jalview.git
7 years agoJAL-2491 first addition of new event
kiramt [Tue, 2 May 2017 07:57:38 +0000 (08:57 +0100)]
JAL-2491 first addition of new event

7 years agoJAL-2489 edited unit test code comment
tcofoegbu [Tue, 25 Apr 2017 14:17:58 +0000 (15:17 +0100)]
JAL-2489 edited unit test code comment

7 years agoJAL-2489 Unit test for bug
tcofoegbu [Tue, 25 Apr 2017 14:14:29 +0000 (15:14 +0100)]
JAL-2489 Unit test for bug

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 25 Apr 2017 11:45:44 +0000 (12:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2489 bug fix
tcofoegbu [Tue, 25 Apr 2017 11:45:36 +0000 (12:45 +0100)]
JAL-2489 bug fix

7 years agoJAL-2487 remove redundant refreshGUI to minimise threading issues
gmungoc [Mon, 24 Apr 2017 13:30:45 +0000 (14:30 +0100)]
JAL-2487 remove redundant refreshGUI to minimise threading issues

7 years agoJAL-2439 Fixed opposite out-by-one problem in wrapped panels
kiramt [Mon, 24 Apr 2017 10:18:26 +0000 (11:18 +0100)]
JAL-2439 Fixed opposite out-by-one problem in wrapped panels

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
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

7 years agoJAL-2439 Fix to hidden column marker being one row too short
kiramt [Mon, 24 Apr 2017 09:51:39 +0000 (10:51 +0100)]
JAL-2439 Fix to hidden column marker being one row too short

7 years agoJAL-2295 Spanish translations for superposition / errors
gmungoc [Fri, 21 Apr 2017 15:12:29 +0000 (16:12 +0100)]
JAL-2295 Spanish translations for superposition / errors

7 years agoJAL-2295 Spanish translations added
gmungoc [Fri, 21 Apr 2017 14:53:55 +0000 (15:53 +0100)]
JAL-2295 Spanish translations added

7 years agoJAL-2361 Spanish text added
gmungoc [Fri, 21 Apr 2017 14:34:04 +0000 (15:34 +0100)]
JAL-2361 Spanish text added

7 years agoJAL-2485 Bug fix to filter out uniprot response header row by excluding the first row
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

7 years agoJAL-2482 added null check
tcofoegbu [Wed, 19 Apr 2017 11:19:45 +0000 (12:19 +0100)]
JAL-2482 added null check

7 years agoJAL-2482 Bugfix
tcofoegbu [Tue, 18 Apr 2017 13:44:19 +0000 (14:44 +0100)]
JAL-2482 Bugfix

7 years agoJAL-2361 tweak layout of warning message
gmungoc [Wed, 12 Apr 2017 15:06:02 +0000 (16:06 +0100)]
JAL-2361 tweak layout of warning message

7 years agoMerge branch 'bug/JAL-2255_seq-fetcher-broken-on-linux' into develop
tcofoegbu [Mon, 10 Apr 2017 16:05:21 +0000 (17:05 +0100)]
Merge branch 'bug/JAL-2255_seq-fetcher-broken-on-linux' into develop

7 years agoJAL-2255 Bug fix bug/JAL-2255_seq-fetcher-broken-on-linux
tcofoegbu [Mon, 10 Apr 2017 16:04:13 +0000 (17:04 +0100)]
JAL-2255 Bug fix

7 years agoMerge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux
tcofoegbu [Mon, 10 Apr 2017 15:54:07 +0000 (16:54 +0100)]
Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

7 years agoJAL-2361 option to save on OK of changed named colour scheme
gmungoc [Mon, 10 Apr 2017 07:48:59 +0000 (08:48 +0100)]
JAL-2361 option to save on OK of changed named colour scheme

7 years agoJAL-2361 make a modified saved scheme the backout checkpoint for Cancel
gmungoc [Thu, 6 Apr 2017 15:52:23 +0000 (16:52 +0100)]
JAL-2361 make a modified saved scheme the backout checkpoint for Cancel

