gmungoc [Fri, 27 May 2016 08:51:36 +0000 (09:51 +0100)]
JAL-1942 small tidy (formatting, explict imports, typed list, spelling)
gmungoc [Fri, 27 May 2016 07:49:56 +0000 (08:49 +0100)]
JAL-1911 correct typo in field name
tcofoegbu [Thu, 26 May 2016 17:19:28 +0000 (18:19 +0100)]
merge
tcofoegbu [Thu, 26 May 2016 17:18:59 +0000 (18:18 +0100)]
JAL-1911 improvement to bugfix - do not save i18n text in preference file
Jim Procter [Thu, 26 May 2016 15:55:15 +0000 (16:55 +0100)]
JAL-2030 - add servlet-api-3.1.jar to installAnywhere build
Jim Procter [Thu, 26 May 2016 15:42:58 +0000 (16:42 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 26 May 2016 15:12:17 +0000 (16:12 +0100)]
merge
tcofoegbu [Thu, 26 May 2016 15:11:40 +0000 (16:11 +0100)]
JAL-1911 bugfix - do not save i18n text in preference file
Jim Procter [Thu, 26 May 2016 15:01:55 +0000 (16:01 +0100)]
JAL-2121 refactor todo
gmungoc [Thu, 26 May 2016 14:55:46 +0000 (15:55 +0100)]
JAL-391 add reverse / complement to command history for Undo / Redo
gmungoc [Thu, 26 May 2016 14:55:19 +0000 (15:55 +0100)]
JAL-2035 relocated a comment
Jim Procter [Thu, 26 May 2016 14:24:49 +0000 (15:24 +0100)]
JAL-2089 update developer doc
Jim Procter [Thu, 26 May 2016 14:21:24 +0000 (15:21 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 26 May 2016 14:19:50 +0000 (15:19 +0100)]
JAL-1400 JAL-2089 allow configurable signature algorithms
JAL-1400 JAL-2089 update developer docs for webstart testing
Jim Procter [Thu, 26 May 2016 14:00:10 +0000 (15:00 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 26 May 2016 13:58:40 +0000 (14:58 +0100)]
JAL-1552 refactor shared dataflavor hander
JAL-1552 fix: fallback to text/plain if other flavors fail
gmungoc [Thu, 26 May 2016 13:11:01 +0000 (14:11 +0100)]
JAL-1670 add non-positional feature with link to demonstrate link from
sequence id context menu
gmungoc [Thu, 26 May 2016 13:05:45 +0000 (14:05 +0100)]
JAL-1993 open sequence fetcher tree on 'fetch sequences'
gmungoc [Thu, 26 May 2016 13:05:02 +0000 (14:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Thu, 26 May 2016 12:03:09 +0000 (13:03 +0100)]
merge
tcofoegbu [Thu, 26 May 2016 12:02:43 +0000 (13:02 +0100)]
JAL-1919 JAL-1479 user help docs
Jim Procter [Thu, 26 May 2016 10:54:03 +0000 (11:54 +0100)]
JAL-1552 extra debug logging for dataflavor if drop has no data
tcofoegbu [Thu, 26 May 2016 10:07:07 +0000 (11:07 +0100)]
merge
tcofoegbu [Thu, 26 May 2016 10:06:02 +0000 (11:06 +0100)]
JAL-1911 bugfix - do not save i18n text in preference file
gmungoc [Thu, 26 May 2016 09:52:38 +0000 (10:52 +0100)]
JAL-1797 non-case-sensitive counting of residues / gaps
gmungoc [Thu, 26 May 2016 09:50:22 +0000 (10:50 +0100)]
JAL-2008 drag to reorder features not available in applet
gmungoc [Thu, 26 May 2016 09:38:07 +0000 (10:38 +0100)]
JAL-2079 update examples to new pfam.xfam.org domain
Jim Procter [Wed, 25 May 2016 17:51:05 +0000 (18:51 +0100)]
JAL-1522 patch - try to pick best text dataflavor
gmungoc [Fri, 20 May 2016 20:00:28 +0000 (21:00 +0100)]
JAL-2114 explicit invalid test cases added
gmungoc [Fri, 20 May 2016 17:30:55 +0000 (18:30 +0100)]
JAL-2114 accept "<123..178" or "123..>178" format
gmungoc [Fri, 20 May 2016 17:18:57 +0000 (18:18 +0100)]
JAL-2115 updated web link for MAFFT (and one typo)
gmungoc [Fri, 20 May 2016 07:51:47 +0000 (08:51 +0100)]
JAL-2049 unit test updated for HGVS syntax, feature group = "Jalview"
gmungoc [Thu, 19 May 2016 16:14:09 +0000 (17:14 +0100)]
JAL-2114 added single-locus case and more error tests
gmungoc [Thu, 19 May 2016 16:01:14 +0000 (17:01 +0100)]
JAL-2114 parser + tests for GenBank location descriptors
tcofoegbu [Wed, 18 May 2016 15:50:26 +0000 (16:50 +0100)]
merge
tcofoegbu [Wed, 18 May 2016 15:49:58 +0000 (16:49 +0100)]
JAL-1563 User documentation for Uniprot FTS
tcofoegbu [Wed, 18 May 2016 15:48:39 +0000 (16:48 +0100)]
JAL-1563 smarter support for advanced querying of Uniprot FTS
gmungoc [Wed, 18 May 2016 12:18:09 +0000 (13:18 +0100)]
JAL-2049 set sequence feature group to "Jalview" for computed protein
