +0000 (09:45 +0100)]
JAL-2104 format tooltips to wrap correctly

8 years agoJAL-1563 updated uniprot FTS config file
tcofoegbu [Wed, 11 May 2016 14:58:21 +0000 (15:58 +0100)]
JAL-1563 updated uniprot FTS config file

8 years agomerge
tcofoegbu [Mon, 9 May 2016 16:48:10 +0000 (17:48 +0100)]
merge

8 years agoJAL-2101 JAL-2071 JAL-1563 Added fix to enable searching for old entry names in Unipr...
tcofoegbu [Mon, 9 May 2016 16:43:56 +0000 (17:43 +0100)]
JAL-2101 JAL-2071 JAL-1563 Added fix to enable searching for old entry names in Uniprot FTS, modified Uniprot FTS data column config file to ensure query consistency with uniprot.org, formatted page range number in FTS summary panel, fixed broken tests, and added Jalview licence header to the Uniprot FTS data column config file

8 years agoJAL-2102 implemented improvement to round FTS's numberic data columns to a configurab...
tcofoegbu [Mon, 9 May 2016 16:36:10 +0000 (17:36 +0100)]
JAL-2102 implemented improvement to round FTS's numberic data columns to a configurable number of significant figures, and added Jalview licence header to the PDB FTS data column config file

8 years agoJAL-2098 identify feature file with "<" in feature type name
gmungoc [Mon, 9 May 2016 14:18:12 +0000 (15:18 +0100)]
JAL-2098 identify feature file with "<" in feature type name

8 years agoJAL-2018 export graduated feature colours correctly
gmungoc [Mon, 9 May 2016 13:41:43 +0000 (14:41 +0100)]
JAL-2018 export graduated feature colours correctly

8 years agoMerge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Fri, 6 May 2016 14:39:04 +0000 (15:39 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop

8 years agoJAL-192 fix javadoc
Jim Procter [Fri, 6 May 2016 14:34:30 +0000 (15:34 +0100)]
JAL-192 fix javadoc

8 years agoJAL-192 JAL-2099 unused variables
Jim Procter [Fri, 6 May 2016 14:31:09 +0000 (15:31 +0100)]
JAL-192 JAL-2099 unused variables

8 years agoJAL-1551 formatting
Jim Procter [Fri, 6 May 2016 14:29:26 +0000 (15:29 +0100)]
JAL-1551 formatting

8 years agoJAL-192 JAL-2099 reuse refactored scale code for wrapped view
Jim Procter [Fri, 6 May 2016 14:29:14 +0000 (15:29 +0100)]
JAL-192 JAL-2099 reuse refactored scale code for wrapped view

8 years agoJAL-192 JAL-2099 factored out calculation from rendering code #3
Jim Procter [Fri, 6 May 2016 14:13:41 +0000 (15:13 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #3

8 years agoJAL-192 JAL-2099 factored out calculation from rendering code #2
Jim Procter [Fri, 6 May 2016 14:03:24 +0000 (15:03 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #2

8 years agoJAL-192 JAL-2099 factored out calculation from rendering code #1
Jim Procter [Fri, 6 May 2016 13:51:38 +0000 (14:51 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #1

8 years agoJAL-2100 centre triangles on hidden column vertical mark and place them below numbers...
Jim Procter [Fri, 6 May 2016 13:21:53 +0000 (14:21 +0100)]
JAL-2100 centre triangles on hidden column vertical mark and place them below numbers on ruler

8 years agoJAL-2100 optimisation
Jim Procter [Fri, 6 May 2016 13:20:41 +0000 (14:20 +0100)]
JAL-2100 optimisation

8 years agoJAL-2100 triangles shown below in jvdesktop unwrapped ruler
Jim Procter [Fri, 6 May 2016 13:09:53 +0000 (14:09 +0100)]
JAL-2100 triangles shown below in jvdesktop unwrapped ruler

8 years agoJAL-192 patch off-by-one for pathological gap case
Jim Procter [Fri, 6 May 2016 13:02:25 +0000 (14:02 +0100)]
JAL-192 patch off-by-one for pathological gap case
JAL-2099 fix incorrect numbering with hidden-columns

8 years agoJAL-2068 better documentation in example script
gmungoc [Thu, 5 May 2016 14:36:08 +0000 (15:36 +0100)]
JAL-2068 better documentation in example script

8 years agoJAL-192 patch for off-by one and pathological case (hide inserted regions + set refer...
Jim Procter [Thu, 5 May 2016 13:25:30 +0000 (14:25 +0100)]
JAL-192 patch for off-by one and pathological case (hide inserted regions + set reference sequence -> column positions numbered with seq-number+’-‘ ! )

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git
gmungoc [Wed, 4 May 2016 15:22:53 +0000 (16:22 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git
into develop

Conflicts:
lib/xercesImpl.jar

8 years agoJAL-2074 reinstated xerces-impl.jar
gmungoc [Wed, 4 May 2016 15:11:43 +0000 (16:11 +0100)]
JAL-2074 reinstated xerces-impl.jar

8 years agoRevert "JAL-2074 removed xerces to explore wierdness"
Jim Procter [Wed, 4 May 2016 15:08:03 +0000 (16:08 +0100)]
Revert "JAL-2074 removed xerces to explore wierdness"

This reverts commit e9ed820777700129be68c32f9fb80a84acd381b9.