7 years agoJAL-2384 JAL-2371 update ResidueShader on change of colour by
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

7 years agoJAL-2361 simplify constructors, select unsaved but applied user defined
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

7 years agoJAL-2361 apply any saved changes to current colour scheme
gmungoc [Wed, 5 Apr 2017 13:21:44 +0000 (14:21 +0100)]
JAL-2361 apply any saved changes to current colour scheme

7 years agoJAL-2314 made non-test method non-public bug/JAL-2314
gmungoc [Mon, 3 Apr 2017 15:51:10 +0000 (16:51 +0100)]
JAL-2314 made non-test method non-public

7 years agoMerge branch 'develop' into bug/JAL-2314
gmungoc [Mon, 3 Apr 2017 13:13:46 +0000 (14:13 +0100)]
Merge branch 'develop' into bug/JAL-2314

7 years agoMerge branch 'develop' into bug/JAL-2461 bug/JAL-2461
gmungoc [Mon, 3 Apr 2017 11:56:53 +0000 (12:56 +0100)]
Merge branch 'develop' into bug/JAL-2461

7 years agoJAL-2405 additional checks for circular reference in context or dataset
gmungoc [Fri, 31 Mar 2017 11:26:45 +0000 (12:26 +0100)]
JAL-2405 additional checks for circular reference in context or dataset

7 years agoJAL-2472 PrivilegedAccessor added
gmungoc [Fri, 31 Mar 2017 11:09:02 +0000 (12:09 +0100)]
JAL-2472 PrivilegedAccessor added

7 years agoMerge branch 'develop' into bug/JAL-2431splitFrameNewView bug/JAL-2431splitFrameNewView
gmungoc [Fri, 31 Mar 2017 09:59:57 +0000 (10:59 +0100)]
Merge branch 'develop' into bug/JAL-2431splitFrameNewView

7 years agoJAL-2430 code tidy, unit test for Jmol hidden column colours
gmungoc [Fri, 31 Mar 2017 09:40:58 +0000 (10:40 +0100)]
JAL-2430 code tidy, unit test for Jmol hidden column colours

7 years agoMerge branch 'develop' into bug/JAL-1608createGroups bug/JAL-1608createGroups
gmungoc [Thu, 30 Mar 2017 14:11:49 +0000 (15:11 +0100)]
Merge branch 'develop' into bug/JAL-1608createGroups

7 years agoJAL-1608 leave Create Group, Remove Group menu items enabled
gmungoc [Thu, 30 Mar 2017 14:10:17 +0000 (15:10 +0100)]
JAL-1608 leave Create Group, Remove Group menu items enabled

7 years agoJAL-2401 code and help tidy for review comments
gmungoc [Thu, 30 Mar 2017 13:40:56 +0000 (14:40 +0100)]
JAL-2401 code and help tidy for review comments

7 years agoJAL-2401 don't apply lower case colour to upper case
gmungoc [Thu, 30 Mar 2017 11:48:42 +0000 (12:48 +0100)]
JAL-2401 don't apply lower case colour to upper case

7 years agoMerge branch 'develop' into bug/JAL-2399textColour bug/JAL-2399textColour
gmungoc [Thu, 30 Mar 2017 11:20:53 +0000 (12:20 +0100)]
Merge branch 'develop' into bug/JAL-2399textColour

7 years agoJAL-2346 JAL-1933 test updated to include Occupancy
gmungoc [Thu, 30 Mar 2017 11:16:43 +0000 (12:16 +0100)]
JAL-2346 JAL-1933 test updated to include Occupancy

7 years agoJAL-2346 always run setup! bug/JAL-2346annotationChoice
gmungoc [Thu, 30 Mar 2017 11:11:12 +0000 (12:11 +0100)]
JAL-2346 always run setup!

