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!)
gmungoc [Mon, 24 Oct 2016 09:46:46 +0000 (10:46 +0100)]
Merge branch 'develop' into bug/JAL-98consensusMemory
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 [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 15:26:51 +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
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
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
kiramt [Tue, 11 Oct 2016 11:01:23 +0000 (12:01 +0100)]
JAL-1552 added acceptDrop call before getTransferable to avoid error
with Java native dnd
gmungoc [Tue, 11 Oct 2016 08:37:28 +0000 (09:37 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
gmungoc [Tue, 11 Oct 2016 08:33:13 +0000 (09:33 +0100)]
JAL-1479 small tidy of error message when Sifts mapping fails
gmungoc [Tue, 11 Oct 2016 08:27:33 +0000 (09:27 +0100)]
JAL-2233 reverted changes to Jmol logging levels
tcofoegbu [Mon, 10 Oct 2016 15:15:49 +0000 (16:15 +0100)]
Merge branch 'bug/JAL-2262_dnd-for-local-structure-files' into develop
tcofoegbu [Mon, 10 Oct 2016 14:59:45 +0000 (15:59 +0100)]
JAL-2262 JAL-2195 unit test for bug
tcofoegbu [Mon, 10 Oct 2016 14:58:55 +0000 (15:58 +0100)]
JAL-2262 JAL-2195 bug fix for mapping local structure files
gmungoc [Thu, 6 Oct 2016 15:16:08 +0000 (16:16 +0100)]
JAL-2254 map error text in root node of EMBL XML response
gmungoc [Thu, 6 Oct 2016 12:55:50 +0000 (13:55 +0100)]
Merge branch 'develop' into bug/JAL-98consensusMemory
gmungoc [Thu, 6 Oct 2016 12:53:37 +0000 (13:53 +0100)]
Merge branch 'develop' into task/JAL-2196pdbeProperties
gmungoc [Thu, 6 Oct 2016 12:14:59 +0000 (13:14 +0100)]
JAL-2252 now buffered read of 3 lines of a time in help files
gmungoc [Thu, 6 Oct 2016 07:52:55 +0000 (08:52 +0100)]
JAL-2245 checks for null added (in case EMBL fetch finds nothing)
Jim Procter [Wed, 5 Oct 2016 22:18:27 +0000 (23:18 +0100)]
JAL-2189 update year in author.props
Jim Procter [Wed, 5 Oct 2016 22:07:28 +0000 (23:07 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 5 Oct 2016 22:06:23 +0000 (23:06 +0100)]
JAL-2189 CITATION file and reorder authors: 2.10: JBP, MC, TCO...
Jim Procter [Wed, 5 Oct 2016 21:15:44 +0000 (22:15 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Wed, 5 Oct 2016 21:15:04 +0000 (22:15 +0100)]
JAL-2252 workaround for link checker not recognising multiline anchors
Jim Procter [Wed, 5 Oct 2016 21:07:18 +0000 (22:07 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Wed, 5 Oct 2016 21:03:24 +0000 (22:03 +0100)]
JAL-2189 updated third party licenses
Jim Procter [Wed, 5 Oct 2016 20:50:09 +0000 (21:50 +0100)]
JAL-2189 release notes
Jim Procter [Wed, 5 Oct 2016 20:49:04 +0000 (21:49 +0100)]
JAL-2036 rebuild menus for each panel before adding to splitframe
Jim Procter [Wed, 5 Oct 2016 20:28:36 +0000 (21:28 +0100)]
JAL-2189 release notes
