Jim Procter [Mon, 15 May 2017 18:23:56 +0000 (19:23 +0100)]
JAL-2507 fix test: knockon from capitalisation on secondary structure from stockholm file
Jim Procter [Mon, 15 May 2017 16:37:17 +0000 (17:37 +0100)]
JAL-2311 disable and relocate Jared service tests to Network (prior to their removal)
Jim Procter [Mon, 15 May 2017 16:26:53 +0000 (17:26 +0100)]
JAL-2507 capitalisation for annotation lines generated from stockholm annotation
Jim Procter [Mon, 15 May 2017 15:56:06 +0000 (16:56 +0100)]
JAL-2507 case insensitive recognition of annotation type
Jim Procter [Mon, 15 May 2017 15:43:12 +0000 (16:43 +0100)]
JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testAlignmentEquivalent asserts
Jim Procter [Mon, 15 May 2017 15:26:02 +0000 (16:26 +0100)]
JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.
Jim Procter [Thu, 11 May 2017 15:20:29 +0000 (16:20 +0100)]
JAL-2509 JAL-2507 allow whitespace in GS annotation lines (removed old code for processing GS column annotation into features)
Jim Procter [Thu, 11 May 2017 15:17:29 +0000 (16:17 +0100)]
JAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test coverage for Annotation equivalence asserts
Jim Procter [Thu, 11 May 2017 14:29:00 +0000 (15:29 +0100)]
JAL-2507 test if an annotation is ‘whitespace’
Jim Procter [Thu, 11 May 2017 14:28:24 +0000 (15:28 +0100)]
JAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitespace annotation
Jim Procter [Tue, 9 May 2017 17:18:27 +0000 (18:18 +0100)]
JAL-2507 spit out tests for ‘{‘ WUSS io from ‘[‘ WUSS io (which may be causing problems via JAL-1863)
Jim Procter [Tue, 9 May 2017 16:58:52 +0000 (17:58 +0100)]
JAL-2509 verify stockholm parser’s bracket regex is working for all WUSS notation
Jim Procter [Tue, 9 May 2017 16:58:27 +0000 (17:58 +0100)]
JAL-2509 extend set of brackets recognised by stockholm parser
Jim Procter [Tue, 9 May 2017 16:57:20 +0000 (17:57 +0100)]
JAL-2507 JAL-2509 extend test to cover round trip of full range of WUSS RNA secondary structure
Jim Procter [Tue, 9 May 2017 15:55:14 +0000 (16:55 +0100)]
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS line
Jim Procter [Tue, 9 May 2017 15:54:15 +0000 (16:54 +0100)]
JAL-2507 output secondary structure regardless of presence of dataset sequence
Jim Procter [Tue, 9 May 2017 15:51:46 +0000 (16:51 +0100)]
JAL-2507 simplify round trip test via AppletFormatAdapter
Jim Procter [Tue, 9 May 2017 14:15:54 +0000 (15:15 +0100)]
JAL-2507 test for alignment+rna annotation -> Stockholm -> roundtrip.