7 years agoJAL-2346 more test coverage for AnnotationColourGradient
gmungoc [Thu, 30 Mar 2017 10:59:58 +0000 (11:59 +0100)]
JAL-2346 more test coverage for AnnotationColourGradient

7 years agoMerge branch 'develop' into bug/JAL-2346annotationChoice
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

7 years agoMerge branch 'develop' into bug/JAL-1608createGroups
gmungoc [Wed, 29 Mar 2017 15:36:03 +0000 (16:36 +0100)]
Merge branch 'develop' into bug/JAL-1608createGroups

7 years agoJAL-2360 fix applet build by separating castor XML dependency from jalview.schemes...
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

7 years agoMerge remote-tracking branch 'origin/develop' into bug/JAL-2314
kiramt [Fri, 24 Mar 2017 09:44:01 +0000 (09:44 +0000)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2314

7 years agoJAL-2314 Tidy up
kiramt [Fri, 24 Mar 2017 09:43:38 +0000 (09:43 +0000)]
JAL-2314 Tidy up

7 years agoJAL-2314 Fixes to DisorderAnnotExportImport test
kiramt [Fri, 24 Mar 2017 09:35:24 +0000 (09:35 +0000)]
JAL-2314 Fixes to DisorderAnnotExportImport test

7 years agoJAL-2464 fix cancel tree print behaviour
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
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

7 years agoJAL-2388 unit test initialisation fix for running full suite
kiramt [Thu, 23 Mar 2017 20:39:51 +0000 (20:39 +0000)]
JAL-2388 unit test initialisation fix for running full suite

7 years agoJAL-2314 Tweaks to stop thread sync issues
kiramt [Thu, 23 Mar 2017 18:47:41 +0000 (18:47 +0000)]
JAL-2314 Tweaks to stop thread sync issues

7 years agoJAL-2464 fix cancel tree print behaviour
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour

7 years agoJAL-2314 Tidies
kiramt [Thu, 23 Mar 2017 14:56:17 +0000 (14:56 +0000)]
JAL-2314 Tidies

7 years agoJAL-2314 Re-annotated unit tests using Jws2Discoverer
kiramt [Thu, 23 Mar 2017 14:17:55 +0000 (14:17 +0000)]
JAL-2314 Re-annotated unit tests using Jws2Discoverer

7 years agoJAL-2461 Removed DAS error stack trace, updated message
kiramt [Wed, 22 Mar 2017 14:21:34 +0000 (14:21 +0000)]
JAL-2461 Removed DAS error stack trace, updated message

7 years agoJAL-2388 Reinstated original overview checks for annotation display
kiramt [Wed, 22 Mar 2017 14:12:50 +0000 (14:12 +0000)]
JAL-2388 Reinstated original overview checks for annotation display

7 years agoMerge remote-tracking branch bug/JAL-2436featureRendererThreading
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

7 years agoMerge remote-tracking branch 'origin/develop' into
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

7 years agoJAL-2311 suppress autocalc'd annotation to isolate the 'real' failure
gmungoc [Wed, 22 Mar 2017 10:51:23 +0000 (10:51 +0000)]
JAL-2311 suppress autocalc'd annotation to isolate the 'real' failure

7 years agoJAL-2307 Fixed SiftsClient unit test
kiramt [Tue, 21 Mar 2017 19:42:32 +0000 (19:42 +0000)]
JAL-2307 Fixed SiftsClient unit test

7 years agoJAL-2306 assert no DAS sources
gmungoc [Tue, 21 Mar 2017 12:41:01 +0000 (12:41 +0000)]
JAL-2306 assert no DAS sources

7 years agoJAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures
gmungoc [Tue, 21 Mar 2017 10:22:57 +0000 (10:22 +0000)]
JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures

7 years agoJAL-2243 update discovered features on opening structure in Chimera
gmungoc [Tue, 21 Mar 2017 09:44:08 +0000 (09:44 +0000)]
JAL-2243 update discovered features on opening structure in Chimera

7 years agoJAL-2438 check for null FeatureRenderer
gmungoc [Tue, 21 Mar 2017 09:43:32 +0000 (09:43 +0000)]
JAL-2438 check for null FeatureRenderer

7 years agoMerge branch 'features/JAL-2388OverviewWindow' into develop
Jim Procter [Tue, 21 Mar 2017 09:05:53 +0000 (09:05 +0000)]
Merge branch 'features/JAL-2388OverviewWindow' into develop

