gmungoc [Fri, 28 Apr 2017 09:07:55 +0000 (10:07 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
Jim Procter [Thu, 27 Apr 2017 17:29:17 +0000 (18:29 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
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)
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
Jim Procter [Thu, 27 Apr 2017 17:04:05 +0000 (18:04 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
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)
Jim Procter [Thu, 27 Apr 2017 16:49:30 +0000 (17:49 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 16:48:46 +0000 (17:48 +0100)]
JAL-1933 applet doc for showOccupancy parameter
Jim Procter [Thu, 27 Apr 2017 16:48:30 +0000 (17:48 +0100)]
JAL-1933 desktop documentation for show occupancy preference
Jim Procter [Thu, 27 Apr 2017 16:43:32 +0000 (17:43 +0100)]
JAL-1933 use constant for preference token
Jim Procter [Thu, 27 Apr 2017 16:40:56 +0000 (17:40 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
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
Jim Procter [Thu, 27 Apr 2017 16:34:47 +0000 (17:34 +0100)]
JAL-1933 desktop preferences for occupancy
Jim Procter [Thu, 27 Apr 2017 16:34:29 +0000 (17:34 +0100)]
JAL-1933 action and label for occupancy
Jim Procter [Thu, 27 Apr 2017 15:39:33 +0000 (16:39 +0100)]
JAL-1933 test for 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
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
Jim Procter [Thu, 27 Apr 2017 15:34:03 +0000 (16:34 +0100)]
JAL-2494 fix: updated behaviour for SequenceGroup.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:32:53 +0000 (16:32 +0100)]
JAL-2494 fixed behaviour for null parameters in line with test
Jim Procter [Thu, 27 Apr 2017 15:25:24 +0000 (16:25 +0100)]
JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:13:25 +0000 (16:13 +0100)]
JAL-2494 test to cover AnnotatedCollectionI.findAnnotations
Jim Procter [Thu, 27 Apr 2017 14:05:42 +0000 (15:05 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 13:58:26 +0000 (14:58 +0100)]
JAL-2432 desktop: filter/select columns by threshold as a percentage
Jim Procter [Thu, 27 Apr 2017 13:57:28 +0000 (14:57 +0100)]
JAL-1933 JAL-2432 code tidy
Jim Procter [Thu, 27 Apr 2017 13:57:13 +0000 (14:57 +0100)]
JAL-2432 left justify value shown after adjusting threshold slider
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
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
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)
Jim Procter [Thu, 27 Apr 2017 10:55:34 +0000 (11:55 +0100)]
JAL-1933 occupancy row has a space below it for counts
Jim Procter [Thu, 27 Apr 2017 10:11:48 +0000 (11:11 +0100)]
Merge branch 'develop' into features/JAL-1933_occupancy
tcofoegbu [Tue, 25 Apr 2017 14:17:58 +0000 (15:17 +0100)]
JAL-2489 edited unit test code comment
tcofoegbu [Tue, 25 Apr 2017 14:14:29 +0000 (15:14 +0100)]
JAL-2489 Unit test for bug
tcofoegbu [Tue, 25 Apr 2017 11:45:44 +0000 (12:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 25 Apr 2017 11:45:36 +0000 (12:45 +0100)]
JAL-2489 bug fix
gmungoc [Mon, 24 Apr 2017 13:30:45 +0000 (14:30 +0100)]
JAL-2487 remove redundant refreshGUI to minimise threading issues
gmungoc [Mon, 24 Apr 2017 11:32:32 +0000 (12:32 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
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
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
gmungoc [Fri, 21 Apr 2017 14:00:20 +0000 (15:00 +0100)]
JAL-2423 tweak tree panel title, add Spanish text
gmungoc [Fri, 21 Apr 2017 13:08:13 +0000 (14:08 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
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
tcofoegbu [Wed, 19 Apr 2017 11:19:45 +0000 (12:19 +0100)]
JAL-2482 added null check
tcofoegbu [Tue, 18 Apr 2017 13:44:19 +0000 (14:44 +0100)]
JAL-2482 Bugfix
gmungoc [Mon, 17 Apr 2017 07:58:24 +0000 (08:58 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Wed, 12 Apr 2017 15:06:02 +0000 (16:06 +0100)]
JAL-2361 tweak layout of warning message
gmungoc [Wed, 12 Apr 2017 14:46:35 +0000 (15:46 +0100)]
JAL-1632 removed check for aligned sequences for Tree calculation
gmungoc [Wed, 12 Apr 2017 13:43:39 +0000 (14:43 +0100)]
JAL-1632 remove unused check for sequences aligned
gmungoc [Wed, 12 Apr 2017 13:42:11 +0000 (14:42 +0100)]
JAL-2403 ensure array held in Matrix is immutable
gmungoc [Wed, 12 Apr 2017 13:41:45 +0000 (14:41 +0100)]
JAL-2403 public static methods to convert distance/similarity matrices
gmungoc [Wed, 12 Apr 2017 10:30:37 +0000 (11:30 +0100)]
JAL-1632 one PCA/Tree per panel, closed when panel is closed
gmungoc [Tue, 11 Apr 2017 13:34:50 +0000 (14:34 +0100)]
JAL-2403 improved ScoreModelI hierarchy as per Kira's review suggestions
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
git://source.jalview.org / jalview.git / log