kiramt [Mon, 31 Oct 2016 09:58:23 +0000 (09:58 +0000)]
JAL-2282 Removed unexpected ; from code
kiramt [Mon, 31 Oct 2016 09:56:36 +0000 (09:56 +0000)]
JAL-2282 Force double-clicking to use sequence_id cases and not accession_id
cases
kiramt [Mon, 31 Oct 2016 09:43:56 +0000 (09:43 +0000)]
Updated messages.
kiramt [Mon, 31 Oct 2016 08:14:49 +0000 (08:14 +0000)]
Use ACCESSION_ID for database accession id, and SEQUENCE_ID for sequence
name.
gmungoc [Thu, 27 Oct 2016 15:21:31 +0000 (16:21 +0100)]
JAL-2282 test assertions for 'other' dbsource
tcofoegbu [Thu, 27 Oct 2016 14:24:27 +0000 (15:24 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 27 Oct 2016 14:24:18 +0000 (15:24 +0100)]
JAL-2280 Improvement to enable drag'n'drop association of mmCIF file structures to sequences
gmungoc [Thu, 27 Oct 2016 09:45:06 +0000 (10:45 +0100)]
JAL-98 refactor bleachColour() to ColorUtils
gmungoc [Thu, 27 Oct 2016 08:03:05 +0000 (09:03 +0100)]
JAL-2287 treat Escape like Cancel in dialog box
gmungoc [Wed, 26 Oct 2016 15:42:51 +0000 (16:42 +0100)]
JAL-2287 Cancel option on Close Chimera? dialog
gmungoc [Wed, 26 Oct 2016 15:22:45 +0000 (16:22 +0100)]
Merge branch 'bug/JAL-98consensusMemory' into develop
gmungoc [Wed, 26 Oct 2016 15:11:17 +0000 (16:11 +0100)]
JAL-2286 modal residue check + commenting
gmungoc [Wed, 26 Oct 2016 15:09:56 +0000 (16:09 +0100)]
JAL-98 null reference to globalColourScheme as it has ref to consensus
gmungoc [Wed, 26 Oct 2016 15:09:21 +0000 (16:09 +0100)]
JAL-2286 javadoc, refactor, unit tests for threshold and conservation
colouring
tcofoegbu [Wed, 26 Oct 2016 10:37:03 +0000 (11:37 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 26 Oct 2016 10:36:20 +0000 (11:36 +0100)]
Merge branch 'features/JAL-2284_export-biojsmsa-via-cli' into develop
tcofoegbu [Wed, 26 Oct 2016 10:31:53 +0000 (11:31 +0100)]
JAL-2284 basic support for exporting BioJS MSA viewer via CLI
gmungoc [Tue, 25 Oct 2016 15:35:51 +0000 (16:35 +0100)]
JAL-2286 use constant for fixed colours
gmungoc [Tue, 25 Oct 2016 15:22:21 +0000 (16:22 +0100)]
JAL-98 javadoc corrected
gmungoc [Tue, 25 Oct 2016 15:21:48 +0000 (16:21 +0100)]
JAL-98 javadoc added
gmungoc [Tue, 25 Oct 2016 15:21:17 +0000 (16:21 +0100)]
JAL-98 minor fixes to / tests for annotation derivation
Jim Procter [Tue, 25 Oct 2016 10:55:28 +0000 (11:55 +0100)]
Merge branch 'releases/Release_2_10_0_Branch_fixmaster' into develop
Jim Procter [Tue, 25 Oct 2016 10:49:32 +0000 (11:49 +0100)]
JAL-2089 patch broken merge to master for Release 2.10.0b1
Jim Procter [Tue, 25 Oct 2016 10:46:04 +0000 (11:46 +0100)]
Merge branch 'releases/Release_2_10_0_Branch'
tcofoegbu [Tue, 25 Oct 2016 10:26:33 +0000 (11:26 +0100)]
Merge branch 'bug/JAL-2277_html-output-wrapped-mode' into develop
Jim Procter [Tue, 25 Oct 2016 10:25:37 +0000 (11:25 +0100)]
Merge branch 'sourcepub' into releases/Release_2_10_0_Branch
