tcofoegbu [Fri, 19 Aug 2016 14:13:10 +0000 (15:13 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 19 Aug 2016 14:13:01 +0000 (15:13 +0100)]
JAL-1803 unit test for PDB chainCode save/restore from Jalview project
gmungoc [Thu, 18 Aug 2016 15:20:50 +0000 (16:20 +0100)]
JAL-2077 using Platform method to check for Ctrl-down
gmungoc [Thu, 18 Aug 2016 15:19:01 +0000 (16:19 +0100)]
JAL-1445 status message '...not containing...' for inverted selection
gmungoc [Thu, 18 Aug 2016 15:16:27 +0000 (16:16 +0100)]
JAL-1693 show warning dialog if unable to make CDS for split frame
gmungoc [Thu, 18 Aug 2016 14:25:52 +0000 (15:25 +0100)]
JAL-1855 fail gracefully if XML has no <sequence> element
gmungoc [Thu, 18 Aug 2016 10:08:23 +0000 (11:08 +0100)]
JAL-2077 handling Cmd-click in scale panel for Mac / Windows
gmungoc [Thu, 18 Aug 2016 09:42:28 +0000 (10:42 +0100)]
JAL-2001 return copy of selection in getSelected()
gmungoc [Wed, 17 Aug 2016 13:55:26 +0000 (14:55 +0100)]
JAL-2146 status message now with formatted residue name / code
gmungoc [Wed, 17 Aug 2016 11:30:57 +0000 (12:30 +0100)]
JAL-2173 don't remove annotation from hidden columns
gmungoc [Wed, 17 Aug 2016 11:22:19 +0000 (12:22 +0100)]
JAL-2172 reverted to not sorting column selection
gmungoc [Wed, 17 Aug 2016 11:16:43 +0000 (12:16 +0100)]
JAL-2105 rest versions updated to 4.6, change log link added
gmungoc [Wed, 17 Aug 2016 10:06:04 +0000 (11:06 +0100)]
JAL-2172 handle case where column selection is not ordered
gmungoc [Tue, 16 Aug 2016 15:52:03 +0000 (16:52 +0100)]
JAL-2172 unit test added
tcofoegbu [Mon, 15 Aug 2016 15:54:17 +0000 (16:54 +0100)]
JAL-1128 fix for truncated bottom boarder pixels in figures generated from wrapped alignment
tcofoegbu [Mon, 15 Aug 2016 15:46:00 +0000 (16:46 +0100)]
JAL-1128 fix for truncated bottom boarder pixels in figures generated from wrapped alignment
tcofoegbu [Mon, 15 Aug 2016 13:54:19 +0000 (14:54 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 15 Aug 2016 13:53:58 +0000 (14:53 +0100)]
JAL-1919 Added improvement to ensure consistence of annotations parsed via JmolParser vs PDBfile parser and fixed unit tests accordingly
gmungoc [Wed, 10 Aug 2016 10:41:20 +0000 (11:41 +0100)]
JAL-2124 i18n of 'All' menu item
gmungoc [Wed, 10 Aug 2016 10:37:01 +0000 (11:37 +0100)]
JAL-2124 i18n of "All" menu item
gmungoc [Wed, 10 Aug 2016 10:34:31 +0000 (11:34 +0100)]
JAL-2146 small optimisation (avoid String creation)
gmungoc [Wed, 10 Aug 2016 10:33:10 +0000 (11:33 +0100)]
JAL-2146 show Column no [Sequence no [Residue / pos]] on mouseover
gmungoc [Mon, 8 Aug 2016 16:16:36 +0000 (17:16 +0100)]
JAL-1577 rebuild menus when secondary structure manually updated
tcofoegbu [Mon, 8 Aug 2016 15:01:32 +0000 (16:01 +0100)]
replaced broken biojsmsa home link in jalveiw help
gmungoc [Mon, 8 Aug 2016 13:42:30 +0000 (14:42 +0100)]
JAL-2119 replaced link with a non-404 alternative
gmungoc [Mon, 8 Aug 2016 13:25:09 +0000 (14:25 +0100)]
JAL-2168 -nonews option also mentioned here
gmungoc [Mon, 8 Aug 2016 13:20:56 +0000 (14:20 +0100)]
JAL-2119 updates to invalid / obsolete help links
gmungoc [Mon, 8 Aug 2016 13:16:44 +0000 (14:16 +0100)]