variants
gmungoc [Wed, 18 May 2016 12:09:50 +0000 (13:09 +0100)]
JAL-2049 use HGVS notation for variant on protein residue
tcofoegbu [Tue, 17 May 2016 11:31:25 +0000 (12:31 +0100)]
JAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
tcofoegbu [Tue, 17 May 2016 11:11:39 +0000 (12:11 +0100)]
merge
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
gmungoc [Fri, 13 May 2016 09:17:57 +0000 (10:17 +0100)]
JAL-2105 capture Ensembl data version, check REST version (per domain)
gmungoc [Thu, 12 May 2016 08:45:17 +0000 (09:45 +0100)]
JAL-2104 format tooltips to wrap correctly
tcofoegbu [Wed, 11 May 2016 14:58:21 +0000 (15:58 +0100)]
JAL-1563 updated uniprot FTS config file
tcofoegbu [Mon, 9 May 2016 16:48:10 +0000 (17:48 +0100)]
merge
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
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
gmungoc [Mon, 9 May 2016 14:18:12 +0000 (15:18 +0100)]
JAL-2098 identify feature file with "<" in feature type name
gmungoc [Mon, 9 May 2016 13:41:43 +0000 (14:41 +0100)]
JAL-2018 export graduated feature colours correctly
Jim Procter [Fri, 6 May 2016 14:39:04 +0000 (15:39 +0100)]
Merge branch 'features/JAL-192_scalerelativetoseq' into develop
Jim Procter [Fri, 6 May 2016 14:34:30 +0000 (15:34 +0100)]
JAL-192 fix javadoc
Jim Procter [Fri, 6 May 2016 14:31:09 +0000 (15:31 +0100)]
JAL-192 JAL-2099 unused variables
Jim Procter [Fri, 6 May 2016 14:29:26 +0000 (15:29 +0100)]
JAL-1551 formatting
Jim Procter [Fri, 6 May 2016 14:29:14 +0000 (15:29 +0100)]
JAL-192 JAL-2099 reuse refactored scale code for wrapped view
Jim Procter [Fri, 6 May 2016 14:13:41 +0000 (15:13 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #3
Jim Procter [Fri, 6 May 2016 14:03:24 +0000 (15:03 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #2
Jim Procter [Fri, 6 May 2016 13:51:38 +0000 (14:51 +0100)]
JAL-192 JAL-2099 factored out calculation from rendering code #1
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
Jim Procter [Fri, 6 May 2016 13:20:41 +0000 (14:20 +0100)]
JAL-2100 optimisation
Jim Procter [Fri, 6 May 2016 13:09:53 +0000 (14:09 +0100)]
JAL-2100 triangles shown below in jvdesktop unwrapped ruler
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
gmungoc [Thu, 5 May 2016 14:36:08 +0000 (15:36 +0100)]
JAL-2068 better documentation in example script
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+’-‘ ! )
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
gmungoc [Wed, 4 May 2016 15:11:43 +0000 (16:11 +0100)]
JAL-2074 reinstated xerces-impl.jar
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.
gmungoc [Wed, 4 May 2016 15:04:26 +0000 (16:04 +0100)]
JAL-2092 hide columns with/without feature
gmungoc [Wed, 4 May 2016 14:03:19 +0000 (15:03 +0100)]
JAL-2074 corrected classpathentry for Groovy 2.4.6
gmungoc [Wed, 4 May 2016 13:55:16 +0000 (14:55 +0100)]
Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop
tcofoegbu [Wed, 4 May 2016 11:58:26 +0000 (12:58 +0100)]
merge
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
gmungoc [Wed, 4 May 2016 08:11:13 +0000 (09:11 +0100)]
JAL-2090 removed test for Java > 1.1 to enable transparency
gmungoc [Tue, 3 May 2016 15:53:21 +0000 (16:53 +0100)]
JAL-2050 hide introns also when fetching Ensembl xrefs for Uniprot
Jim Procter [Tue, 3 May 2016 15:04:43 +0000 (16:04 +0100)]
Merge branch 'r291_docs' into develop
tcofoegbu [Tue, 3 May 2016 14:18:43 +0000 (15:18 +0100)]
JAL-2091 disable pagination buttons during initialisation
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
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
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)
Jim Procter [Mon, 2 May 2016 11:21:06 +0000 (12:21 +0100)]
JAL-1270 capitalise test groups
Jim Procter [Mon, 2 May 2016 11:19:54 +0000 (12:19 +0100)]
JAL-2089 JAL-1551 formatting
Jim Procter [Mon, 2 May 2016 11:19:23 +0000 (12:19 +0100)]
JAL-2089 release 2.9.1 entry in release notes
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
git://source.jalview.org / jalview.git / log