8 years agoJAL-2092 hide columns with/without feature
gmungoc [Wed, 4 May 2016 15:04:26 +0000 (16:04 +0100)]
JAL-2092 hide columns with/without feature

8 years agoJAL-2074 corrected classpathentry for Groovy 2.4.6
gmungoc [Wed, 4 May 2016 14:03:19 +0000 (15:03 +0100)]
JAL-2074 corrected classpathentry for Groovy 2.4.6

8 years agoMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop
gmungoc [Wed, 4 May 2016 13:55:16 +0000 (14:55 +0100)]
Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop

8 years agomerge
tcofoegbu [Wed, 4 May 2016 11:58:26 +0000 (12:58 +0100)]
merge

8 years agoJAL-1563 JAL-2091 Added total result count to Uniprot pagination, implemented caching...
tcofoegbu [Wed, 4 May 2016 11:57:56 +0000 (12:57 +0100)]
JAL-1563 JAL-2091 Added total result count to Uniprot pagination, implemented caching of selections for FTS services pagination, and added horizontal scrollbar to structure chooser summary table

8 years agoJAL-2090 removed test for Java > 1.1 to enable transparency
gmungoc [Wed, 4 May 2016 08:11:13 +0000 (09:11 +0100)]
JAL-2090 removed test for Java > 1.1 to enable transparency

8 years agoJAL-2050 hide introns also when fetching Ensembl xrefs for Uniprot
gmungoc [Tue, 3 May 2016 15:53:21 +0000 (16:53 +0100)]
JAL-2050 hide introns also when fetching Ensembl xrefs for Uniprot

8 years agoMerge branch 'r291_docs' into develop
Jim Procter [Tue, 3 May 2016 15:04:43 +0000 (16:04 +0100)]
Merge branch 'r291_docs' into develop

8 years agoJAL-2091 disable pagination buttons during initialisation
tcofoegbu [Tue, 3 May 2016 14:18:43 +0000 (15:18 +0100)]
JAL-2091 disable pagination buttons during initialisation

8 years agoJAL-1563 JAL-2091 Added generic pagination for FTS Service, pagination for PDB FTS...
tcofoegbu [Tue, 3 May 2016 13:22:59 +0000 (14:22 +0100)]
JAL-1563 JAL-2091 Added generic pagination for FTS Service, pagination for PDB FTS, error handling for Uniprot FTS rest client and minor refactoring/housekeeping

8 years agoJAL-1563 Fixed Uniprot FTS result-set count error, added blank image placeholder...
tcofoegbu [Mon, 2 May 2016 11:46:48 +0000 (12:46 +0100)]
JAL-1563 Fixed Uniprot FTS result-set count error, added blank image placeholder to prevent UI from jittering during a search operation, reverted timer for search textfield back to 1.5ses

8 years agoJAL-1270 move some Network tests to External (require third-party services)
Jim Procter [Mon, 2 May 2016 11:22:32 +0000 (12:22 +0100)]
JAL-1270 move some Network tests to External (require third-party services)

8 years agoJAL-1270 capitalise test groups
Jim Procter [Mon, 2 May 2016 11:21:06 +0000 (12:21 +0100)]
JAL-1270 capitalise test groups

8 years agoJAL-2089 JAL-1551 formatting
Jim Procter [Mon, 2 May 2016 11:19:54 +0000 (12:19 +0100)]
JAL-2089 JAL-1551 formatting

8 years agoJAL-2089 release 2.9.1 entry in release notes
Jim Procter [Mon, 2 May 2016 11:19:23 +0000 (12:19 +0100)]
JAL-2089 release 2.9.1 entry in release notes

8 years agomerge
tcofoegbu [Fri, 29 Apr 2016 15:54:18 +0000 (16:54 +0100)]
merge

8 years agoJAL-1563 house keeping/updated API doc for new method added for FTS pagination merge/JAL-1563_uniprot-free-text-search
tcofoegbu [Fri, 29 Apr 2016 15:50:02 +0000 (16:50 +0100)]
JAL-1563 house keeping/updated API doc for new method added for FTS pagination