JAL-2168 document '-nonews' parameter
gmungoc [Fri, 5 Aug 2016 13:53:23 +0000 (14:53 +0100)]
JAL-2168 skip news feed if parameter "-nonews" is supplied
gmungoc [Fri, 5 Aug 2016 13:11:43 +0000 (14:11 +0100)]
JAL-1448 always use UK locale for formatted date properties
gmungoc [Fri, 5 Aug 2016 10:22:14 +0000 (11:22 +0100)]
JAL-2164 add transferred annotation to sequence
gmungoc [Thu, 4 Aug 2016 14:35:18 +0000 (15:35 +0100)]
JAL-2164 changed to be Java 1.7 compliant
gmungoc [Thu, 4 Aug 2016 09:55:50 +0000 (10:55 +0100)]
JAL-2008 handle fast mouse drag of feature ordering correctly
gmungoc [Thu, 4 Aug 2016 09:11:06 +0000 (10:11 +0100)]
JAL-2015 convert Color from colour picker to FeatureColour
Jim Procter [Tue, 2 Aug 2016 15:22:43 +0000 (16:22 +0100)]
JAL-2046 additional logic to suppress spurious implementation-error warnings
Jim Procter [Tue, 2 Aug 2016 14:56:19 +0000 (15:56 +0100)]
Merge branch 'efficiency/JAL-2034_JAL-1421' into develop
Jim Procter [Tue, 2 Aug 2016 14:46:58 +0000 (15:46 +0100)]
JAL-2034 show greyed out image during overview update
Jim Procter [Tue, 2 Aug 2016 13:16:06 +0000 (14:16 +0100)]
Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
Jim Procter [Tue, 2 Aug 2016 13:15:35 +0000 (14:15 +0100)]
JAL-2068 reinstated false return value for notifyWorking
(prevents multiple worker threads starting when new view created)
* documentation for AlignCalcManagerI
Jim Procter [Tue, 2 Aug 2016 10:05:53 +0000 (11:05 +0100)]
Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
Jim Procter [Mon, 1 Aug 2016 20:13:52 +0000 (21:13 +0100)]
JAL-2164 TODO: make test pass for JMOL_PARSER
Jim Procter [Mon, 1 Aug 2016 20:13:22 +0000 (21:13 +0100)]
JAL-2164 JAL-1919 JAL-1270 use structure import settings to properly configure for test
Jim Procter [Mon, 1 Aug 2016 19:16:42 +0000 (20:16 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 1 Aug 2016 16:21:08 +0000 (17:21 +0100)]
JAL-2164 bugfix to convert insCodes of '\000' to ' ' in JmolParser, this fixes the xml marshalling bug
Jim Procter [Mon, 1 Aug 2016 14:40:24 +0000 (15:40 +0100)]
Merge branch 'bug/JAL-2154projectMappings' into develop
Jim Procter [Mon, 1 Aug 2016 13:00:19 +0000 (14:00 +0100)]
Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects' into develop
Jim Procter [Mon, 1 Aug 2016 12:46:09 +0000 (13:46 +0100)]
JAL-2164 prevent jalview news from opening
Jim Procter [Mon, 1 Aug 2016 12:45:05 +0000 (13:45 +0100)]
JAL-2164 clear the desktop before testStoreAndRecoverExpandedViews
Jim Procter [Mon, 1 Aug 2016 10:54:34 +0000 (11:54 +0100)]
Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects' into develop
Jim Procter [Mon, 1 Aug 2016 07:49:54 +0000 (08:49 +0100)]
JAL-1772 make sure we actually return reference to AlignFrame that is visible after views are gathered
Jim Procter [Fri, 29 Jul 2016 16:37:32 +0000 (17:37 +0100)]
JAL-1772 JAL-2164 make expanded view save/restore test pass when run in isolation (problem may be that load returns an alignFrame that isn’t actually the one shown in the desktop…)
Jim Procter [Fri, 29 Jul 2016 16:36:51 +0000 (17:36 +0100)]