Jim Procter [Tue, 25 Oct 2016 10:24:40 +0000 (11:24 +0100)]
Merge branch 'sourcepub' into develop
Jim Procter [Tue, 25 Oct 2016 10:24:04 +0000 (11:24 +0100)]
JAL-2089 update What's new for 2.10.0b1
tcofoegbu [Tue, 25 Oct 2016 10:22:10 +0000 (11:22 +0100)]
JAL-2277 Improvement to support html+svg export in wrap mode
gmungoc [Tue, 25 Oct 2016 09:01:38 +0000 (10:01 +0100)]
JAL-98 field comments updated
gmungoc [Tue, 25 Oct 2016 09:01:11 +0000 (10:01 +0100)]
JAL-98 small efficiency fix + commenting
gmungoc [Tue, 25 Oct 2016 09:00:25 +0000 (10:00 +0100)]
JAL-98 javadoc / comments updated
Jim Procter [Tue, 25 Oct 2016 08:32:09 +0000 (09:32 +0100)]
Merge branch 'releases/Release_2_10_0_Branch'
Jim Procter [Tue, 25 Oct 2016 08:31:18 +0000 (09:31 +0100)]
Merge branch 'sourcepub' into releases/Release_2_10_0_Branch
Jim Procter [Tue, 25 Oct 2016 08:30:43 +0000 (09:30 +0100)]
Merge branch 'sourcepub' into develop
Jim Procter [Tue, 25 Oct 2016 08:30:06 +0000 (09:30 +0100)]
JAL-1683 reinstate replacetoken patterns so source replacement happens!
Jim Procter [Mon, 24 Oct 2016 21:25:05 +0000 (22:25 +0100)]
Merge branch 'sourcepub' into develop
Jim Procter [Mon, 24 Oct 2016 21:23:29 +0000 (22:23 +0100)]
Merge branch 'sourcepub' into releases/Release_2_10_0_Branch
Jim Procter [Mon, 24 Oct 2016 21:20:48 +0000 (22:20 +0100)]
JAL-1683 replace version and year in licence header when generating source tarsal
Jim Procter [Mon, 24 Oct 2016 20:27:52 +0000 (21:27 +0100)]
Merge branch 'releases/Release_2_10_0_Branch'
gmungoc [Mon, 24 Oct 2016 18:12:09 +0000 (19:12 +0100)]
JAL-98 fixme comment removed - nothing to do
gmungoc [Mon, 24 Oct 2016 18:11:28 +0000 (19:11 +0100)]
JAL-98 ResidueCount 100% test coverage (and bug fixes!)
kiramt [Mon, 24 Oct 2016 17:29:46 +0000 (18:29 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 24 Oct 2016 15:46:59 +0000 (16:46 +0100)]
Unit tests for UrlLink
Jim Procter [Mon, 24 Oct 2016 15:11:39 +0000 (16:11 +0100)]
Merge branch 'develop' into releases/Release_2_10_0_Branch
Jim Procter [Mon, 24 Oct 2016 15:11:02 +0000 (16:11 +0100)]
JAL-2089 bump version and release branch info
Jim Procter [Mon, 24 Oct 2016 14:46:43 +0000 (15:46 +0100)]
Merge branch 'develop' into releases/Release_2_10_0_Branch
Jim Procter [Mon, 24 Oct 2016 14:46:14 +0000 (15:46 +0100)]
JAL-2089 release notes for JAL-2234
Jim Procter [Mon, 24 Oct 2016 14:43:56 +0000 (15:43 +0100)]
Merge branch 'patch/JAL-2234_renameFER1_ARATH' into develop
Jim Procter [Mon, 24 Oct 2016 14:43:05 +0000 (15:43 +0100)]
JAL-2234 reordered seqs (after sequence data was reordered) so files match the example project files
Jim Procter [Mon, 24 Oct 2016 14:42:12 +0000 (15:42 +0100)]
JAL-2234 rename seqs for linked jalview examples
Jim Procter [Mon, 24 Oct 2016 14:24:54 +0000 (15:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_0_Branch
Jim Procter [Mon, 24 Oct 2016 14:23:12 +0000 (15:23 +0100)]