8 years agoJAL-1563 Further increased swing timer for search textfield to 2500ms, removed 1200ms...
tcofoegbu [Fri, 29 Apr 2016 15:01:50 +0000 (16:01 +0100)]
JAL-1563 Further increased swing timer for search textfield to 2500ms, removed 1200ms delay which was initially added to enable the search summary table initialise without interference, and implemented pagination for Uniprot FTS

8 years agoJAL-2051 better checking of retrieved / duplicated accession ids
gmungoc [Fri, 29 Apr 2016 14:59:23 +0000 (15:59 +0100)]
JAL-2051 better checking of retrieved / duplicated accession ids

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Apr 2016 14:57:58 +0000 (15:57 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoMerge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Fri, 29 Apr 2016 14:24:02 +0000 (15:24 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop

8 years agoJAL-192 need visible and actual sequence limits for scale
Jim Procter [Fri, 29 Apr 2016 13:52:59 +0000 (14:52 +0100)]
JAL-192 need visible and actual sequence limits for scale

8 years agoJAL-192 fix bounds when no hidden regions, and when sequence contained in hidden...
Jim Procter [Fri, 29 Apr 2016 11:41:31 +0000 (12:41 +0100)]
JAL-192 fix bounds when no hidden regions, and when sequence contained in hidden region

8 years agoJAL-192 scale origin relative to start of reference sequence, & deal gracefully with...
Jim Procter [Fri, 29 Apr 2016 09:44:30 +0000 (10:44 +0100)]
JAL-192 scale origin relative to start of reference sequence, & deal gracefully with reference sequence being completely hidden

8 years agoJAL-966 JAL-1553
 todo: remove UI components from Column Selection code
Jim Procter [Fri, 29 Apr 2016 09:43:29 +0000 (10:43 +0100)]
JAL-966 JAL-1553
 todo: remove UI components from Column Selection code

8 years agoJAL-1551 formatting

Jim Procter [Fri, 29 Apr 2016 09:42:02 +0000 (10:42 +0100)]
JAL-1551 formatting


8 years agoJAL-192 ‘efficiently’ locate visible bounds for a sequence (needs scalability testing)
Jim Procter [Fri, 29 Apr 2016 09:41:46 +0000 (10:41 +0100)]
JAL-192 ‘efficiently’ locate visible bounds for a sequence (needs scalability testing)

8 years agoJAL-1551 formatting
Jim Procter [Fri, 29 Apr 2016 09:39:48 +0000 (10:39 +0100)]
JAL-1551 formatting

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Apr 2016 08:25:21 +0000 (09:25 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-1563 increased swing timer for search action from 500ms to 1500ms
tcofoegbu [Thu, 28 Apr 2016 14:13:36 +0000 (15:13 +0100)]
JAL-1563 increased swing timer for search action from 500ms to 1500ms

8 years agoJAL-2083 removed use of reflection for Groovy
gmungoc [Thu, 28 Apr 2016 13:38:48 +0000 (14:38 +0100)]
JAL-2083 removed use of reflection for Groovy

8 years agoJAL-1563 fixed failing tests for FTS Rest Client core
tcofoegbu [Thu, 28 Apr 2016 12:07:17 +0000 (13:07 +0100)]
JAL-1563 fixed failing tests for FTS Rest Client core

8 years agoJAL-1563 Increased default response size to 500, and tweaked 'Organism' and 'Gene...
tcofoegbu [Thu, 28 Apr 2016 12:06:22 +0000 (13:06 +0100)]
JAL-1563 Increased default response size to 500, and tweaked 'Organism' and 'Gene Names' column width parameters

8 years agoJAL-1563 Implemented hack to make table both scrollable and resizable and made Unipro...
tcofoegbu [Thu, 28 Apr 2016 12:03:06 +0000 (13:03 +0100)]
JAL-1563 Implemented hack to make table both scrollable and resizable and made Uniprot responses to be sorted by score

8 years agoJAL-1563 Added Id (Uniprot Id) to the dynamic column config file and changed primary...
tcofoegbu [Wed, 27 Apr 2016 17:57:37 +0000 (18:57 +0100)]
JAL-1563 Added Id (Uniprot Id) to the dynamic column config file and changed primary key from 'entry name' to 'Id'. Also fixed generic batch retrieval mode when the search target is set to the primary key column

8 years agoMerge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Wed, 27 Apr 2016 16:02:13 +0000 (17:02 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop

8 years agoJAL-192 fix off-by-one for alignment ruler with no reference
Jim Procter [Wed, 27 Apr 2016 16:02:02 +0000 (17:02 +0100)]
JAL-192 fix off-by-one for alignment ruler with no reference

8 years agoMerge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Wed, 27 Apr 2016 15:45:57 +0000 (16:45 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop

8 years agoJAL-192 show reference sequence position and residue in ruler
Jim Procter [Wed, 27 Apr 2016 15:36:28 +0000 (16:36 +0100)]
JAL-192 show reference sequence position and residue in ruler