JAL-2164 JAL-1772 explodeViews can be static, so make it so
tcofoegbu [Fri, 29 Jul 2016 16:06:27 +0000 (17:06 +0100)]
JAL-1957 JAL-1479 updated SIFTS user docs
Jim Procter [Fri, 29 Jul 2016 15:07:38 +0000 (16:07 +0100)]
JAL-2164 revert tests depending on import of legacy jalview projects
Jim Procter [Fri, 29 Jul 2016 14:02:29 +0000 (15:02 +0100)]
JAL-2154 disable visual delay only after completed import
Jim Procter [Fri, 29 Jul 2016 14:02:03 +0000 (15:02 +0100)]
JAL-2154 register any new dataset codon frames only when all data imported
Jim Procter [Fri, 29 Jul 2016 14:01:07 +0000 (15:01 +0100)]
JAL-2154 only include mappings in dbref/alcodon in dataset XML
tcofoegbu [Fri, 29 Jul 2016 09:38:38 +0000 (10:38 +0100)]
JAL-2157 fixed Jalview2xmlTest
Jim Procter [Wed, 27 Jul 2016 16:41:59 +0000 (17:41 +0100)]
JAL-2154 toString for forward references
Jim Procter [Wed, 27 Jul 2016 13:57:40 +0000 (14:57 +0100)]
Merge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles' into bug/JAL-2154projectMappings
Jim Procter [Wed, 27 Jul 2016 09:29:09 +0000 (10:29 +0100)]
JAL-2163 set title for the alignframe from restored view state
Jim Procter [Wed, 27 Jul 2016 10:57:24 +0000 (11:57 +0100)]
JAL-2156 resolve and add complementary views for saveAlignment
Jim Procter [Wed, 27 Jul 2016 10:55:51 +0000 (11:55 +0100)]
JAL-2156 refactor saveState & saveAlignment to common method
Jim Procter [Wed, 27 Jul 2016 09:29:46 +0000 (10:29 +0100)]
JAL-2156 getter for AlignFrame(s) held in a splitframe
tcofoegbu [Wed, 27 Jul 2016 12:02:46 +0000 (13:02 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 27 Jul 2016 12:02:07 +0000 (13:02 +0100)]
JAL-1919 added codes for End-2-End scan for sequence consistency for PDB files parse with JmolParser vs. Jalview's PDBfile parser
Jim Procter [Tue, 26 Jul 2016 11:59:31 +0000 (12:59 +0100)]
JAL-2157 todo: verify parser/file format enums and static/dynamic status these fields
tcofoegbu [Tue, 26 Jul 2016 10:57:46 +0000 (11:57 +0100)]
JAL-2157 bugfix for issues from enum refactoring
tcofoegbu [Mon, 25 Jul 2016 14:05:01 +0000 (15:05 +0100)]
JAL-2157 bugfix for regression from commit
82a6c8e2e25b7534168b68b2c89b9cf195f815a5
Jim Procter [Sun, 24 Jul 2016 13:05:12 +0000 (14:05 +0100)]
JAL-2154 formatting
Jim Procter [Sun, 24 Jul 2016 13:04:15 +0000 (14:04 +0100)]
JAL-2154 keep track of incomplete sequences and report if they weren’t resolved
Jim Procter [Sun, 24 Jul 2016 12:58:45 +0000 (13:58 +0100)]
JAL-2154 systematic pattern for defining/resolving forward references to sequences
Jim Procter [Sat, 23 Jul 2016 10:09:48 +0000 (11:09 +0100)]
JAL-2154 patch the hack (Jalview2XML tests pass)
tcofoegbu [Fri, 22 Jul 2016 16:13:53 +0000 (17:13 +0100)]
JAL-2148 Bugfix in structureImportSettings string-to-enum conversion and further enhancement to deal with Atoms from multi-model entries
tcofoegbu [Thu, 21 Jul 2016 16:20:56 +0000 (17:20 +0100)]
Resolve merge conflict for StructureImportSettings
tcofoegbu [Thu, 21 Jul 2016 16:12:10 +0000 (17:12 +0100)]
JAL-2148 fix to heuristically determine chain termination positions. This aids in decision making w.r.t CA HETATMs inclusion