gmungoc [Tue, 9 May 2017 09:16:50 +0000 (10:16 +0100)]
JAL-1632 correct i18n and NPE
gmungoc [Mon, 8 May 2017 14:40:19 +0000 (15:40 +0100)]
JAL-1933 Spanish tooltips for annotation
gmungoc [Mon, 8 May 2017 13:54:56 +0000 (14:54 +0100)]
JAL-1632 i18n for warning messages
gmungoc [Mon, 8 May 2017 12:17:04 +0000 (13:17 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2515' into develop
kiramt [Mon, 8 May 2017 08:23:31 +0000 (09:23 +0100)]
JAL-2515 Id panel in applet updated for NPE on urlProvider
kiramt [Mon, 8 May 2017 08:06:22 +0000 (09:06 +0100)]
JAL-2512 And corresponding test
kiramt [Mon, 8 May 2017 07:59:46 +0000 (08:59 +0100)]
JAL-2512 And applet
kiramt [Mon, 8 May 2017 07:54:41 +0000 (08:54 +0100)]
JAL-2512 Fix to show non-gap positions in None colour scheme
gmungoc [Thu, 4 May 2017 16:08:59 +0000 (17:08 +0100)]
JAL-2506 allow graduated colour as default in new Sequence Feature
dialog
gmungoc [Thu, 4 May 2017 15:13:06 +0000 (16:13 +0100)]
JAL-2510 ensure modified feature type is displayed
gmungoc [Thu, 4 May 2017 14:56:42 +0000 (15:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 May 2017 14:56:32 +0000 (15:56 +0100)]
JAL-2504 allow feature type to be specified for Create Features dialog
Jim Procter [Thu, 4 May 2017 13:10:44 +0000 (14:10 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholmoutput' into develop
Jim Procter [Thu, 4 May 2017 13:10:03 +0000 (14:10 +0100)]
Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop
Jim Procter [Thu, 4 May 2017 13:09:44 +0000 (14:09 +0100)]
Merge branch 'features/JAL-2393customMatrices' into develop
Jim Procter [Thu, 4 May 2017 13:04:36 +0000 (14:04 +0100)]
JAL-1656 make RNAML->Stockholm round trip test pass by ignoring differences in secondary structure annotation visibility
Jim Procter [Thu, 4 May 2017 13:03:42 +0000 (14:03 +0100)]
JAL-2507 JAL-2509 allow differences in visibility of annotation rows to be ignored when comparing round-tripped alignments
Jim Procter [Thu, 4 May 2017 13:02:24 +0000 (14:02 +0100)]
JAL-2507 JAL-2509 new assert to compare secondary structure in two annotation rows
Jim Procter [Thu, 4 May 2017 12:56:11 +0000 (13:56 +0100)]
fix for JAL-2509 - don’t replace all bracket types with ()
Jim Procter [Thu, 4 May 2017 10:37:19 +0000 (11:37 +0100)]
fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label or 'isRNA' RNA secondary structure annotation flag
tcofoegbu [Thu, 4 May 2017 10:06:37 +0000 (11:06 +0100)]
Merge branch 'features/JAL-2473_set-minimium-dimensions' into develop
tcofoegbu [Thu, 4 May 2017 10:03:14 +0000 (11:03 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2473_set-minimium-dimensions
Jim Procter [Thu, 4 May 2017 08:53:10 +0000 (09:53 +0100)]
Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop
Jim Procter [Thu, 4 May 2017 08:52:21 +0000 (09:52 +0100)]
Merge branch 'features/JAL-2393customMatrices' into develop
Jim Procter [Wed, 3 May 2017 16:48:11 +0000 (17:48 +0100)]
JAL-2393 JAL-2416 refresh the score model menu when updating gui enabled/disabled settings
Jim Procter [Wed, 3 May 2017 16:43:55 +0000 (17:43 +0100)]
JAL-2503 show threshold slider for quantitative annotation rows
Jim Procter [Wed, 3 May 2017 16:35:47 +0000 (17:35 +0100)]
JAL-2503 AlignmentAnnotation.isQuantitative() test
gmungoc [Wed, 3 May 2017 14:51:36 +0000 (15:51 +0100)]
JAL-2246 basic sanity test of fetching example accessions
