jalview.git
7 years agoJAL-2434 check all sequences when determining superposable columns
gmungoc [Fri, 28 Apr 2017 11:37:42 +0000 (12:37 +0100)]
JAL-2434 check all sequences when determining superposable columns

7 years agoJAL-2434 use a constant for StructureMapping.NO_CHAIN (space)
gmungoc [Fri, 28 Apr 2017 09:06:58 +0000 (10:06 +0100)]
JAL-2434 use a constant for StructureMapping.NO_CHAIN (space)

7 years agoJAL-2136 merged develop into branch to fix build failure
tcofoegbu [Tue, 18 Apr 2017 10:49:54 +0000 (11:49 +0100)]
JAL-2136 merged develop into branch to fix build failure

7 years agoJAL-2136 corrected error in annotation file
tcofoegbu [Tue, 18 Apr 2017 10:37:36 +0000 (11:37 +0100)]
JAL-2136 corrected error in annotation file

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-2136 JAL-2137 Added improvement to enable explicit and dynamic definition of...
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

7 years agoJAL-2136 fixed failing unit test for Phyre2Client
tcofoegbu [Tue, 28 Mar 2017 17:12:43 +0000 (18:12 +0100)]
JAL-2136 fixed failing unit test for Phyre2Client

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

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-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-2463 bugfix
tcofoegbu [Thu, 23 Mar 2017 12:02:33 +0000 (12:02 +0000)]
JAL-2463 bugfix

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 agoMerge JAL-2136_phyre2_integration to develop
tcofoegbu [Mon, 20 Mar 2017 15:14:27 +0000 (15:14 +0000)]
Merge JAL-2136_phyre2_integration to 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-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less... merge/JAL-2136_phyre2_integration
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

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-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file...
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

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-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation...
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.

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

7 years agoJAL-2295 avoid quotes breaking attribute value parsing
gmungoc [Wed, 8 Mar 2017 11:15:27 +0000 (11:15 +0000)]
JAL-2295 avoid quotes breaking attribute value parsing