8 years agoJAL-1563 Added fix to prevent swing timer from reinitiating search action when jalvie...
tcofoegbu [Wed, 27 Apr 2016 15:36:20 +0000 (16:36 +0100)]
JAL-1563 Added fix to prevent swing timer from reinitiating search action when jalview gains focus on the FTS interface

8 years agoJAL-1366 JAL-2086 reinstate bolding of reference sequence
Jim Procter [Wed, 27 Apr 2016 15:35:19 +0000 (16:35 +0100)]
JAL-1366 JAL-2086 reinstate bolding of reference sequence

8 years agoJAL-2085 JAL-2086 fix hiddenRepSequence and new referenceSeq getter
Jim Procter [Wed, 27 Apr 2016 15:34:06 +0000 (16:34 +0100)]
JAL-2085 JAL-2086 fix hiddenRepSequence and new referenceSeq getter

8 years agoJAL-1563 further modificaiton of the uniprot data column configuration file
tcofoegbu [Wed, 27 Apr 2016 13:45:47 +0000 (14:45 +0100)]
JAL-1563 further modificaiton of the uniprot data column configuration file

8 years agoJAL-1563 Modified Uniprot data column configurations and improved implementation...
tcofoegbu [Wed, 27 Apr 2016 12:57:28 +0000 (13:57 +0100)]
JAL-1563 Modified Uniprot data column configurations and improved implementation to cope with when there are discrepancies between search code and column code

8 years agore-enabled new uniprot sequence fetcher on spike branch
tcofoegbu [Wed, 27 Apr 2016 10:51:31 +0000 (11:51 +0100)]
re-enabled new uniprot sequence fetcher on spike branch

8 years agoJAL-2079 fix broken cherry-pick conflict merge
Jim Procter [Tue, 26 Apr 2016 17:25:36 +0000 (18:25 +0100)]
JAL-2079 fix broken cherry-pick conflict merge

8 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 26 Apr 2016 16:49:08 +0000 (17:49 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

8 years agoJAL-2079 update GPL header for new Xfam tests
Jim Procter [Tue, 26 Apr 2016 16:48:33 +0000 (17:48 +0100)]
JAL-2079 update GPL header for new Xfam tests

8 years agoJAL-2079 use new service to retrieve Rfam Seed alignment
Jim Procter [Tue, 26 Apr 2016 16:33:02 +0000 (17:33 +0100)]
JAL-2079 use new service to retrieve Rfam Seed alignment

8 years agoJAL-2084 JAL-2079 removed RFAM(Full) from Xfam Network tests
Jim Procter [Tue, 26 Apr 2016 16:08:58 +0000 (17:08 +0100)]
JAL-2084 JAL-2079 removed RFAM(Full) from Xfam Network tests

8 years agoJAL-2079 disable RFAM(Full) source until we can retrieve data
Jim Procter [Tue, 26 Apr 2016 15:58:34 +0000 (16:58 +0100)]
JAL-2079 disable RFAM(Full) source until we can retrieve data

8 years agoJAL-2079 update URL for RFAM and PFAM sources
Jim Procter [Tue, 26 Apr 2016 15:57:05 +0000 (16:57 +0100)]
JAL-2079 update URL for RFAM and PFAM sources

8 years agomerge
tcofoegbu [Tue, 26 Apr 2016 16:42:45 +0000 (17:42 +0100)]
merge

8 years agoJAL-2079 allow prefix+<XFAMID>+suffix type URL signature
Jim Procter [Tue, 26 Apr 2016 15:53:34 +0000 (16:53 +0100)]
JAL-2079 allow prefix+<XFAMID>+suffix type URL signature

8 years agoJAL-1563 reverted to old uniprot fetcher to enable Geoff's presentation tomorrow
tcofoegbu [Tue, 26 Apr 2016 16:42:02 +0000 (17:42 +0100)]
JAL-1563 reverted to old uniprot fetcher to enable Geoff's presentation tomorrow

8 years agoJAL-2077 reinstate JAL-1554 fix for left-then-right click workaround to prevent ID...
Jim Procter [Tue, 26 Apr 2016 13:56:07 +0000 (14:56 +0100)]
JAL-2077 reinstate JAL-1554 fix for left-then-right click workaround to prevent ID links opening

8 years agoJAL-2077 reinstate annotation label popup by handling at MousePressed rather than...
Jim Procter [Tue, 26 Apr 2016 13:38:23 +0000 (14:38 +0100)]
JAL-2077 reinstate annotation label popup by handling at MousePressed rather than MouseClicked

8 years agoJAL-1981 catch any exception when setting QuaQua look and feel
gmungoc [Tue, 26 Apr 2016 11:16:18 +0000 (12:16 +0100)]
JAL-1981 catch any exception when setting QuaQua look and feel