Jim Procter [Wed, 5 Oct 2016 20:08:48 +0000 (21:08 +0100)]
JAL-2189 tidy up release notes
Jim Procter [Wed, 5 Oct 2016 19:58:12 +0000 (20:58 +0100)]
JAL-2189 tweak ensembl release notes
Jim Procter [Wed, 5 Oct 2016 16:56:39 +0000 (17:56 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
JAL-2189 merge formatting and licensing updates to develop
Jim Procter [Wed, 5 Oct 2016 16:56:17 +0000 (17:56 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 5 Oct 2016 16:53:20 +0000 (17:53 +0100)]
JAL-2189 formatting and release notes
Jim Procter [Wed, 5 Oct 2016 16:52:54 +0000 (17:52 +0100)]
JAL-2189 license header
Jim Procter [Wed, 5 Oct 2016 16:32:54 +0000 (17:32 +0100)]
JAL-2189 apply license
Jim Procter [Wed, 5 Oct 2016 15:52:19 +0000 (16:52 +0100)]
JAL-2189 format help
Jim Procter [Wed, 5 Oct 2016 15:33:28 +0000 (16:33 +0100)]
JAL-2189 format tests
Jim Procter [Wed, 5 Oct 2016 15:31:57 +0000 (16:31 +0100)]
JAL-2189 formatting and GPL
Jim Procter [Wed, 5 Oct 2016 15:28:14 +0000 (16:28 +0100)]
JAL-2189 source formatting
gmungoc [Wed, 5 Oct 2016 15:17:59 +0000 (16:17 +0100)]
Merge branch 'develop' into task/JAL-2196pdbeProperties
Conflicts:
src/jalview/datamodel/PDBEntry.java
test/jalview/ws/dbsources/UniprotTest.java
tcofoegbu [Wed, 5 Oct 2016 15:13:33 +0000 (16:13 +0100)]
QQMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 5 Oct 2016 15:13:16 +0000 (16:13 +0100)]
JAL-1563 JAL-1479 minor house-keeping for Uniprot FTS & SIFTS user docs
Jim Procter [Wed, 5 Oct 2016 15:03:09 +0000 (16:03 +0100)]
Revert "JAL-2245 Castor mapping and code changes for change to ENA XML format"
This reverts commit
30b2b47cbdfa35b127b0fb09e911815cddd9ed7b.
Jim Procter [Wed, 5 Oct 2016 14:59:59 +0000 (15:59 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 5 Oct 2016 14:53:01 +0000 (15:53 +0100)]
JAL-2189 release notes/whats new
Jim Procter [Wed, 5 Oct 2016 14:52:49 +0000 (15:52 +0100)]
JAL-2189 JAL-2152 Chimera 1.11.1 minimum version requirement
gmungoc [Wed, 5 Oct 2016 14:12:01 +0000 (15:12 +0100)]
JAL-1191 revert to using SequenceOntologyLite due to downstream
dependencies
gmungoc [Wed, 5 Oct 2016 13:24:54 +0000 (14:24 +0100)]
JAL-1191 configure full SO for desktop, SOLite for applet (without
breaking the build)
gmungoc [Wed, 5 Oct 2016 11:52:45 +0000 (12:52 +0100)]
JAL-2245 defence against NullPointer if no EMBL data unmarshalled
gmungoc [Wed, 5 Oct 2016 11:51:11 +0000 (12:51 +0100)]
JAL-1191 use full SO in desktop application
gmungoc [Wed, 5 Oct 2016 11:49:44 +0000 (12:49 +0100)]
JAL-2105 update Ensembl REST version to 4.7
gmungoc [Wed, 5 Oct 2016 11:01:31 +0000 (12:01 +0100)]
JAL-1191 refined warning message
gmungoc [Wed, 5 Oct 2016 10:23:53 +0000 (11:23 +0100)]
JAL-1191 added mRNA isA transcript to SequenceOntologyLite (because
Ensembl now returning coding features as mRNA not transcript!)
