Jim Procter [Thu, 27 Apr 2017 10:11:48 +0000 (11:11 +0100)]
Merge branch 'develop' into features/JAL-1933_occupancy
gmungoc [Wed, 26 Apr 2017 11:02:20 +0000 (12:02 +0100)]
JAL-2490 findFeaturesAtRes with performant feature lookup
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
gmungoc [Tue, 25 Apr 2017 13:46:54 +0000 (14:46 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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 12:00:12 +0000 (13:00 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Mon, 24 Apr 2017 11:32:32 +0000 (12:32 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 24 Apr 2017 11:19:41 +0000 (12:19 +0100)]
JAL-2424 final contig now an inclusive range
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
gmungoc [Thu, 20 Apr 2017 15:44:50 +0000 (16:44 +0100)]
JAL-2483 JAL-2481 findAllFeatures without scanning all features
gmungoc [Wed, 19 Apr 2017 15:23:35 +0000 (16:23 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 19 Apr 2017 12:21:13 +0000 (13:21 +0100)]
JAL-2480 cache min-max score values per sequence and feature type
tcofoegbu [Wed, 19 Apr 2017 11:19:45 +0000 (12:19 +0100)]
JAL-2482 added null check
gmungoc [Wed, 19 Apr 2017 08:09:46 +0000 (09:09 +0100)]
JAL-2483 use SequenceFeatures to look up groups, types, feature lengths
tcofoegbu [Tue, 18 Apr 2017 13:44:19 +0000 (14:44 +0100)]
JAL-2482 Bugfix
gmungoc [Tue, 18 Apr 2017 10:53:38 +0000 (11:53 +0100)]
JAL-2480 subtract from total length on deleting feature
gmungoc [Tue, 18 Apr 2017 10:23:22 +0000 (11:23 +0100)]
JAL-2480 more test coverage
gmungoc [Tue, 18 Apr 2017 09:36:00 +0000 (10:36 +0100)]
JAL-2480 test coverage / bug fixes / javadoc
gmungoc [Tue, 18 Apr 2017 08:42:45 +0000 (09:42 +0100)]
JAL-2480 SequenceFeaturesI encapsulates features api
gmungoc [Mon, 17 Apr 2017 14:44:20 +0000 (15:44 +0100)]
JAL-2446 comment updates
gmungoc [Mon, 17 Apr 2017 14:12:29 +0000 (15:12 +0100)]
JAL-2446 promote Range from test to src to replace SubList
gmungoc [Mon, 17 Apr 2017 12:37:39 +0000 (13:37 +0100)]
JAL-2446 tidied up / generalised binary search in FeatureStore
gmungoc [Mon, 17 Apr 2017 09:30:59 +0000 (10:30 +0100)]
JAL-2446 add call to SequenceFeatures.delete(); use varargs for type
gmungoc [Mon, 17 Apr 2017 07:59:05 +0000 (08:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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 [Wed, 12 Apr 2017 09:51:55 +0000 (10:51 +0100)]
JAL-2446 getGroups, getFeatures for positional/non-positional features
gmungoc [Tue, 11 Apr 2017 14:24:59 +0000 (15:24 +0100)]
JAL-2446 find feature types for one or more groups (vararg)
tcofoegbu [Tue, 11 Apr 2017 14:20:36 +0000 (15:20 +0100)]
Pull from develop
kiramt [Tue, 11 Apr 2017 13:58:08 +0000 (14:58 +0100)]
JAL-2479 Moved some network-dependent unit tests into Network group
gmungoc [Tue, 11 Apr 2017 13:34:50 +0000 (14:34 +0100)]
JAL-2403 improved ScoreModelI hierarchy as per Kira's review suggestions
tcofoegbu [Tue, 11 Apr 2017 12:43:07 +0000 (13:43 +0100)]
JAL-2473 removed unused fields in JalviewDialog
gmungoc [Tue, 11 Apr 2017 11:17:14 +0000 (12:17 +0100)]
JAL-2446 getFeatureTypesForGroup() added
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 [Tue, 11 Apr 2017 07:46:54 +0000 (08:46 +0100)]
JAL-2446 added getFeatureGroups
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 14:40:59 +0000 (15:40 +0100)]
JAL-2446 SequenceFeatures.hasFeatures() added
tcofoegbu [Mon, 10 Apr 2017 11:44:40 +0000 (12:44 +0100)]
JAL-2473 added improvement to apply default / custom minimum dimension for various Jalview dialogs / windows. This is to prevent some components from disappearing when the dialogs / windows are resized downwards below certain dimensions
gmungoc [Mon, 10 Apr 2017 08:53:53 +0000 (09:53 +0100)]
JAL-2446 FeatureStore.isEmpty() added
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 [Fri, 7 Apr 2017 10:35:27 +0000 (11:35 +0100)]
JAL-2446 fix size maintenance during add
gmungoc [Fri, 7 Apr 2017 09:26:37 +0000 (10:26 +0100)]
JAL-2446 added delete/contains to pseudo-random tests, fail fixes
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 [Thu, 6 Apr 2017 15:08:36 +0000 (16:08 +0100)]
JAL-2446 added contains, delete, checks for inclusion on add + tests
gmungoc [Thu, 6 Apr 2017 11:07:13 +0000 (12:07 +0100)]
JAL-2446 pseudo-random test of findOverlaps, bug fix for for add
overlapping range at end
gmungoc [Wed, 5 Apr 2017 15:31:21 +0000 (16:31 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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 [Wed, 5 Apr 2017 08:14:28 +0000 (09:14 +0100)]
JAL-2446 various get and find methods added with test coverage
gmungoc [Wed, 5 Apr 2017 08:13:53 +0000 (09:13 +0100)]
JAL-2446 method isNonPositional() added
gmungoc [Tue, 4 Apr 2017 15:19:01 +0000 (16:19 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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 [Mon, 3 Apr 2017 09:07:03 +0000 (10:07 +0100)]
JAL-2446 pseudo-random generator unit test, and fixes arising
gmungoc [Fri, 31 Mar 2017 13:18:59 +0000 (14:18 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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
git://source.jalview.org / jalview.git / log