gmungoc [Mon, 1 May 2017 12:51:13 +0000 (13:51 +0100)]
JAL-2434 omit unmapped positions from mapping
gmungoc [Fri, 28 Apr 2017 14:55:32 +0000 (15:55 +0100)]
JAL-2495 highlight all mapped sequences from structure pick
gmungoc [Fri, 28 Apr 2017 11:37:42 +0000 (12:37 +0100)]
JAL-2434 check all sequences when determining superposable columns
gmungoc [Fri, 28 Apr 2017 09:06:58 +0000 (10:06 +0100)]
JAL-2434 use a constant for StructureMapping.NO_CHAIN (space)
tcofoegbu [Tue, 18 Apr 2017 10:49:54 +0000 (11:49 +0100)]
JAL-2136 merged develop into branch to fix build failure
tcofoegbu [Tue, 18 Apr 2017 10:37:36 +0000 (11:37 +0100)]
JAL-2136 corrected error in annotation file
gmungoc [Wed, 12 Apr 2017 15:06:02 +0000 (16:06 +0100)]
JAL-2361 tweak layout of warning message
tcofoegbu [Mon, 10 Apr 2017 16:05:21 +0000 (17:05 +0100)]
Merge branch 'bug/JAL-2255_seq-fetcher-broken-on-linux' into develop
tcofoegbu [Mon, 10 Apr 2017 16:04:13 +0000 (17:04 +0100)]
JAL-2255 Bug fix
tcofoegbu [Mon, 10 Apr 2017 15:54:07 +0000 (16:54 +0100)]
Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux
gmungoc [Mon, 10 Apr 2017 07:48:59 +0000 (08:48 +0100)]
JAL-2361 option to save on OK of changed named colour scheme
gmungoc [Thu, 6 Apr 2017 15:52:23 +0000 (16:52 +0100)]
JAL-2361 make a modified saved scheme the backout checkpoint for Cancel
gmungoc [Wed, 5 Apr 2017 15:14:39 +0000 (16:14 +0100)]
JAL-2384 JAL-2371 update ResidueShader on change of colour by
conservation / pid
gmungoc [Wed, 5 Apr 2017 14:47:10 +0000 (15:47 +0100)]
JAL-2361 simplify constructors, select unsaved but applied user defined
colour scheme in menu
gmungoc [Wed, 5 Apr 2017 13:21:44 +0000 (14:21 +0100)]
JAL-2361 apply any saved changes to current colour scheme
gmungoc [Mon, 3 Apr 2017 15:51:10 +0000 (16:51 +0100)]
JAL-2314 made non-test method non-public
gmungoc [Mon, 3 Apr 2017 13:13:46 +0000 (14:13 +0100)]
Merge branch 'develop' into bug/JAL-2314
gmungoc [Mon, 3 Apr 2017 11:56:53 +0000 (12:56 +0100)]
Merge branch 'develop' into bug/JAL-2461
gmungoc [Fri, 31 Mar 2017 11:26:45 +0000 (12:26 +0100)]
JAL-2405 additional checks for circular reference in context or dataset
gmungoc [Fri, 31 Mar 2017 11:09:02 +0000 (12:09 +0100)]
JAL-2472 PrivilegedAccessor added
gmungoc [Fri, 31 Mar 2017 09:59:57 +0000 (10:59 +0100)]
Merge branch 'develop' into bug/JAL-2431splitFrameNewView
gmungoc [Fri, 31 Mar 2017 09:40:58 +0000 (10:40 +0100)]
JAL-2430 code tidy, unit test for Jmol hidden column colours
gmungoc [Thu, 30 Mar 2017 14:11:49 +0000 (15:11 +0100)]
Merge branch 'develop' into bug/JAL-1608createGroups
gmungoc [Thu, 30 Mar 2017 14:10:17 +0000 (15:10 +0100)]
JAL-1608 leave Create Group, Remove Group menu items enabled
gmungoc [Thu, 30 Mar 2017 13:40:56 +0000 (14:40 +0100)]
JAL-2401 code and help tidy for review comments
gmungoc [Thu, 30 Mar 2017 11:48:42 +0000 (12:48 +0100)]
JAL-2401 don't apply lower case colour to upper case
gmungoc [Thu, 30 Mar 2017 11:20:53 +0000 (12:20 +0100)]
Merge branch 'develop' into bug/JAL-2399textColour
gmungoc [Thu, 30 Mar 2017 11:16:43 +0000 (12:16 +0100)]
JAL-2346 JAL-1933 test updated to include Occupancy
gmungoc [Thu, 30 Mar 2017 11:11:12 +0000 (12:11 +0100)]
JAL-2346 always run setup!
