jalview.git
7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...
tcofoegbu [Mon, 1 May 2017 17:26:52 +0000 (18:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 1 May 2017 17:16:56 +0000 (18:16 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2482 bug fix
tcofoegbu [Mon, 1 May 2017 17:13:55 +0000 (18:13 +0100)]
JAL-2482 bug fix

7 years agoJAL-2482 unit test for bug fix
tcofoegbu [Mon, 1 May 2017 17:08:05 +0000 (18:08 +0100)]
JAL-2482 unit test for bug fix

7 years agoJAL-2489 JAL-2371 reinstate calls to
gmungoc [Mon, 1 May 2017 15:44:23 +0000 (16:44 +0100)]
JAL-2489 JAL-2371 reinstate calls to
ColourSchemeProperty.getColourName() to handle null case

7 years agoJAL-2465 missed commit for refactore renaming of getPdbFile() method to getStructureF...
tcofoegbu [Tue, 28 Mar 2017 17:08:15 +0000 (18:08 +0100)]
JAL-2465 missed commit for refactore renaming of getPdbFile() method to getStructureFile()

7 years agoJAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()
tcofoegbu [Tue, 28 Mar 2017 17:03:41 +0000 (18:03 +0100)]
JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()

7 years agoJAL-2465 unit test for bugfix
tcofoegbu [Tue, 28 Mar 2017 17:04:46 +0000 (18:04 +0100)]
JAL-2465 unit test for bugfix

7 years agoMerge remote-tracking branch
gmungoc [Mon, 1 May 2017 13:18:38 +0000 (14:18 +0100)]
Merge remote-tracking branch
'origin/bug/JAL-2479unitteststoNetworkGroup' into develop

7 years agoMerge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 17:29:17 +0000 (18:29 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop

7 years agoJAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default (allows... features/JAL-1933_occupancy
Jim Procter [Thu, 27 Apr 2017 17:22:47 +0000 (18:22 +0100)]
JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default (allows jalview.gui.AnnotationChooserTest to pass)

7 years agoJAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default
Jim Procter [Thu, 27 Apr 2017 17:21:29 +0000 (18:21 +0100)]
JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default

7 years agoMerge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 17:04:05 +0000 (18:04 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop

7 years agoJAL-1933 don't show occupancy row when testing conservation thread runs even when...
Jim Procter [Thu, 27 Apr 2017 17:02:54 +0000 (18:02 +0100)]
JAL-1933 don't show occupancy row when testing conservation thread runs even when only quality calculation is enabled in preferences (JAL-1306)

7 years agoMerge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 16:49:30 +0000 (17:49 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop

7 years agoJAL-1933 applet doc for showOccupancy parameter
Jim Procter [Thu, 27 Apr 2017 16:48:46 +0000 (17:48 +0100)]
JAL-1933 applet doc for showOccupancy parameter

7 years agoJAL-1933 desktop documentation for show occupancy preference
Jim Procter [Thu, 27 Apr 2017 16:48:30 +0000 (17:48 +0100)]
JAL-1933 desktop documentation for show occupancy preference

7 years agoJAL-1933 use constant for preference token
Jim Procter [Thu, 27 Apr 2017 16:43:32 +0000 (17:43 +0100)]
JAL-1933 use constant for preference token

7 years agoMerge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 16:40:56 +0000 (17:40 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop

7 years agoJAL-1933 consensus calculation doesn’t depend on occupancy row being materialised
Jim Procter [Thu, 27 Apr 2017 16:39:38 +0000 (17:39 +0100)]
JAL-1933 consensus calculation doesn’t depend on occupancy row being materialised

7 years agoJAL-1933 desktop preferences for occupancy
Jim Procter [Thu, 27 Apr 2017 16:34:47 +0000 (17:34 +0100)]
JAL-1933 desktop preferences for occupancy

7 years agoJAL-1933 action and label for occupancy
Jim Procter [Thu, 27 Apr 2017 16:34:29 +0000 (17:34 +0100)]
JAL-1933 action and label for occupancy