JAL-2089 tweak release note for JAL-2283
Jim Procter [Mon, 24 Oct 2016 14:20:07 +0000 (15:20 +0100)]
JAL-2089 documented additional JAL-2272 CMD-click issue and reformatted 2.10.0b1 release notes a little
Jim Procter [Mon, 24 Oct 2016 14:16:38 +0000 (15:16 +0100)]
Merge branch 'bug/JAL-2272cmdClickGroupEdit' into develop
Jim Procter [Mon, 24 Oct 2016 13:52:35 +0000 (14:52 +0100)]
Merge branch 'bug/JAL-2283consColourEnabled' into develop
gmungoc [Mon, 24 Oct 2016 13:50:53 +0000 (14:50 +0100)]
JAL-2272 Cmd-drag to group edit sequences on Mac (Ctrl-click for popup
menu)
gmungoc [Mon, 24 Oct 2016 13:32:23 +0000 (14:32 +0100)]
JAL-2283 corrected preferences settings for test
Jim Procter [Mon, 24 Oct 2016 13:13:04 +0000 (14:13 +0100)]
Merge branch 'develop' into releases/Release_2_10_0_Branch
Jim Procter [Mon, 24 Oct 2016 12:50:52 +0000 (13:50 +0100)]
JAL-2089 JAL-2195 release notes
Jim Procter [Mon, 24 Oct 2016 12:50:39 +0000 (13:50 +0100)]
JAL-2089 JAL-2283 release notes
kiramt [Mon, 24 Oct 2016 12:37:22 +0000 (13:37 +0100)]
Fixed dialog box messages in English and Spanish. Adjustments to dialog
box spacing.
Jim Procter [Mon, 24 Oct 2016 12:34:54 +0000 (13:34 +0100)]
Merge branch 'bug/JAL-2283consColourEnabled' into develop
Jim Procter [Mon, 24 Oct 2016 11:40:45 +0000 (12:40 +0100)]
JAL-2044 documentation
gmungoc [Mon, 24 Oct 2016 09:46:46 +0000 (10:46 +0100)]
Merge branch 'develop' into bug/JAL-98consensusMemory
kiramt [Mon, 24 Oct 2016 09:38:56 +0000 (10:38 +0100)]
Correct Preferences to check for SEQUENCE_NAME as well as SEQUENCE_ID on
initialisation.
gmungoc [Mon, 24 Oct 2016 09:18:53 +0000 (10:18 +0100)]
JAL-2283 set 'by conservation' correctly when changing colour schem
kiramt [Mon, 24 Oct 2016 09:16:25 +0000 (10:16 +0100)]
Code tidy up. Unit test passes.
kiramt [Sat, 22 Oct 2016 16:55:23 +0000 (17:55 +0100)]
Working links menu
kiramt [Fri, 21 Oct 2016 13:37:04 +0000 (14:37 +0100)]
Factored URL Link constants out into UrlConstants file.
kiramt [Fri, 21 Oct 2016 07:08:23 +0000 (08:08 +0100)]
Created (failing) unit test for addFeatureLinks
Jim Procter [Thu, 20 Oct 2016 11:21:33 +0000 (12:21 +0100)]
Merge branch 'releases/Release_2_10_Branch' into releases/Release_2_10_0_Branch
Jim Procter [Thu, 20 Oct 2016 11:21:08 +0000 (12:21 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Thu, 20 Oct 2016 11:20:01 +0000 (12:20 +0100)]
JAL-2089 update release date for 2.10.0b1 to Tuesday 25th Oct and fix duplicate anchor name
Jim Procter [Thu, 20 Oct 2016 11:17:15 +0000 (12:17 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 19 Oct 2016 16:11:16 +0000 (17:11 +0100)]
JAL-2269 JAL-2195 review and revised test
* cut down DNMT1_MOUSE.pdb file to a stub and renamed to examples/testdata/localstruct.pdb
* added comments explaining test behaviour
* remove try/catch - exceptions should cause test to fail.