gmungoc [Thu, 30 Mar 2017 10:59:58 +0000 (11:59 +0100)]
JAL-2346 more test coverage for AnnotationColourGradient
gmungoc [Thu, 30 Mar 2017 10:01:08 +0000 (11:01 +0100)]
Merge branch 'develop' into bug/JAL-2346annotationChoice
Conflicts:
src/jalview/gui/AnnotationRowFilter.java
gmungoc [Wed, 29 Mar 2017 15:36:03 +0000 (16:36 +0100)]
Merge branch 'develop' into bug/JAL-1608createGroups
tcofoegbu [Tue, 28 Mar 2017 17:20:10 +0000 (18:20 +0100)]
JAL-2136 JAL-2137 Added improvement to enable explicit and dynamic definition of STRUCTMODEL data via HEADER_STRUCT_MODEL annotation, updated test annotation file, and added unit test accordingly
tcofoegbu [Tue, 28 Mar 2017 17:12:43 +0000 (18:12 +0100)]
JAL-2136 fixed failing unit test for Phyre2Client
tcofoegbu [Tue, 28 Mar 2017 17:08:15 +0000 (18:08 +0100)]
JAL-2465 missed commit for refactore renaming of getPdbFile() method to getStructureFile()
tcofoegbu [Tue, 28 Mar 2017 17:04:46 +0000 (18:04 +0100)]
JAL-2465 unit test for bugfix
tcofoegbu [Tue, 28 Mar 2017 17:03:41 +0000 (18:03 +0100)]
JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()
Jim Procter [Fri, 24 Mar 2017 15:28:49 +0000 (15:28 +0000)]
JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes.ColourSchemes to jalview.schemes.ColourSchemeLoader
kiramt [Fri, 24 Mar 2017 09:44:01 +0000 (09:44 +0000)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2314
kiramt [Fri, 24 Mar 2017 09:43:38 +0000 (09:43 +0000)]
JAL-2314 Tidy up
kiramt [Fri, 24 Mar 2017 09:35:24 +0000 (09:35 +0000)]
JAL-2314 Fixes to DisorderAnnotExportImport test
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour
kiramt [Thu, 23 Mar 2017 20:40:10 +0000 (20:40 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Thu, 23 Mar 2017 20:39:51 +0000 (20:39 +0000)]
JAL-2388 unit test initialisation fix for running full suite
kiramt [Thu, 23 Mar 2017 18:47:41 +0000 (18:47 +0000)]
JAL-2314 Tweaks to stop thread sync issues
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour
kiramt [Thu, 23 Mar 2017 14:56:17 +0000 (14:56 +0000)]
JAL-2314 Tidies
kiramt [Thu, 23 Mar 2017 14:17:55 +0000 (14:17 +0000)]
JAL-2314 Re-annotated unit tests using Jws2Discoverer
tcofoegbu [Thu, 23 Mar 2017 12:02:33 +0000 (12:02 +0000)]
JAL-2463 bugfix
kiramt [Wed, 22 Mar 2017 14:21:34 +0000 (14:21 +0000)]
JAL-2461 Removed DAS error stack trace, updated message
kiramt [Wed, 22 Mar 2017 14:12:50 +0000 (14:12 +0000)]
JAL-2388 Reinstated original overview checks for annotation display
kiramt [Wed, 22 Mar 2017 13:53:57 +0000 (13:53 +0000)]
Merge remote-tracking branch
'origin/bug/JAL-2436featureRendererThreading' into develop
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
kiramt [Wed, 22 Mar 2017 12:36:24 +0000 (12:36 +0000)]
Merge remote-tracking branch 'origin/develop' into
bug/JAL-2436featureRendererThreading