gmungoc [Tue, 4 Oct 2016 15:03:18 +0000 (16:03 +0100)]
Merge branch 'bug/JAL-2245enaXmlChange' into develop
gmungoc [Tue, 4 Oct 2016 14:12:19 +0000 (15:12 +0100)]
Merge branch 'bug/JAL-2210_hack_for_Release_2_10' into develop
gmungoc [Tue, 4 Oct 2016 14:11:25 +0000 (15:11 +0100)]
JAL-2245 Castor mapping and code changes for change to ENA XML format
gmungoc [Tue, 4 Oct 2016 13:55:59 +0000 (14:55 +0100)]
JAL-2232 some fix / partial fix of failing tests
Jim Procter [Tue, 4 Oct 2016 13:28:02 +0000 (14:28 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Tue, 4 Oct 2016 13:27:22 +0000 (14:27 +0100)]
JAL-2189 release notes
gmungoc [Tue, 4 Oct 2016 12:50:02 +0000 (13:50 +0100)]
JAL-2232 added test that failed before last fix, passes after it
gmungoc [Tue, 4 Oct 2016 10:58:56 +0000 (11:58 +0100)]
JAL-2232 JAL-2154 update dbrefs to newly created dataset sequence
Jim Procter [Tue, 4 Oct 2016 09:56:46 +0000 (10:56 +0100)]
JAL-2189 link to feature sorting documentation
Jim Procter [Tue, 4 Oct 2016 09:55:47 +0000 (10:55 +0100)]
JAL-2189 JAL-2005 mention alignment order preservation when equivalent sequences are sorted.
Jim Procter [Tue, 4 Oct 2016 09:46:33 +0000 (10:46 +0100)]
JAL-2189 release notes
Jim Procter [Tue, 4 Oct 2016 09:44:44 +0000 (10:44 +0100)]
JAL-2005 JAL-599 test alignment and features for checking feature sort behaviour
gmungoc [Mon, 3 Oct 2016 16:13:57 +0000 (17:13 +0100)]
JAL-2110 javadoc formatting only
gmungoc [Mon, 3 Oct 2016 16:11:50 +0000 (17:11 +0100)]
JAL-2110 JAL-1705 handle not found (400) better
gmungoc [Mon, 3 Oct 2016 15:10:21 +0000 (16:10 +0100)]
JAL-2110 additional tests for setDatasetSequence, javadoc for isProtein
Jim Procter [Mon, 3 Oct 2016 14:08:01 +0000 (15:08 +0100)]
JAL-2189 update RELEASE file
Jim Procter [Mon, 3 Oct 2016 14:06:34 +0000 (15:06 +0100)]
JAL-2189 more release notes
Jim Procter [Mon, 3 Oct 2016 14:06:26 +0000 (15:06 +0100)]
JAL-2189 ensembl sequence fetching, locus view and variant annotation transfer docs
gmungoc [Mon, 3 Oct 2016 13:21:26 +0000 (14:21 +0100)]
JAL-98 throw exception (unhandled) for int overthrow while counting
Jim Procter [Mon, 3 Oct 2016 13:11:32 +0000 (14:11 +0100)]
JAL-2189 release notes
gmungoc [Mon, 3 Oct 2016 11:45:47 +0000 (12:45 +0100)]
JAL-98 use Profile to store consensus, ResidueCount for fast compact
counting
gmungoc [Mon, 3 Oct 2016 10:07:12 +0000 (11:07 +0100)]
JAL-98 bespoke fast percentage formatter for consensus tooltip
Jim Procter [Mon, 3 Oct 2016 08:21:48 +0000 (09:21 +0100)]
JAL-2210 use addDBRef to ensure normalisation (just in case the uniprot record is not normalised!)
Jim Procter [Mon, 3 Oct 2016 08:21:10 +0000 (09:21 +0100)]
JAL-2210 need to add both transcript and product, and Ensembl needs to be marked as a primary ref on protein, otherwise the ensembl peptide ids on uniprot don’t match up with the ones retrieved from ensembl
Jim Procter [Mon, 3 Oct 2016 08:18:03 +0000 (09:18 +0100)]
JAL-2210 JAL-2232 remove version number from ENACDS excession
Jim Procter [Mon, 3 Oct 2016 08:17:05 +0000 (09:17 +0100)]
JAL-2210 hack to remove EMBL from Protein crossrefs, and ENSEMBL from CDS crossers.
Jim Procter [Mon, 3 Oct 2016 08:16:14 +0000 (09:16 +0100)]
JAL-2210 explicit ‘doNotAdd’ list to prevent sequences retrieved from being added whose references have already been remapped to local dataset sequences
git://source.jalview.org / jalview.git / log