Jim Procter [Tue, 31 May 2016 18:02:01 +0000 (19:02 +0100)]
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
Jim Procter [Tue, 31 May 2016 17:58:10 +0000 (18:58 +0100)]
JAL-1551 JAL-2106 javadoc
Jim Procter [Tue, 31 May 2016 17:57:46 +0000 (18:57 +0100)]
JAL-2110 abstract methods should never reference their implementing classes
tcofoegbu [Tue, 31 May 2016 16:56:31 +0000 (17:56 +0100)]
merge
tcofoegbu [Tue, 31 May 2016 16:55:18 +0000 (17:55 +0100)]
JAL-1563 minor user doc update
tcofoegbu [Tue, 31 May 2016 16:52:29 +0000 (17:52 +0100)]
JAL-1944 fix for visible seqs sometimes been replaced with hidden ones while exporting sequences with the option 'Export Hidden Sequences' set to false
gmungoc [Tue, 31 May 2016 16:32:08 +0000 (17:32 +0100)]
JAL-2023 adjustments to mappings added for split frame to avoid
duplication and ensure saved in project
gmungoc [Tue, 31 May 2016 16:29:02 +0000 (17:29 +0100)]
JAL-2110 refactor + tests to allow a dbref version to update "0" or
"source:0"
Jim Procter [Tue, 31 May 2016 15:34:35 +0000 (16:34 +0100)]
Merge branch 'features/JAL-2113_emblXml1.2' into develop
Jim Procter [Tue, 31 May 2016 15:33:21 +0000 (16:33 +0100)]
Merge branch 'develop' into features/JAL-2113_emblXml1.2
JAL-2113 JAL-1919 mmcif/pdb configurable retrieval from EBI/PDBe - verfied as working
Jim Procter [Tue, 31 May 2016 14:18:36 +0000 (15:18 +0100)]
Merge branch 'jims/291patches' into develop
gmungoc [Tue, 31 May 2016 09:17:46 +0000 (10:17 +0100)]
JAL-1011 JAL-1989 don't mirror column-only selections in unrelated views
gmungoc [Tue, 31 May 2016 06:53:45 +0000 (07:53 +0100)]
JAL-2123 use "rlabel" command to highlight with label on mouseover
tcofoegbu [Mon, 30 May 2016 16:01:16 +0000 (17:01 +0100)]
JAL-2038 fix to enable case-insensitive file name <--> sequence id matching during a drag & drop pdb file association operation
Jim Procter [Mon, 30 May 2016 15:40:30 +0000 (16:40 +0100)]
JAL-553 JAL-1557 always send selections after triggering the PaintRefreser for a view
Jim Procter [Mon, 30 May 2016 15:39:41 +0000 (16:39 +0100)]
JAL-1557 allow group associated rows to be used to create/edit current selection
Jim Procter [Mon, 30 May 2016 14:45:29 +0000 (15:45 +0100)]
JAL-2077 release notes
Jim Procter [Mon, 30 May 2016 14:45:20 +0000 (15:45 +0100)]
JAL-2077 fix: convenience method and checks for CMD+Click to toggle selections
Jim Procter [Mon, 30 May 2016 14:43:06 +0000 (15:43 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 30 May 2016 14:41:19 +0000 (15:41 +0100)]
JAL-2089 update release date for 2.9.1
gmungoc [Mon, 30 May 2016 13:59:35 +0000 (14:59 +0100)]
JAL-1670 JAL-2018 updated unit test for added example feature
gmungoc [Mon, 30 May 2016 13:47:17 +0000 (14:47 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 30 May 2016 13:46:13 +0000 (14:46 +0100)]
JAL-1989 equals method strengthened to fully match selection/hidden cols
gmungoc [Mon, 30 May 2016 13:45:08 +0000 (14:45 +0100)]
JAL-2119 help links checker added to /utils
Jim Procter [Mon, 30 May 2016 11:02:44 +0000 (12:02 +0100)]
JAL-1552 fix JAL-2122 resolve File->string before adding to List<String>.
gmungoc [Mon, 30 May 2016 06:48:57 +0000 (07:48 +0100)]
JAL-2119 updated Valdar group link
gmungoc [Sun, 29 May 2016 19:49:25 +0000 (20:49 +0100)]
JAL-2119 fixes for broken links in help files
gmungoc [Fri, 27 May 2016 14:24:15 +0000 (15:24 +0100)]
JAL-1989 tightened up use of flag for 'column selection changed'
gmungoc [Fri, 27 May 2016 14:21:54 +0000 (15:21 +0100)]
JAL-1989 added hashCode and equals, renamed field to avoid name conflict
gmungoc [Fri, 27 May 2016 14:06:46 +0000 (15:06 +0100)]
JAL-1911 use existing object when setting 'Prompt each time' selected
tcofoegbu [Fri, 27 May 2016 10:17:44 +0000 (11:17 +0100)]
merge
tcofoegbu [Fri, 27 May 2016 10:17:14 +0000 (11:17 +0100)]
JAL-1823 improvement to all chain code specification from manual pdb entry mode
tcofoegbu [Fri, 27 May 2016 10:15:32 +0000 (11:15 +0100)]
JAL-1911 further improvement to bugfix - do not save i18n text in preference file
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
gmungoc [Thu, 26 May 2016 09:27:02 +0000 (10:27 +0100)]
JAL-2113 additions to embl_mapping.xml / data models / tests
Jim Procter [Wed, 25 May 2016 17:51:05 +0000 (18:51 +0100)]
JAL-1522 patch - try to pick best text dataflavor
gmungoc [Mon, 23 May 2016 13:34:22 +0000 (14:34 +0100)]
JAL-2113 remove spaces in sequence from unmarshalling newlines
gmungoc [Mon, 23 May 2016 12:07:38 +0000 (13:07 +0100)]
JAL-2114 save 'raw' ENA location as a sequence feature attribute
gmungoc [Mon, 23 May 2016 10:47:35 +0000 (11:47 +0100)]
JAL-2113 tidy variable naming / javadoc
gmungoc [Mon, 23 May 2016 10:07:16 +0000 (11:07 +0100)]
JAL-2113 EBIFetchClient refactor / unit tests / remove unused fields and
parameters
gmungoc [Mon, 23 May 2016 08:02:14 +0000 (09:02 +0100)]
Merge branch 'develop' into features/JAL-2113_emblXml1.2
gmungoc [Fri, 20 May 2016 20:00:28 +0000 (21:00 +0100)]
JAL-2114 explicit invalid test cases added
gmungoc [Fri, 20 May 2016 19:54:08 +0000 (20:54 +0100)]
JAL-2113 corrected test to use valid location syntax
gmungoc [Fri, 20 May 2016 19:47:55 +0000 (20:47 +0100)]
JAL-2113 removed classes deleted from mapping
gmungoc [Fri, 20 May 2016 19:24:01 +0000 (20:24 +0100)]
JAL-2113 embl_mapping.xml and code updated for EMBL XML v1.2
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
git://source.jalview.org / jalview.git / log