gmungoc [Mon, 2 May 2016 08:06:28 +0000 (09:06 +0100)]
JAL-1812 bind Groovy to Jalview rather than Desktop, remove reflection
tcofoegbu [Fri, 29 Apr 2016 15:54:18 +0000 (16:54 +0100)]
merge
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
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
gmungoc [Fri, 29 Apr 2016 14:59:23 +0000 (15:59 +0100)]
JAL-2051 better checking of retrieved / duplicated accession ids
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
Jim Procter [Fri, 29 Apr 2016 14:24:02 +0000 (15:24 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Fri, 29 Apr 2016 13:52:59 +0000 (14:52 +0100)]
JAL-192 need visible and actual sequence limits for scale
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
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
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
Jim Procter [Fri, 29 Apr 2016 09:42:02 +0000 (10:42 +0100)]
JAL-1551 formatting
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)
Jim Procter [Fri, 29 Apr 2016 09:39:48 +0000 (10:39 +0100)]
JAL-1551 formatting
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
tcofoegbu [Thu, 28 Apr 2016 14:13:36 +0000 (15:13 +0100)]
JAL-1563 increased swing timer for search action from 500ms to 1500ms
gmungoc [Thu, 28 Apr 2016 13:38:48 +0000 (14:38 +0100)]
JAL-2083 removed use of reflection for Groovy
tcofoegbu [Thu, 28 Apr 2016 12:07:17 +0000 (13:07 +0100)]
JAL-1563 fixed failing tests for FTS Rest Client core
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
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
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
Jim Procter [Wed, 27 Apr 2016 16:02:13 +0000 (17:02 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop
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
Jim Procter [Wed, 27 Apr 2016 15:45:57 +0000 (16:45 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Wed, 27 Apr 2016 15:36:28 +0000 (16:36 +0100)]
JAL-192 show reference sequence position and residue in ruler
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
Jim Procter [Wed, 27 Apr 2016 15:35:19 +0000 (16:35 +0100)]
JAL-1366 JAL-2086 reinstate bolding of reference sequence
Jim Procter [Wed, 27 Apr 2016 15:34:06 +0000 (16:34 +0100)]
JAL-2085 JAL-2086 fix hiddenRepSequence and new referenceSeq getter
tcofoegbu [Wed, 27 Apr 2016 13:45:47 +0000 (14:45 +0100)]
JAL-1563 further modificaiton of the uniprot data column configuration file
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
tcofoegbu [Wed, 27 Apr 2016 10:51:31 +0000 (11:51 +0100)]
re-enabled new uniprot sequence fetcher on spike branch
Jim Procter [Tue, 26 Apr 2016 17:25:36 +0000 (18:25 +0100)]
JAL-2079 fix broken cherry-pick conflict merge
Jim Procter [Tue, 26 Apr 2016 16:49:08 +0000 (17:49 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 26 Apr 2016 16:48:33 +0000 (17:48 +0100)]
JAL-2079 update GPL header for new Xfam tests
Jim Procter [Tue, 26 Apr 2016 16:33:02 +0000 (17:33 +0100)]
JAL-2079 use new service to retrieve Rfam Seed alignment
Jim Procter [Tue, 26 Apr 2016 16:08:58 +0000 (17:08 +0100)]
JAL-2084 JAL-2079 removed RFAM(Full) from Xfam Network tests
Jim Procter [Tue, 26 Apr 2016 15:58:34 +0000 (16:58 +0100)]
JAL-2079 disable RFAM(Full) source until we can retrieve data
Jim Procter [Tue, 26 Apr 2016 15:57:05 +0000 (16:57 +0100)]
JAL-2079 update URL for RFAM and PFAM sources
tcofoegbu [Tue, 26 Apr 2016 16:42:45 +0000 (17:42 +0100)]
merge
Jim Procter [Tue, 26 Apr 2016 15:53:34 +0000 (16:53 +0100)]
JAL-2079 allow prefix+<XFAMID>+suffix type URL signature
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
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
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
gmungoc [Tue, 26 Apr 2016 11:16:18 +0000 (12:16 +0100)]
JAL-1981 catch any exception when setting QuaQua look and feel
Jim Procter [Tue, 26 Apr 2016 12:39:58 +0000 (13:39 +0100)]
Merge branch 'bug/JAL-2080_javaws_slow_291' into develop
Jim Procter [Tue, 26 Apr 2016 10:45:04 +0000 (11:45 +0100)]
JAL-2080 removed all 'Class-Path' references in libs
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
Jim Procter [Tue, 26 Apr 2016 09:57:22 +0000 (10:57 +0100)]
JAL-2080 mark jalview.jar as main jar resource
tcofoegbu [Tue, 26 Apr 2016 12:01:21 +0000 (13:01 +0100)]
merge
tcofoegbu [Tue, 26 Apr 2016 12:00:43 +0000 (13:00 +0100)]
JAL-2071 improvement to get column data files as InputStream
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
tcofoegbu [Tue, 26 Apr 2016 11:09:40 +0000 (12:09 +0100)]
JAL-2071 changed extension for data column config files
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
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