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
gmungoc [Wed, 22 Mar 2017 10:51:23 +0000 (10:51 +0000)]
JAL-2311 suppress autocalc'd annotation to isolate the 'real' failure
kiramt [Tue, 21 Mar 2017 19:42:32 +0000 (19:42 +0000)]
JAL-2307 Fixed SiftsClient unit test
gmungoc [Tue, 21 Mar 2017 12:41:01 +0000 (12:41 +0000)]
JAL-2306 assert no DAS sources
gmungoc [Tue, 21 Mar 2017 10:22:57 +0000 (10:22 +0000)]
JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures
gmungoc [Tue, 21 Mar 2017 09:44:08 +0000 (09:44 +0000)]
JAL-2243 update discovered features on opening structure in Chimera
gmungoc [Tue, 21 Mar 2017 09:43:32 +0000 (09:43 +0000)]
JAL-2438 check for null FeatureRenderer
Jim Procter [Tue, 21 Mar 2017 09:05:53 +0000 (09:05 +0000)]
Merge branch 'features/JAL-2388OverviewWindow' into develop
Jim Procter [Mon, 20 Mar 2017 16:05:00 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2421overviewboxflicker' into develop
tcofoegbu [Mon, 20 Mar 2017 15:14:27 +0000 (15:14 +0000)]
Merge JAL-2136_phyre2_integration to develop
kiramt [Mon, 20 Mar 2017 08:12:15 +0000 (08:12 +0000)]
JAL-2388 Comment typo
tcofoegbu [Fri, 17 Mar 2017 15:41:01 +0000 (15:41 +0000)]
JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less stringent and backwards compatible, Link query and template sequences, transfer annotation from model to template sequence
kiramt [Fri, 17 Mar 2017 14:11:11 +0000 (14:11 +0000)]
JAL-2388 ViewportRanges unit test
kiramt [Fri, 17 Mar 2017 13:47:15 +0000 (13:47 +0000)]
JAL-2437 Synchronization corrections and unit tests
kiramt [Fri, 17 Mar 2017 07:24:00 +0000 (07:24 +0000)]
JAL-2388 Renamed column and row subtraction functions
Jim Procter [Thu, 16 Mar 2017 18:15:03 +0000 (18:15 +0000)]
Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop
Jim Procter [Thu, 16 Mar 2017 17:42:25 +0000 (17:42 +0000)]
JAL-1933 refactor parameter for code clarity
kiramt [Thu, 16 Mar 2017 17:30:14 +0000 (17:30 +0000)]
JAL-2388 Applied ViewportRanges to code
kiramt [Thu, 16 Mar 2017 13:32:40 +0000 (13:32 +0000)]
JAL-2388 Renamed viewport position props to viewport ranges
kiramt [Thu, 16 Mar 2017 12:13:05 +0000 (12:13 +0000)]
JAL-2388 Unit test update
kiramt [Thu, 16 Mar 2017 12:12:52 +0000 (12:12 +0000)]
JAL-2388 Applet update for overview panel
kiramt [Thu, 16 Mar 2017 12:12:31 +0000 (12:12 +0000)]
JAL-2439 Out-by-one in setting endRes/endSeq
gmungoc [Wed, 15 Mar 2017 16:31:28 +0000 (16:31 +0000)]
JAL-2431 show cDNA consensus after New View in split frame
kiramt [Wed, 15 Mar 2017 14:58:36 +0000 (14:58 +0000)]
JAL-2388 Unit tests and tidies
gmungoc [Wed, 15 Mar 2017 12:55:25 +0000 (12:55 +0000)]
JAL-2443 push getResidueBoxColour inside getResidueColour
gmungoc [Wed, 15 Mar 2017 12:49:51 +0000 (12:49 +0000)]
JAL-2438 corrected getFeatureRenderer()