Jim Procter [Thu, 21 Jul 2016 12:03:21 +0000 (13:03 +0100)]
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
JAL-1919 JAL-2148 regularise use of jalview.datamodel.PDBEntry.Type for PDB/mmCIF file type
JAL-1919 JAL-2148 use new enum jalview.structure.StructureImportSettings.StructureParser
gmungoc [Wed, 20 Jul 2016 16:14:45 +0000 (17:14 +0100)]
JAL-2154 poke JSeq start/end into Vamsas sequence
Jim Procter [Wed, 20 Jul 2016 15:25:25 +0000 (16:25 +0100)]
JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annotation from 3D data
Jim Procter [Wed, 20 Jul 2016 15:19:08 +0000 (16:19 +0100)]
JAL-1926 JAL-2106 don’t use PDB database constant as a file format string
Jim Procter [Wed, 20 Jul 2016 15:18:01 +0000 (16:18 +0100)]
JAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMAT’ property values
Jim Procter [Wed, 20 Jul 2016 13:30:29 +0000 (14:30 +0100)]
JAL-1926 JAL-2106 remove startRes/endRes fields - not used
gmungoc [Wed, 20 Jul 2016 09:00:57 +0000 (10:00 +0100)]
JAL-2023 stronger check for whether to start cdna consensus
gmungoc [Wed, 20 Jul 2016 09:00:24 +0000 (10:00 +0100)]
JAL-2023 avoid writing / loading empty mappings
gmungoc [Wed, 20 Jul 2016 08:05:29 +0000 (09:05 +0100)]
JAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons
gmungoc [Wed, 20 Jul 2016 05:09:01 +0000 (06:09 +0100)]
JAL-2068 AnnotationWorker create/update annotation, not delete / re-add
gmungoc [Tue, 19 Jul 2016 17:31:02 +0000 (18:31 +0100)]
JAL-2068 small refactor to reuse shared method
gmungoc [Tue, 19 Jul 2016 17:30:24 +0000 (18:30 +0100)]
JAL-2068 update rather than recreate AlignmentAnnotation on run()
gmungoc [Tue, 19 Jul 2016 15:21:18 +0000 (16:21 +0100)]
JAL-391 corrected handling of gapped sequences
tcofoegbu [Tue, 19 Jul 2016 11:49:48 +0000 (12:49 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 19 Jul 2016 11:49:35 +0000 (12:49 +0100)]
JAL-1919 set default structure file format to mmCIF, refactored some StructureImportSetting variables, removed mmCIF from DBRefSource, updated tests
Jim Procter [Tue, 19 Jul 2016 10:20:03 +0000 (11:20 +0100)]
Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
Jim Procter [Mon, 18 Jul 2016 16:03:04 +0000 (17:03 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 27 Oct 2015 12:17:25 +0000 (12:17 +0000)]
JAL-666 patch JAL-1947 in applet where overview is under sampled when lost of sequences are hidden in the viewport (hangover from applet not supporting hidden rows)
gmungoc [Mon, 18 Jul 2016 15:39:34 +0000 (16:39 +0100)]
JAL-2105 check content of Ensembl REST ping response
gmungoc [Mon, 18 Jul 2016 15:38:53 +0000 (16:38 +0100)]
JAL-2099 ensure initial setting of scaleAbove reaches viewport
gmungoc [Mon, 18 Jul 2016 15:36:58 +0000 (16:36 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 18 Jul 2016 15:36:44 +0000 (16:36 +0100)]
JAL-2099 JAL-2100 port scale number / hidden column mark changes to
applet
Jim Procter [Mon, 18 Jul 2016 15:29:34 +0000 (16:29 +0100)]
JAL-2068 clearer instructions on how to use script (and modify it!)
Jim Procter [Mon, 18 Jul 2016 15:29:15 +0000 (16:29 +0100)]
JAL-2068 clarify comments
git://source.jalview.org / jalview.git / log