gmungoc [Tue, 11 Apr 2017 10:48:40 +0000 (11:48 +0100)]
JAL-2428 Javadoc
gmungoc [Tue, 11 Apr 2017 07:59:47 +0000 (08:59 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 10 Apr 2017 18:24:04 +0000 (19:24 +0100)]
JAL-2403 unit tests for PCA.computeSimilarity, signature simplified
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 15:21:35 +0000 (16:21 +0100)]
JAL-2403 removed remaining jvCalcMode references from PCA
gmungoc [Mon, 10 Apr 2017 14:49:26 +0000 (15:49 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 10 Apr 2017 14:49:05 +0000 (15:49 +0100)]
JAL-2416 test updated for reinstatement of '*' row/column in blosum62
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 [Sun, 9 Apr 2017 07:07:31 +0000 (08:07 +0100)]
JAL-2393 remove unused commented code
gmungoc [Fri, 7 Apr 2017 13:27:45 +0000 (14:27 +0100)]
JAL-2393 code tidying for review comments
gmungoc [Fri, 7 Apr 2017 13:16:55 +0000 (14:16 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
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
gmungoc [Wed, 29 Mar 2017 14:21:43 +0000 (15:21 +0100)]
JAL-2416 JAL-728 reduced dependency on Blosum62 implementation details
gmungoc [Wed, 29 Mar 2017 11:38:18 +0000 (12:38 +0100)]
JAL-2416 revert to '*' not '-' in score matrix, handle gaps explicitly
in AlignSeq
gmungoc [Wed, 29 Mar 2017 08:20:13 +0000 (09:20 +0100)]
JAL-2416 explicit constant for unknown/unknown identity score (*
diagonal), comments
gmungoc [Tue, 28 Mar 2017 15:40:38 +0000 (16:40 +0100)]
JAL-2416 format matrix more readably
gmungoc [Tue, 28 Mar 2017 11:55:33 +0000 (12:55 +0100)]
JAL-2403 JAL-2416 pairwise score unexpected symbols as minimum matrix
substitution score (or 1 for identity) (reproduces '*' score column)
gmungoc [Tue, 28 Mar 2017 11:01:05 +0000 (12:01 +0100)]
JAL-2416 JAL-2403 remove unused '*' row/column from score matrices
gmungoc [Tue, 28 Mar 2017 10:59:42 +0000 (11:59 +0100)]
JAL-2403 further test coverage for ScoreMatrix, min/max getters
gmungoc [Tue, 28 Mar 2017 09:18:43 +0000 (10:18 +0100)]
JAL-2416 more test coverage of matrix parser
gmungoc [Mon, 27 Mar 2017 18:14:17 +0000 (19:14 +0100)]
JAL-2416 parse score matrices in either NCBI or AAindex format
gmungoc [Mon, 27 Mar 2017 18:13:44 +0000 (19:13 +0100)]
JAL-2416 amended to AAindex format
gmungoc [Mon, 27 Mar 2017 18:13:20 +0000 (19:13 +0100)]
JAL-2416 amended to (as near as possible) strict NCBI format
gmungoc [Mon, 27 Mar 2017 13:27:35 +0000 (14:27 +0100)]
JAL-2416 class Javadoc updates prior to parsing changes
gmungoc [Mon, 27 Mar 2017 13:25:59 +0000 (14:25 +0100)]
JAL-2468 change score model in PCAModel when switching
peptide/nucleotide
gmungoc [Mon, 27 Mar 2017 12:49:06 +0000 (13:49 +0100)]
JAL-2416 tidy up after switch from ' ' to '-' in score matrices
gmungoc [Mon, 27 Mar 2017 12:12:37 +0000 (13:12 +0100)]
JAL-2416 score matrix gap symbol (if any) dynamically determined
gmungoc [Mon, 27 Mar 2017 11:40:35 +0000 (12:40 +0100)]
JAL-2416 tooltip with descriptions for score models drop-down list
gmungoc [Mon, 27 Mar 2017 10:48:49 +0000 (11:48 +0100)]
JAL-2416 add score model description field for tooltip in PCA panel
gmungoc [Mon, 27 Mar 2017 10:02:47 +0000 (11:02 +0100)]
JAL-2403 SWDistanceModel now SmithWatermanModel - a similarity model
gmungoc [Mon, 27 Mar 2017 09:16:21 +0000 (10:16 +0100)]
JAL-2416 use '-' not space for gap in score matrices
gmungoc [Mon, 27 Mar 2017 09:10:13 +0000 (10:10 +0100)]
JAL-2428 unused method deleted
gmungoc [Mon, 27 Mar 2017 09:09:22 +0000 (10:09 +0100)]
JAL-2403 PIDDistanceModel deleted as superseded by PIDModel
gmungoc [Mon, 27 Mar 2017 08:11:47 +0000 (09:11 +0100)]
JAL-2428 pass AlignmentView to TreeModel so Show Input Data works
gmungoc [Fri, 24 Mar 2017 16:59:32 +0000 (16:59 +0000)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Fri, 24 Mar 2017 16:30:04 +0000 (16:30 +0000)]
JAL-2428 simplify TreeModel constructors, add getOriginalData
gmungoc [Fri, 24 Mar 2017 16:28:29 +0000 (16:28 +0000)]
JAL-2428 use 'correct' name for selected score model
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
gmungoc [Fri, 24 Mar 2017 14:47:49 +0000 (14:47 +0000)]
JAL-1632 TreeChooser renamed CalculationChooser, text improved, i18n
gmungoc [Fri, 24 Mar 2017 12:21:33 +0000 (12:21 +0000)]
JAL-1632 named parameters
gmungoc [Fri, 24 Mar 2017 09:58:15 +0000 (09:58 +0000)]
JAL-2398 corrected BLOSUM62 C -> R score in resource file!
gmungoc [Fri, 24 Mar 2017 09:57:31 +0000 (09:57 +0000)]
JAL-2416 tests added for ScoreMatrix
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
gmungoc [Fri, 24 Mar 2017 09:30:47 +0000 (09:30 +0000)]
JAL-838 move two callers off Comparison.PID and deprecate it
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 16:39:46 +0000 (16:39 +0000)]
JAL-2397 scale PCA by PID to alignment width to match SeqSpace
gmungoc [Thu, 23 Mar 2017 16:12:14 +0000 (16:12 +0000)]
JAL-2397 formatting only
gmungoc [Thu, 23 Mar 2017 16:11:37 +0000 (16:11 +0000)]
JAL-1632 suppress PID parameter options in Tree/PCA chooser for now
gmungoc [Thu, 23 Mar 2017 16:10:21 +0000 (16:10 +0000)]
JAL-838 class javadoc added
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour
gmungoc [Thu, 23 Mar 2017 15:01:29 +0000 (15:01 +0000)]
JAL-2393 code tidy and comments, PIDDistanceModel deprecated
gmungoc [Thu, 23 Mar 2017 15:00:59 +0000 (15:00 +0000)]
JAL-2393 updated test for removal of PIDDistanceModel
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
gmungoc [Thu, 23 Mar 2017 09:17:31 +0000 (09:17 +0000)]
Merge branch 'develop' into features/JAL-2393customMatrices
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
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
git://source.jalview.org / jalview.git / log