Jim Procter [Fri, 10 Jun 2016 08:19:28 +0000 (09:19 +0100)]
Merge branch 'r291_docs' into develop
Jim Procter [Fri, 10 Jun 2016 08:18:58 +0000 (09:18 +0100)]
JAL-2089 docs for June 10th
Jim Procter [Wed, 8 Jun 2016 15:38:56 +0000 (16:38 +0100)]
JAL-2089 signed off bug release notes
Jim Procter [Wed, 8 Jun 2016 15:37:51 +0000 (16:37 +0100)]
JAL-1941 remove improper test tag from Annotate3D test helper
Jim Procter [Mon, 6 Jun 2016 08:48:31 +0000 (09:48 +0100)]
JAL-2089 documenting for 8th june RC1
Jim Procter [Fri, 10 Jun 2016 08:01:03 +0000 (09:01 +0100)]
JAL-1941 added test URL and notes about PyRNA restclient
Jim Procter [Fri, 10 Jun 2016 08:00:41 +0000 (09:00 +0100)]
JAL-1941 Annotate3d tests should be in network group
tcofoegbu [Wed, 8 Jun 2016 15:59:23 +0000 (16:59 +0100)]
JAL-1479 JAL- Fix to eradicate duplicate mapping output and further improvement for DBRef re-fetching and matching issue
tcofoegbu [Mon, 6 Jun 2016 13:49:31 +0000 (14:49 +0100)]
JAL-1919, JAL-1960 fix to disable refetching dbrefs when viewing structures
tcofoegbu [Mon, 6 Jun 2016 11:55:58 +0000 (12:55 +0100)]
JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export hidden sequences is enabled
tcofoegbu [Thu, 2 Jun 2016 16:36:57 +0000 (17:36 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
merge
tcofoegbu [Thu, 2 Jun 2016 16:36:49 +0000 (17:36 +0100)]
JAL-2020 fix for Jmol choking jalview while loading a structure
gmungoc [Thu, 2 Jun 2016 15:20:28 +0000 (16:20 +0100)]
JAL-2124 additional Spanish text strings
gmungoc [Thu, 2 Jun 2016 14:06:48 +0000 (15:06 +0100)]
JAL-1424 corrected typos in message text keys
gmungoc [Thu, 2 Jun 2016 14:06:01 +0000 (15:06 +0100)]
JAL-1424 removed duplicate entry and unneeded full stops
tcofoegbu [Thu, 2 Jun 2016 10:30:36 +0000 (11:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
merge
Jim Procter [Thu, 2 Jun 2016 10:29:47 +0000 (11:29 +0100)]
JAL-2125 remove SHA256 digest manifest and signatures for VARNA jar
tcofoegbu [Thu, 2 Jun 2016 10:29:21 +0000 (11:29 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
merge
tcofoegbu [Thu, 2 Jun 2016 10:29:12 +0000 (11:29 +0100)]
JAL-1944 java doc update and minor house keeping
Jim Procter [Thu, 2 Jun 2016 10:05:30 +0000 (11:05 +0100)]
JAL-2125 remove SHA256 digest manifest and signatures for Jmol jar
Jim Procter [Wed, 1 Jun 2016 15:52:49 +0000 (16:52 +0100)]
Merge branch 'testfix/JAL-2038' into develop
Jim Procter [Wed, 1 Jun 2016 15:52:24 +0000 (16:52 +0100)]
JAL-2038 fix tests for case insensitive eSequenceIdMatcher
Jim Procter [Wed, 1 Jun 2016 15:51:31 +0000 (16:51 +0100)]
JAL-2038 ensure bare Strings are lowercased before equals called
tcofoegbu [Wed, 1 Jun 2016 15:34:00 +0000 (16:34 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
merge
tcofoegbu [Wed, 1 Jun 2016 15:33:46 +0000 (16:33 +0100)]
JAL-1944 updated bugfix implementation
gmungoc [Wed, 1 Jun 2016 14:11:30 +0000 (15:11 +0100)]
JAL-1424 clearer messaging
gmungoc [Wed, 1 Jun 2016 14:01:30 +0000 (15:01 +0100)]
JAL-1424 utility to check resource bundle labels used in code (and some
fixes arising)
Jim Procter [Wed, 1 Jun 2016 13:34:42 +0000 (14:34 +0100)]
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
Jim Procter [Wed, 1 Jun 2016 13:33:27 +0000 (14:33 +0100)]
fix build
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
git://source.jalview.org / jalview.git / log