tcofoegbu [Tue, 26 Apr 2016 10:19:52 +0000 (11:19 +0100)]
JAL-2071 House keeping
tcofoegbu [Tue, 26 Apr 2016 09:28:01 +0000 (10:28 +0100)]
JAL-2074 removed hard-coded groovy lib path in classpath
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
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
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
tcofoegbu [Mon, 25 Apr 2016 15:14:17 +0000 (16:14 +0100)]
develop merge
Jim Procter [Mon, 25 Apr 2016 15:10:04 +0000 (16:10 +0100)]
JAL-2074 backed out groovy upgrade - back to 1.8.2
tcofoegbu [Mon, 25 Apr 2016 15:06:29 +0000 (16:06 +0100)]
develop merge
Jim Procter [Mon, 25 Apr 2016 14:47:09 +0000 (15:47 +0100)]
JAL-2074 groovy-all didn’t get added :q
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
gmungoc [Mon, 25 Apr 2016 13:03:33 +0000 (14:03 +0100)]
JAL-2078 fixed broken link to groovy page
tcofoegbu [Mon, 25 Apr 2016 10:36:59 +0000 (11:36 +0100)]
JAL-2071 added unit tests for FTSRestClient
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
Jim Procter [Sun, 24 Apr 2016 12:18:38 +0000 (13:18 +0100)]
JAL-1551 JAL-2077 formatting
Jim Procter [Sun, 24 Apr 2016 12:17:30 +0000 (13:17 +0100)]
JAL-2077 - reinstate popups on osx
Jim Procter [Sun, 24 Apr 2016 10:28:48 +0000 (11:28 +0100)]
Merge branch 'JAL-2075_features_hiddeng' into develop
Jim Procter [Sun, 24 Apr 2016 10:14:01 +0000 (11:14 +0100)]
JAL-2075 test showing hidden columns bug in feature score model
Jim Procter [Sun, 24 Apr 2016 10:12:20 +0000 (11:12 +0100)]
JAL-2075 refactor FeatureScoreModel to native testNG asserts
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
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
Jim Procter [Sat, 23 Apr 2016 17:36:11 +0000 (18:36 +0100)]
JAL-2075 findPosition for SeqCigar (with test)
Jim Procter [Sat, 23 Apr 2016 17:35:09 +0000 (18:35 +0100)]
JAL-2075 formatting
tcofoegbu [Fri, 22 Apr 2016 15:42:23 +0000 (16:42 +0100)]
JAL-1563 JAL-2071 Update and completed implementation for UniProt FTS support
tcofoegbu [Fri, 22 Apr 2016 15:33:47 +0000 (16:33 +0100)]
JAL-2071 further refactoring, optimisation, and house keeping for the generic Free Text Search implementation
gmungoc [Fri, 22 Apr 2016 15:16:55 +0000 (16:16 +0100)]
JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame Calculate menu
gmungoc [Fri, 22 Apr 2016 15:12:28 +0000 (16:12 +0100)]
JAL-2068 code and test for case of minValue == maxValue
gmungoc [Fri, 22 Apr 2016 15:03:28 +0000 (16:03 +0100)]
JAL-2068 framework and example scripts for pluggable alignment
annotation workers
gmungoc [Fri, 22 Apr 2016 14:37:40 +0000 (15:37 +0100)]
JAL-2068 Javadoc added
gmungoc [Fri, 22 Apr 2016 14:23:05 +0000 (15:23 +0100)]
JAL-2068 redundant implements clauses removed
gmungoc [Fri, 22 Apr 2016 14:20:00 +0000 (15:20 +0100)]
JAL-2068 convenience helper method for graduated score colour
gmungoc [Thu, 21 Apr 2016 09:56:53 +0000 (10:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 20 Apr 2016 16:03:06 +0000 (17:03 +0100)]
Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop
Jim Procter [Wed, 20 Apr 2016 16:00:53 +0000 (17:00 +0100)]
JAL-2074 updated URLs and removed 'how to get groovy' classpath stuff
Jim Procter [Wed, 20 Apr 2016 15:59:07 +0000 (16:59 +0100)]
JAL-2074 updated groovy-all to 2.4.6-indy
Jim Procter [Wed, 20 Apr 2016 10:56:57 +0000 (11:56 +0100)]
fix for JAL-2072
tcofoegbu [Tue, 19 Apr 2016 14:37:47 +0000 (15:37 +0100)]
JAL-2071 architectural improvement for Plugable Free Text Search Services
gmungoc [Mon, 18 Apr 2016 09:19:06 +0000 (10:19 +0100)]
JAL-2067 fixed broken link
gmungoc [Thu, 14 Apr 2016 13:36:34 +0000 (14:36 +0100)]
JAL-2041 add ID,clinical_significance to feature attributes (for export)
gmungoc [Thu, 14 Apr 2016 12:32:09 +0000 (13:32 +0100)]
JAL-2041 clinical_significance shown on sequence feature tooltip
gmungoc [Thu, 14 Apr 2016 12:30:03 +0000 (13:30 +0100)]
JAL-1421 typed map / lists, explicit imports, method refactoring
gmungoc [Thu, 14 Apr 2016 11:20:29 +0000 (12:20 +0100)]
JAL-2049 small refactor of constructors to avoid code duplication
gmungoc [Thu, 14 Apr 2016 11:17:28 +0000 (12:17 +0100)]
JAL-1421 type parameter added to some collections
gmungoc [Thu, 14 Apr 2016 11:06:29 +0000 (12:06 +0100)]
JAL-2049 revised computePeptideVariants to transfer id, clinical_sig
gmungoc [Thu, 14 Apr 2016 11:04:15 +0000 (12:04 +0100)]
JAL-1705 refactored/utility methods to detect e.g. 'PhenCode_variation'
gmungoc [Thu, 14 Apr 2016 11:00:38 +0000 (12:00 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 14 Apr 2016 10:17:05 +0000 (11:17 +0100)]
JAL-653 test updated for 'use ID for description'
git://source.jalview.org / jalview.git / log