7 years agoMerge branch 'bug/JAL-2421overviewboxflicker' into develop
Jim Procter [Mon, 20 Mar 2017 16:05:00 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2421overviewboxflicker' into develop

7 years agoJAL-2388 Comment typo
kiramt [Mon, 20 Mar 2017 08:12:15 +0000 (08:12 +0000)]
JAL-2388 Comment typo

7 years agoJAL-2388 ViewportRanges unit test
kiramt [Fri, 17 Mar 2017 14:11:11 +0000 (14:11 +0000)]
JAL-2388 ViewportRanges unit test

7 years agoJAL-2437 Synchronization corrections and unit tests
kiramt [Fri, 17 Mar 2017 13:47:15 +0000 (13:47 +0000)]
JAL-2437 Synchronization corrections and unit tests

7 years agoJAL-2388 Renamed column and row subtraction functions
kiramt [Fri, 17 Mar 2017 07:24:00 +0000 (07:24 +0000)]
JAL-2388 Renamed column and row subtraction functions

7 years agoMerge branch 'merges/develop_JAL2295setChimeraAttributes' into develop
Jim Procter [Thu, 16 Mar 2017 18:15:03 +0000 (18:15 +0000)]
Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop

7 years agoJAL-1933 refactor parameter for code clarity
Jim Procter [Thu, 16 Mar 2017 17:42:25 +0000 (17:42 +0000)]
JAL-1933 refactor parameter for code clarity

7 years agoJAL-2388 Applied ViewportRanges to code
kiramt [Thu, 16 Mar 2017 17:30:14 +0000 (17:30 +0000)]
JAL-2388 Applied ViewportRanges to code

7 years agoJAL-2388 Renamed viewport position props to viewport ranges
kiramt [Thu, 16 Mar 2017 13:32:40 +0000 (13:32 +0000)]
JAL-2388 Renamed viewport position props to viewport ranges

7 years agoJAL-2388 Unit test update
kiramt [Thu, 16 Mar 2017 12:13:05 +0000 (12:13 +0000)]
JAL-2388 Unit test update

7 years agoJAL-2388 Applet update for overview panel
kiramt [Thu, 16 Mar 2017 12:12:52 +0000 (12:12 +0000)]
JAL-2388 Applet update for overview panel

7 years agoJAL-2439 Out-by-one in setting endRes/endSeq
kiramt [Thu, 16 Mar 2017 12:12:31 +0000 (12:12 +0000)]
JAL-2439 Out-by-one in setting endRes/endSeq

7 years agoJAL-2431 show cDNA consensus after New View in split frame
gmungoc [Wed, 15 Mar 2017 16:31:28 +0000 (16:31 +0000)]
JAL-2431 show cDNA consensus after New View in split frame

7 years agoJAL-2388 Unit tests and tidies
kiramt [Wed, 15 Mar 2017 14:58:36 +0000 (14:58 +0000)]
JAL-2388 Unit tests and tidies

7 years agoJAL-2443 push getResidueBoxColour inside getResidueColour
gmungoc [Wed, 15 Mar 2017 12:55:25 +0000 (12:55 +0000)]
JAL-2443 push getResidueBoxColour inside getResidueColour

7 years agoJAL-2438 corrected getFeatureRenderer()
gmungoc [Wed, 15 Mar 2017 12:49:51 +0000 (12:49 +0000)]
JAL-2438 corrected getFeatureRenderer()

7 years agoJAL-2442 applet feature transparency also on overview or structure
gmungoc [Wed, 15 Mar 2017 12:47:36 +0000 (12:47 +0000)]
JAL-2442 applet feature transparency also on overview or structure

7 years agoJAL-2438 handle null FeatureRenderer in FeatureColourFinder
gmungoc [Wed, 15 Mar 2017 11:49:39 +0000 (11:49 +0000)]
JAL-2438 handle null FeatureRenderer in FeatureColourFinder

