jalview.git
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

8 years agoMerge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4 groovy/JAL-2074_upgradeto2.4.4
Jim Procter [Tue, 26 Apr 2016 12:41:21 +0000 (13:41 +0100)]
Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4

8 years agoMerge branch 'bug/JAL-2080_javaws_slow_291' into develop
Jim Procter [Tue, 26 Apr 2016 12:39:58 +0000 (13:39 +0100)]
Merge branch 'bug/JAL-2080_javaws_slow_291' into develop

8 years agoJAL-2080 removed all 'Class-Path' references in libs
Jim Procter [Tue, 26 Apr 2016 10:45:04 +0000 (11:45 +0100)]
JAL-2080 removed all 'Class-Path' references in libs

8 years agoJAL-2080 removed classpath references to Xerces and commons-logging in jar manifest
Jim Procter [Tue, 26 Apr 2016 10:23:53 +0000 (11:23 +0100)]
JAL-2080 removed classpath references to Xerces and commons-logging in jar manifest

8 years agoJAL-2080 mark jalview.jar as main jar resource
Jim Procter [Tue, 26 Apr 2016 09:57:22 +0000 (10:57 +0100)]
JAL-2080 mark jalview.jar as main jar resource

8 years agomerge
tcofoegbu [Tue, 26 Apr 2016 12:01:21 +0000 (13:01 +0100)]
merge

8 years agoJAL-2071 improvement to get column data files as InputStream
tcofoegbu [Tue, 26 Apr 2016 12:00:43 +0000 (13:00 +0100)]
JAL-2071 improvement to get column data files as InputStream

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 Apr 2016 11:17:41 +0000 (12:17 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-2071 changed extension for data column config files
tcofoegbu [Tue, 26 Apr 2016 11:09:40 +0000 (12:09 +0100)]
JAL-2071 changed extension for data column config files

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 Apr 2016 10:41:35 +0000 (11:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-2071 resolved fts data column config file path for PDB and UniProt
tcofoegbu [Tue, 26 Apr 2016 10:22:34 +0000 (11:22 +0100)]
JAL-2071 resolved fts data column config file path for PDB and UniProt

8 years agoJAL-2071 House keeping
tcofoegbu [Tue, 26 Apr 2016 10:19:52 +0000 (11:19 +0100)]
JAL-2071 House keeping

8 years agoJAL-2074 removed hard-coded groovy lib path in classpath
tcofoegbu [Tue, 26 Apr 2016 09:28:01 +0000 (10:28 +0100)]
JAL-2074 removed hard-coded groovy lib path in classpath

8 years agoJAL-2071 improvement to reduce webservice requests to Free Text Search (FTS) services...
tcofoegbu [Tue, 26 Apr 2016 09:21:56 +0000 (10:21 +0100)]
JAL-2071 improvement to reduce webservice requests to Free Text Search (FTS) services by using swing timer to deffer textfield actions until user stops typing for a certain amount of time

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 Apr 2016 07:59:54 +0000 (08:59 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-2074 disable security manager at start up re: http://lopica.sourceforge.net/faq...
Jim Procter [Mon, 25 Apr 2016 20:35:20 +0000 (21:35 +0100)]
JAL-2074 disable security manager at start up re: lopica.sourceforge.net/faq.html#nosandbox

8 years agoJAL-2074 removed xerces to explore wierdness
Jim Procter [Mon, 25 Apr 2016 16:12:19 +0000 (17:12 +0100)]
JAL-2074 removed xerces to explore wierdness

8 years agoJAL-2074 reinstate upgrade to groovy 2.8.4-indy
Jim Procter [Mon, 25 Apr 2016 15:31:07 +0000 (16:31 +0100)]
JAL-2074 reinstate upgrade to groovy 2.8.4-indy

8 years agoJAL-2074 reinstate upgrade to groovy 2.8.4-indy
Jim Procter [Mon, 25 Apr 2016 15:27:41 +0000 (16:27 +0100)]
JAL-2074 reinstate upgrade to groovy 2.8.4-indy

