Jim Procter [Mon, 20 Jun 2016 08:02:29 +0000 (09:02 +0100)]
JAL-2110 List now used for AlignCodonFrame references
Jim Procter [Mon, 20 Jun 2016 07:58:10 +0000 (08:58 +0100)]
JAL-2110 copy alcodonframes only if copy constructor called on dataset alignmentI instance
Jim Procter [Sun, 19 Jun 2016 10:55:19 +0000 (11:55 +0100)]
JAL-2110 distinct alignedcodonframe entries for tests
Jim Procter [Sun, 19 Jun 2016 10:19:45 +0000 (11:19 +0100)]
JAL-2110 test alcodonframes must be distinct
Jim Procter [Sun, 19 Jun 2016 07:29:58 +0000 (08:29 +0100)]
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview.datamodel.Alignment from AlignmentI
Jim Procter [Thu, 16 Jun 2016 12:50:55 +0000 (13:50 +0100)]
JAL-2110 todo - select mappings involving sequences in alignment
Jim Procter [Thu, 16 Jun 2016 12:50:16 +0000 (13:50 +0100)]
JAL-2110 change test for desired behaviour of getCodonFrame()
Jim Procter [Thu, 16 Jun 2016 12:47:05 +0000 (13:47 +0100)]
JAL-2110 equals and hashcode should check fromSeq
Jim Procter [Thu, 16 Jun 2016 12:38:33 +0000 (13:38 +0100)]
JAL-2110 throw implementation error if not given a dataset for CDS alignment synthesis
Jim Procter [Thu, 16 Jun 2016 12:18:36 +0000 (13:18 +0100)]
JAL-2110 typo caused infinite loop
Jim Procter [Wed, 15 Jun 2016 15:49:21 +0000 (16:49 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
@gmungoc verified correct to raise exceptions for unsupported join grammar expressions
gmungoc [Wed, 15 Jun 2016 10:25:07 +0000 (11:25 +0100)]
JAL-2025 unit tests added
gmungoc [Wed, 15 Jun 2016 08:20:04 +0000 (09:20 +0100)]
JAL-2101 unit test updated to match config file
tcofoegbu [Tue, 14 Jun 2016 16:48:04 +0000 (17:48 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 14 Jun 2016 16:47:55 +0000 (17:47 +0100)]
JAL-2102 right justify 'Mass' in uniprot FTS, and 'Max Observed Residue' in PDB FTS, and correct 'Miscellaneous' spelling
gmungoc [Tue, 14 Jun 2016 13:57:59 +0000 (14:57 +0100)]
JAL-2114 more helpful reporting of parse failures
gmungoc [Tue, 14 Jun 2016 12:44:53 +0000 (13:44 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Tue, 14 Jun 2016 11:31:34 +0000 (12:31 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 14 Jun 2016 11:28:11 +0000 (12:28 +0100)]
JAL-2110 fixes to dbref resolution and mappings, use same dataset for
dna/cds/protein
gmungoc [Tue, 14 Jun 2016 11:26:04 +0000 (12:26 +0100)]
JAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonicalised to UNIPROT
tcofoegbu [Tue, 14 Jun 2016 11:24:40 +0000 (12:24 +0100)]
JAL-2047 trapped block that could likely cause ClassCastException
tcofoegbu [Tue, 14 Jun 2016 10:17:44 +0000 (11:17 +0100)]
JAL-2047 resolved structure chooser's displayed column configuration updating, added horizontal scrollbar to structure chooser summary table and minor house keeping
gmungoc [Tue, 14 Jun 2016 07:05:53 +0000 (08:05 +0100)]
JAL-1686 JAL-2110 equals and/or hashCode method added
tcofoegbu [Fri, 10 Jun 2016 14:56:48 +0000 (15:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 10 Jun 2016 14:56:39 +0000 (15:56 +0100)]
JAL-1479 updated SIFTS FTP download URL, added improvement to ensure that new SIFTS file are successfully downloaded before overwriting the outdated cached ones, and added fix for PDB RESNUM transfer via JMol parser
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
gmungoc [Thu, 9 Jun 2016 13:55:45 +0000 (14:55 +0100)]
JAL-2110 work in progress
gmungoc [Thu, 9 Jun 2016 13:53:10 +0000 (14:53 +0100)]
Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef
gmungoc [Thu, 9 Jun 2016 13:46:35 +0000 (14:46 +0100)]
JAL-2114 corrected Javadoc
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
gmungoc [Fri, 3 Jun 2016 08:00:04 +0000 (09:00 +0100)]
JAL-2110 random stuff
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 15:26:27 +0000 (16:26 +0100)]
Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef
gmungoc [Thu, 2 Jun 2016 15:20:28 +0000 (16:20 +0100)]
JAL-2124 additional Spanish text strings
gmungoc [Thu, 2 Jun 2016 14:10:23 +0000 (15:10 +0100)]
Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef
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
git://source.jalview.org / jalview.git / log