kiramt [Tue, 25 Apr 2017 13:52:45 +0000 (14:52 +0100)]
JAL-2388 Missed file from previous commit
kiramt [Tue, 25 Apr 2017 13:52:11 +0000 (14:52 +0100)]
JAL-2388 Reverted and re-did applet changes
kiramt [Tue, 25 Apr 2017 12:59:18 +0000 (13:59 +0100)]
JAL-2388 Tidies and other corrections so applet compiles
kiramt [Tue, 25 Apr 2017 12:33:37 +0000 (13:33 +0100)]
JAL-2388 And corrected OverviewCanvas for applet
kiramt [Tue, 25 Apr 2017 12:26:21 +0000 (13:26 +0100)]
JAL-2388 Updated applet to show/hide hidden regions in overview
kiramt [Tue, 25 Apr 2017 11:15:50 +0000 (12:15 +0100)]
JAL-2388 Working hidden regions hide/show in desktop
kiramt [Mon, 24 Apr 2017 13:13:18 +0000 (14:13 +0100)]
Merge remote-tracking branch
'origin/features/JAL-2388hiddencolumnschanges' into
features/JAL-2388OverviewWindow
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
src/jalview/viewmodel/OverviewDimensions.java
kiramt [Mon, 24 Apr 2017 13:01:34 +0000 (14:01 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Mon, 24 Apr 2017 13:00:31 +0000 (14:00 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
kiramt [Mon, 24 Apr 2017 12:59:47 +0000 (13:59 +0100)]
JAL-2388 Finished split of hidden columns and selected columns
kiramt [Mon, 24 Apr 2017 10:18:26 +0000 (11:18 +0100)]
JAL-2439 Fixed opposite out-by-one problem in wrapped panels
kiramt [Mon, 24 Apr 2017 09:52:12 +0000 (10:52 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 24 Apr 2017 09:51:39 +0000 (10:51 +0100)]
JAL-2439 Fix to hidden column marker being one row too short
kiramt [Mon, 24 Apr 2017 09:37:33 +0000 (10:37 +0100)]
JAL-2388 Hidden cols separated from column selection (almost complete)
gmungoc [Fri, 21 Apr 2017 15:12:29 +0000 (16:12 +0100)]
JAL-2295 Spanish translations for superposition / errors
gmungoc [Fri, 21 Apr 2017 14:53:55 +0000 (15:53 +0100)]
JAL-2295 Spanish translations added
gmungoc [Fri, 21 Apr 2017 14:34:04 +0000 (15:34 +0100)]
JAL-2361 Spanish text added
tcofoegbu [Fri, 21 Apr 2017 11:33:31 +0000 (12:33 +0100)]
JAL-2485 Bug fix to filter out uniprot response header row by excluding the first row
kiramt [Fri, 21 Apr 2017 11:21:23 +0000 (12:21 +0100)]
JAL-2388 Tidies
kiramt [Fri, 21 Apr 2017 09:42:24 +0000 (10:42 +0100)]
JAL-2388 Make sure resizing still works
kiramt [Fri, 21 Apr 2017 09:03:37 +0000 (10:03 +0100)]
JAL-2388 Alignment col and row collections with iterators
tcofoegbu [Wed, 19 Apr 2017 11:19:45 +0000 (12:19 +0100)]
JAL-2482 added null check
kiramt [Wed, 19 Apr 2017 11:01:30 +0000 (12:01 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388OverviewWindow
Conflicts:
resources/lang/Messages_es.properties
tcofoegbu [Tue, 18 Apr 2017 13:44:19 +0000 (14:44 +0100)]
JAL-2482 Bugfix
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
kiramt [Wed, 29 Mar 2017 09:53:39 +0000 (10:53 +0100)]
JAL-2388 New rendering code, extensions to support hiding hidden cols
kiramt [Wed, 29 Mar 2017 09:51:59 +0000 (10:51 +0100)]
JAL-2388 New iterators and tests
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 11:36:35 +0000 (11:36 +0000)]
JAL-2388 Removing AlignmentPanel dependency (mostly)
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
kiramt [Thu, 23 Mar 2017 13:46:36 +0000 (13:46 +0000)]
JAL-2388 Factored out applet overview canvas, threading adjustments
kiramt [Wed, 22 Mar 2017 16:29:45 +0000 (16:29 +0000)]
JAL-2388 Rationalised overview panel drawing thread
kiramt [Wed, 22 Mar 2017 14:47:23 +0000 (14:47 +0000)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388OverviewWindow
Conflicts:
src/jalview/gui/OverviewPanel.java
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 [Wed, 22 Mar 2017 10:29:16 +0000 (10:29 +0000)]
JAL-2388 Minor changes to thread flags
kiramt [Tue, 21 Mar 2017 19:42:32 +0000 (19:42 +0000)]
JAL-2307 Fixed SiftsClient unit test
kiramt [Tue, 21 Mar 2017 15:38:01 +0000 (15:38 +0000)]
JAL-2388 Unpleasant but operational refactor into OverviewCanvas
gmungoc [Tue, 21 Mar 2017 12:41:01 +0000 (12:41 +0000)]
JAL-2306 assert no DAS sources
kiramt [Tue, 21 Mar 2017 11:26:31 +0000 (11:26 +0000)]
JAL-2388 Made ViewportRanges final
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
kiramt [Mon, 20 Mar 2017 08:12:15 +0000 (08:12 +0000)]
JAL-2388 Comment typo
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'
git://source.jalview.org / jalview.git / log