8 years agoJAL-2074 add the groovy 1.8.2 library back to classpath
Jim Procter [Mon, 25 Apr 2016 15:21:19 +0000 (16:21 +0100)]
JAL-2074 add the groovy 1.8.2 library back to classpath

8 years agodevelop merge
tcofoegbu [Mon, 25 Apr 2016 15:14:17 +0000 (16:14 +0100)]
develop merge

8 years agoJAL-2074 backed out groovy upgrade - back to 1.8.2
Jim Procter [Mon, 25 Apr 2016 15:10:04 +0000 (16:10 +0100)]
JAL-2074 backed out groovy upgrade - back to 1.8.2

8 years agodevelop merge
tcofoegbu [Mon, 25 Apr 2016 15:06:29 +0000 (16:06 +0100)]
develop merge

8 years agoJAL-2074 groovy-all didn’t get added :q
Jim Procter [Mon, 25 Apr 2016 14:47:09 +0000 (15:47 +0100)]
JAL-2074 groovy-all didn’t get added :q

8 years agoJAL-2074 switch to non-indy groovy to see if class loader problem remains
Jim Procter [Mon, 25 Apr 2016 13:42:40 +0000 (14:42 +0100)]
JAL-2074 switch to non-indy groovy to see if class loader problem remains

8 years agoJAL-2078 fixed broken link to groovy page
gmungoc [Mon, 25 Apr 2016 13:03:33 +0000 (14:03 +0100)]
JAL-2078 fixed broken link to groovy page

8 years agoJAL-2071 added unit tests for FTSRestClient features/JAL-1563_uniprot-free-text-search
tcofoegbu [Mon, 25 Apr 2016 10:36:59 +0000 (11:36 +0100)]
JAL-2071 added unit tests for FTSRestClient

8 years agoJAL-1812 JAL-2068 only allow one Groovy console open at a time
gmungoc [Mon, 25 Apr 2016 09:26:20 +0000 (10:26 +0100)]
JAL-1812 JAL-2068 only allow one Groovy console open at a time

8 years agoJAL-1551 JAL-2077 formatting
Jim Procter [Sun, 24 Apr 2016 12:18:38 +0000 (13:18 +0100)]
JAL-1551 JAL-2077 formatting

8 years agoJAL-2077 - reinstate popups on osx
Jim Procter [Sun, 24 Apr 2016 12:17:30 +0000 (13:17 +0100)]
JAL-2077 - reinstate popups on osx

8 years agoMerge branch 'JAL-2075_features_hiddeng' into develop
Jim Procter [Sun, 24 Apr 2016 10:28:48 +0000 (11:28 +0100)]
Merge branch 'JAL-2075_features_hiddeng' into develop

8 years agoJAL-2075 test showing hidden columns bug in feature score model
Jim Procter [Sun, 24 Apr 2016 10:14:01 +0000 (11:14 +0100)]
JAL-2075 test showing hidden columns bug in feature score model

8 years agoJAL-2075 refactor FeatureScoreModel to native testNG asserts
Jim Procter [Sun, 24 Apr 2016 10:12:20 +0000 (11:12 +0100)]
JAL-2075 refactor FeatureScoreModel to native testNG asserts

8 years agoJAL-2075 make GroovyConsole a singleton so tests requiring a valid AlignFrame but...
Jim Procter [Sun, 24 Apr 2016 10:10:32 +0000 (11:10 +0100)]
JAL-2075 make GroovyConsole a singleton so tests requiring a valid AlignFrame but no desktop can run

8 years agoJAL-2075 fix: use AlignmentView.getVisibleContigs and SeqCigar.findPosition to locate...
Jim Procter [Sat, 23 Apr 2016 17:37:04 +0000 (18:37 +0100)]
JAL-2075 fix: use AlignmentView.getVisibleContigs and SeqCigar.findPosition to locate aligned features

8 years agoJAL-2075 findPosition for SeqCigar (with test)
Jim Procter [Sat, 23 Apr 2016 17:36:11 +0000 (18:36 +0100)]
JAL-2075 findPosition for SeqCigar (with test)