7 years agoJAL-2438 refactored checks for 'no features displayed'
gmungoc [Wed, 15 Mar 2017 11:29:05 +0000 (11:29 +0000)]
JAL-2438 refactored checks for 'no features displayed'

7 years agoJAL-2438 clarify code and javadoc, reinstate updateFeatures() check
gmungoc [Wed, 15 Mar 2017 09:19:06 +0000 (09:19 +0000)]
JAL-2438 clarify code and javadoc, reinstate updateFeatures() check

7 years agoMerge branch 'develop' into bug/JAL-2436featureRendererThreading
gmungoc [Wed, 15 Mar 2017 08:49:59 +0000 (08:49 +0000)]
Merge branch 'develop' into bug/JAL-2436featureRendererThreading

7 years agoMerge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Wed, 15 Mar 2017 07:54:22 +0000 (07:54 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow

7 years agoJAL-2388 Working overview panel
kiramt [Tue, 14 Mar 2017 16:42:01 +0000 (16:42 +0000)]
JAL-2388 Working overview panel

7 years agoJAL-2439 Fixes to out-by-one sequence indexing in gui classes
kiramt [Tue, 14 Mar 2017 16:41:33 +0000 (16:41 +0000)]
JAL-2439 Fixes to out-by-one sequence indexing in gui classes

7 years agoJAL-2388 New hidden cols/seqs functions to support overview panel
kiramt [Tue, 14 Mar 2017 16:06:34 +0000 (16:06 +0000)]
JAL-2388 New hidden cols/seqs functions to support overview panel

7 years agoJAL-2438 unit test, fixes, Javadoc updates
gmungoc [Tue, 14 Mar 2017 15:07:19 +0000 (15:07 +0000)]
JAL-2438 unit test, fixes, Javadoc updates

7 years agoJAL-2438 unit tests for FeatureColourFinder (transparency tbc!)
gmungoc [Tue, 14 Mar 2017 12:25:35 +0000 (12:25 +0000)]
JAL-2438 unit tests for FeatureColourFinder (transparency tbc!)

7 years agoJAL-2438 Javadoc updates
gmungoc [Tue, 14 Mar 2017 12:25:09 +0000 (12:25 +0000)]
JAL-2438 Javadoc updates

7 years agoJAL-2438 comment/Javadoc tidies
gmungoc [Tue, 14 Mar 2017 09:42:40 +0000 (09:42 +0000)]
JAL-2438 comment/Javadoc tidies

7 years agoJAL-2438 corrected handling of default colour
gmungoc [Mon, 13 Mar 2017 17:00:19 +0000 (17:00 +0000)]
JAL-2438 corrected handling of default colour

7 years agoJAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not
gmungoc [Mon, 13 Mar 2017 16:42:23 +0000 (16:42 +0000)]
JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not
cloned for structure viewers

7 years agoJAL-2437 Fixed reordering of sequences when hiding and revealing
kiramt [Fri, 10 Mar 2017 16:11:58 +0000 (16:11 +0000)]
JAL-2437 Fixed reordering of sequences when hiding and revealing

7 years agoJAL-2388 Moving some alignment panel logic into overview (in progress)
kiramt [Fri, 10 Mar 2017 12:08:45 +0000 (12:08 +0000)]
JAL-2388 Moving some alignment panel logic into overview (in progress)

7 years agoJAL-2426 Checks on conservation thread in case we are shutting down
kiramt [Tue, 28 Feb 2017 12:25:11 +0000 (12:25 +0000)]
JAL-2426 Checks on conservation thread in case we are shutting down

7 years agoJAL-2426 Removal of NPE in conservation thread when closing Jalview
kiramt [Tue, 28 Feb 2017 14:50:10 +0000 (14:50 +0000)]
JAL-2426 Removal of NPE in conservation thread when closing Jalview

7 years agoJAL-2388 Minor fix for annotation graph, removed unit test dep on gui
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

7 years agoJAL-2430 colour columns hidden in alignment gray on structure
gmungoc [Wed, 8 Mar 2017 14:41:45 +0000 (14:41 +0000)]
JAL-2430 colour columns hidden in alignment gray on structure