Jim Procter [Wed, 3 May 2017 11:17:56 +0000 (12:17 +0100)]
Merge branch 'features/JAL-2432_annotbypercent' into develop
Jim Procter [Wed, 3 May 2017 11:15:34 +0000 (12:15 +0100)]
JAL-1933 JAL-2501 i18n for all auto calculated descriptions
Jim Procter [Wed, 3 May 2017 10:56:47 +0000 (11:56 +0100)]
JAL-1933 show occupancy in tooltip for row
gmungoc [Wed, 3 May 2017 10:52:24 +0000 (11:52 +0100)]
JAL-2246 test a Uniprot fetch
Jim Procter [Wed, 3 May 2017 10:47:16 +0000 (11:47 +0100)]
JAL-2432 honour percentage checkbox when entering values in text box
Jim Procter [Wed, 3 May 2017 10:46:23 +0000 (11:46 +0100)]
JAL-2432 applet: only enable percent checkbox when threshold is active
Jim Procter [Wed, 3 May 2017 10:40:04 +0000 (11:40 +0100)]
JAL-2432 percentage checkbox follows threshold value field
gmungoc [Wed, 3 May 2017 09:46:10 +0000 (10:46 +0100)]
JAL-2105 Ensembl REST now at 5.0
gmungoc [Wed, 3 May 2017 09:43:52 +0000 (10:43 +0100)]
JAL-2485 JAL-2246 test Uniprot FTS summary
Jim Procter [Wed, 3 May 2017 08:47:26 +0000 (09:47 +0100)]
JAL-2432 recover state for ‘display percentage’ checkbox
Jim Procter [Wed, 3 May 2017 08:46:32 +0000 (09:46 +0100)]
JAL-2432 simplify code
Jim Procter [Tue, 2 May 2017 16:59:01 +0000 (17:59 +0100)]
JAL-1632 validate CalculationChooser when selection or alignment changes
Jim Procter [Tue, 2 May 2017 16:58:30 +0000 (17:58 +0100)]
JAL-1632 enable/disable CalculationChooser buttons on focus
Jim Procter [Tue, 2 May 2017 16:56:13 +0000 (17:56 +0100)]
JAL-1632 compare size of input against minimums for calculation and enable/disable buttons
Jim Procter [Tue, 2 May 2017 16:54:41 +0000 (17:54 +0100)]
JAL-1632 OK->Calculate, Cancel->Close buttons
Jim Procter [Tue, 2 May 2017 16:53:53 +0000 (17:53 +0100)]
JAL-1632 removed ‘tree’ option and changed dialog layout
gmungoc [Tue, 2 May 2017 14:35:39 +0000 (15:35 +0100)]
JAL-1933 Spanish for Occupancy
Jim Procter [Tue, 2 May 2017 13:17:23 +0000 (14:17 +0100)]
JAL-2424 fixme’s removed
Jim Procter [Tue, 2 May 2017 13:16:25 +0000 (14:16 +0100)]
JAL-2424 update assert to correct width for normalising similarity scores
Jim Procter [Tue, 2 May 2017 13:15:52 +0000 (14:15 +0100)]
JAL-2424 resolved, assert updated to pass (1f != 1d)
Jim Procter [Tue, 2 May 2017 12:46:06 +0000 (13:46 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
Jim Procter [Tue, 2 May 2017 12:37:58 +0000 (13:37 +0100)]
Merge branch 'bug/JAL-2424getVisibleContigs' into develop
gmungoc [Tue, 2 May 2017 09:42:13 +0000 (10:42 +0100)]
JAL-2499 inlined two 1-line methods
gmungoc [Tue, 2 May 2017 09:30:58 +0000 (10:30 +0100)]
JAL-2499 JAL-2403 push 'configure for view' inside ScoreModels, defer
creating model for PCA/Tree, tidy Javadoc
gmungoc [Tue, 2 May 2017 08:28:30 +0000 (09:28 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
tcofoegbu [Mon, 1 May 2017 17:16:56 +0000 (18:16 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 1 May 2017 17:13:55 +0000 (18:13 +0100)]
JAL-2482 bug fix
tcofoegbu [Mon, 1 May 2017 17:08:05 +0000 (18:08 +0100)]
JAL-2482 unit test for bug fix
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
gmungoc [Mon, 1 May 2017 13:18:38 +0000 (14:18 +0100)]
Merge remote-tracking branch
'origin/bug/JAL-2479unitteststoNetworkGroup' into develop
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
git://source.jalview.org / jalview.git / log