7 years agoJAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting
Jim Procter [Thu, 27 Apr 2017 15:39:33 +0000 (16:39 +0100)]
JAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting

7 years agoJAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY .jalview_properties setting
Jim Procter [Thu, 27 Apr 2017 15:39:12 +0000 (16:39 +0100)]
JAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY .jalview_properties setting

7 years agoJAL-1933 only create and add occupancy row to alignment view if showOccupancy viewpor...
Jim Procter [Thu, 27 Apr 2017 15:38:22 +0000 (16:38 +0100)]
JAL-1933 only create and add occupancy row to alignment view if showOccupancy viewport attribute is set

7 years agoJAL-2494 fix: updated behaviour for SequenceGroup.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:34:03 +0000 (16:34 +0100)]
JAL-2494 fix: updated behaviour for SequenceGroup.findAnnotations

7 years agoJAL-2494 fixed behaviour for null parameters in line with test
Jim Procter [Thu, 27 Apr 2017 15:32:53 +0000 (16:32 +0100)]
JAL-2494 fixed behaviour for null parameters in line with test

7 years agoJAL-2494 javadoc for AnnotatedCollectionI.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:25:24 +0000 (16:25 +0100)]
JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations

7 years agoJAL-2494 test to cover AnnotatedCollectionI.findAnnotations

Jim Procter [Thu, 27 Apr 2017 15:13:25 +0000 (16:13 +0100)]
JAL-2494 test to cover AnnotatedCollectionI.findAnnotations


7 years agoMerge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 14:05:42 +0000 (15:05 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop

7 years agoJAL-2432 desktop: filter/select columns by threshold as a percentage
Jim Procter [Thu, 27 Apr 2017 13:58:26 +0000 (14:58 +0100)]
JAL-2432 desktop: filter/select columns by threshold as a percentage

7 years agoJAL-1933 JAL-2432 code tidy
Jim Procter [Thu, 27 Apr 2017 13:57:28 +0000 (14:57 +0100)]
JAL-1933 JAL-2432 code tidy

7 years agoJAL-2432 left justify value shown after adjusting threshold slider
Jim Procter [Thu, 27 Apr 2017 13:57:13 +0000 (14:57 +0100)]
JAL-2432 left justify value shown after adjusting threshold slider

7 years agoJAL-1933 JAL-2432 percentile filter for select/hide columns by annotation in applet
Jim Procter [Thu, 27 Apr 2017 13:56:28 +0000 (14:56 +0100)]
JAL-1933 JAL-2432 percentile filter for select/hide columns by annotation in applet

7 years agoJAL-1933 shade occupancy from light grey to black for high -> low occupancy
Jim Procter [Thu, 27 Apr 2017 10:57:50 +0000 (11:57 +0100)]
JAL-1933 shade occupancy from light grey to black for high -> low occupancy

7 years agoJAL-1933 don’t show symbol counts under histogram (also loses tooltip)
Jim Procter [Thu, 27 Apr 2017 10:56:47 +0000 (11:56 +0100)]
JAL-1933 don’t show symbol counts under histogram (also loses tooltip)

7 years agoJAL-1933 occupancy row has a space below it for counts
Jim Procter [Thu, 27 Apr 2017 10:55:34 +0000 (11:55 +0100)]
JAL-1933 occupancy row has a space below it for counts

7 years agoMerge branch 'develop' into features/JAL-1933_occupancy
Jim Procter [Thu, 27 Apr 2017 10:11:48 +0000 (11:11 +0100)]
Merge branch 'develop' into features/JAL-1933_occupancy

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 agoJAL-2479 Moved some network-dependent unit tests into Network group bug/JAL-2479unitteststoNetworkGroup
kiramt [Tue, 11 Apr 2017 13:58:08 +0000 (14:58 +0100)]
JAL-2479 Moved some network-dependent unit tests into Network group

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