gmungoc [Wed, 15 Mar 2017 12:47:36 +0000 (12:47 +0000)]
JAL-2442 applet feature transparency also on overview or structure
gmungoc [Wed, 15 Mar 2017 11:49:39 +0000 (11:49 +0000)]
JAL-2438 handle null FeatureRenderer in FeatureColourFinder
gmungoc [Wed, 15 Mar 2017 11:29:05 +0000 (11:29 +0000)]
JAL-2438 refactored checks for 'no features displayed'
gmungoc [Wed, 15 Mar 2017 09:19:06 +0000 (09:19 +0000)]
JAL-2438 clarify code and javadoc, reinstate updateFeatures() check
gmungoc [Wed, 15 Mar 2017 08:49:59 +0000 (08:49 +0000)]
Merge branch 'develop' into bug/JAL-2436featureRendererThreading
kiramt [Wed, 15 Mar 2017 07:54:22 +0000 (07:54 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Tue, 14 Mar 2017 16:42:01 +0000 (16:42 +0000)]
JAL-2388 Working overview panel
kiramt [Tue, 14 Mar 2017 16:41:33 +0000 (16:41 +0000)]
JAL-2439 Fixes to out-by-one sequence indexing in gui classes
kiramt [Tue, 14 Mar 2017 16:06:34 +0000 (16:06 +0000)]
JAL-2388 New hidden cols/seqs functions to support overview panel
tcofoegbu [Tue, 14 Mar 2017 15:35:50 +0000 (15:35 +0000)]
JAL-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file specification, improved implementation to link the Fasta mapping file to Phyre2 model entry, and moved Phyre2 model info from sequence detail to PDBEntry properties
gmungoc [Tue, 14 Mar 2017 15:07:19 +0000 (15:07 +0000)]
JAL-2438 unit test, fixes, Javadoc updates
gmungoc [Tue, 14 Mar 2017 12:25:35 +0000 (12:25 +0000)]
JAL-2438 unit tests for FeatureColourFinder (transparency tbc!)
gmungoc [Tue, 14 Mar 2017 12:25:09 +0000 (12:25 +0000)]
JAL-2438 Javadoc updates
gmungoc [Tue, 14 Mar 2017 09:42:40 +0000 (09:42 +0000)]
JAL-2438 comment/Javadoc tidies
gmungoc [Mon, 13 Mar 2017 17:00:19 +0000 (17:00 +0000)]
JAL-2438 corrected handling of default colour
gmungoc [Mon, 13 Mar 2017 16:42:23 +0000 (16:42 +0000)]
JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not
cloned for structure viewers
kiramt [Fri, 10 Mar 2017 16:11:58 +0000 (16:11 +0000)]
JAL-2437 Fixed reordering of sequences when hiding and revealing
tcofoegbu [Fri, 10 Mar 2017 14:29:21 +0000 (14:29 +0000)]
JAL-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation to register Phyre2 model file from AnnotationFile such that it could be properly processed Phyre2 client on structure viewing.
kiramt [Fri, 10 Mar 2017 12:08:45 +0000 (12:08 +0000)]
JAL-2388 Moving some alignment panel logic into overview (in progress)
kiramt [Tue, 28 Feb 2017 12:25:11 +0000 (12:25 +0000)]
JAL-2426 Checks on conservation thread in case we are shutting down
kiramt [Tue, 28 Feb 2017 14:50:10 +0000 (14:50 +0000)]
JAL-2426 Removal of NPE in conservation thread when closing Jalview
kiramt [Thu, 9 Mar 2017 10:29:06 +0000 (10:29 +0000)]
JAL-2388 Minor fix for annotation graph, removed unit test dep on gui
git://source.jalview.org / jalview.git / log