Jim Procter [Wed, 19 Oct 2016 15:52:33 +0000 (16:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 19 Oct 2016 15:26:51 +0000 (16:26 +0100)]
JAL-2089 update 2.10.0b1 release date
Jim Procter [Tue, 18 Oct 2016 16:42:37 +0000 (17:42 +0100)]
JAL-2089 release notes and new known defects
Jim Procter [Tue, 18 Oct 2016 14:22:19 +0000 (15:22 +0100)]
JAL-2039 release notes
Jim Procter [Tue, 18 Oct 2016 14:21:37 +0000 (15:21 +0100)]
JAL-2245 release notes
Jim Procter [Tue, 18 Oct 2016 14:20:48 +0000 (15:20 +0100)]
JAL-2089 2.10.0b1 release notes
Jim Procter [Tue, 18 Oct 2016 14:20:06 +0000 (15:20 +0100)]
JAL-2039 rejig instructions for Structure Chooser and clarify what happens after ‘View’ is pressed
kiramt [Mon, 17 Oct 2016 13:38:15 +0000 (14:38 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-1552dragndroptake2' into develop
kiramt [Mon, 17 Oct 2016 13:36:16 +0000 (14:36 +0100)]
acceptDrop call added before getTransferable in alignment frame drag and
drop.
tcofoegbu [Mon, 17 Oct 2016 11:32:38 +0000 (12:32 +0100)]
JAL-2262 JAL-2195 Improvement to set PDBId availability in a flag
kiramt [Mon, 17 Oct 2016 08:24:58 +0000 (09:24 +0100)]
Re-attempt to fix JAL-1552 by removing extra calls to acceptDrop.
gmungoc [Fri, 14 Oct 2016 10:12:00 +0000 (11:12 +0100)]
Merge branch 'releases/Release_2_10_Branch' into task/JAL-2196pdbeProperties
gmungoc [Thu, 13 Oct 2016 15:43:52 +0000 (16:43 +0100)]
JAL-2253 2 second timeout on ping URL, default 5 minutes on others
Jim Procter [Thu, 13 Oct 2016 14:02:51 +0000 (15:02 +0100)]
JAL-2234 switch FER1_ARATH and FER2_ARATH in ferredoxin tree
gmungoc [Thu, 13 Oct 2016 10:13:37 +0000 (11:13 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
gmungoc [Thu, 13 Oct 2016 09:58:06 +0000 (10:58 +0100)]
JAL-1479 revise warning message to suit all contexts
gmungoc [Thu, 13 Oct 2016 09:56:37 +0000 (10:56 +0100)]
JAL-2044 increase Jmol file load timeout from 5 to 20 seconds
gmungoc [Thu, 13 Oct 2016 09:55:42 +0000 (10:55 +0100)]
JAL-2044 ensure AAStructureBindingModel.pdbEntry has no file duplicated;
pull up modelFileNames
gmungoc [Thu, 13 Oct 2016 09:50:27 +0000 (10:50 +0100)]
JAL-2044 include model name in progress bar message opening file
Jim Procter [Wed, 12 Oct 2016 12:55:58 +0000 (13:55 +0100)]
JAL-2234 switched FER1_ARATH and FER2_ARATH in example projects
tcofoegbu [Tue, 11 Oct 2016 12:03:24 +0000 (13:03 +0100)]
Merge branch 'features/JAL-2039_Offer_cached_structurefiles_immediately' into develop
tcofoegbu [Tue, 11 Oct 2016 12:01:39 +0000 (13:01 +0100)]
JAL-2039 improvement to offer cached structure view immediately when cached structures exists
gmungoc [Tue, 11 Oct 2016 11:10:18 +0000 (12:10 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
gmungoc [Tue, 11 Oct 2016 11:09:37 +0000 (12:09 +0100)]
JAL-2241 check for null jprovider when processing New View action
git://source.jalview.org / jalview.git / log