Jim Procter [Wed, 17 May 2017 15:10:15 +0000 (16:10 +0100)]
Merge branch 'bug/JAL-2510amendFeatures' into develop
Jim Procter [Wed, 17 May 2017 14:41:04 +0000 (15:41 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 17 May 2017 14:39:43 +0000 (15:39 +0100)]
JAL-2447 experimental section in ‘Whats New’
Jim Procter [Wed, 17 May 2017 14:39:17 +0000 (15:39 +0100)]
JAL-2447 JAL-2295 JAL-2296 documenting as experimental features
Jim Procter [Wed, 17 May 2017 13:46:38 +0000 (14:46 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 17 May 2017 13:31:54 +0000 (14:31 +0100)]
Merge branch 'features/JAL-2447experimentalFlag' into develop
Jim Procter [Wed, 17 May 2017 13:28:08 +0000 (14:28 +0100)]
JAL-2418 release notes
gmungoc [Wed, 17 May 2017 12:07:13 +0000 (13:07 +0100)]
JAL-2504 use (and update) defaults for new feature only if not supplied
gmungoc [Wed, 17 May 2017 07:59:07 +0000 (08:59 +0100)]
Merge branch 'develop' into bug/JAL-2510amendFeatures
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Jim Procter [Tue, 16 May 2017 16:36:01 +0000 (17:36 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 16 May 2017 16:27:35 +0000 (17:27 +0100)]
JAL-2418 release notes
Jim Procter [Tue, 16 May 2017 15:51:31 +0000 (16:51 +0100)]
JAL-384 documentation on custom colours groovy examples
Jim Procter [Tue, 16 May 2017 15:35:15 +0000 (16:35 +0100)]
JAL-384 - groovy scripts for conserved/unconserved colourscheme requests
Jim Procter [Tue, 16 May 2017 15:30:07 +0000 (16:30 +0100)]
JAL-2418 release notes
Jim Procter [Tue, 16 May 2017 13:54:17 +0000 (14:54 +0100)]
JAL-2418 JAL-2316 added to new features
Jim Procter [Tue, 16 May 2017 13:30:04 +0000 (14:30 +0100)]
JAL-2316 tweaking docs and links in help
Jim Procter [Tue, 16 May 2017 12:46:14 +0000 (13:46 +0100)]
JAL-2418 release 2.10.2 release notes template
Jim Procter [Tue, 16 May 2017 12:45:29 +0000 (13:45 +0100)]
alternative patch for JAL-2339 readability in java-help
gmungoc [Tue, 16 May 2017 12:40:27 +0000 (13:40 +0100)]
JAL-2403 simplify instantiation / configuration of score model for view
kiramt [Tue, 16 May 2017 10:34:09 +0000 (11:34 +0100)]
JAL-2522 Missed fix to applet
kiramt [Tue, 16 May 2017 09:37:48 +0000 (10:37 +0100)]
JAL-2388 Rationalised hashCode method in HiddenColumns
Jim Procter [Tue, 16 May 2017 08:48:31 +0000 (09:48 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
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 16:37:43 +0000 (17:37 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
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
gmungoc [Mon, 15 May 2017 15:55:54 +0000 (16:55 +0100)]
JAL-2532 new feature types and colour changes from Amend Features
retained after Cancel in Feature Settings
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’.
kiramt [Mon, 15 May 2017 14:50:28 +0000 (15:50 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 15 May 2017 14:50:07 +0000 (15:50 +0100)]
JAL-2388 Add missed optimisation
Jim Procter [Mon, 15 May 2017 11:14:20 +0000 (12:14 +0100)]
Merge branch 'features/JAL-2376_add-horizontal-bar' into develop
Jim Procter [Mon, 15 May 2017 11:07:39 +0000 (12:07 +0100)]
JAL-2371 create a default ResidueShader when constructing the viewport
Jim Procter [Fri, 12 May 2017 14:48:16 +0000 (15:48 +0100)]
Merge branch 'features/JAL-2435splitScreenFont' into develop
Jim Procter [Fri, 12 May 2017 14:47:10 +0000 (15:47 +0100)]
JAL-2418 broken help ref
Jim Procter [Fri, 12 May 2017 14:46:27 +0000 (15:46 +0100)]
JAL-2435 documentation and what’s new
Jim Procter [Fri, 12 May 2017 14:42:17 +0000 (15:42 +0100)]
JAL-2435 mention new checkbox in linked cDNA/Protein view documentation
Jim Procter [Fri, 12 May 2017 14:41:45 +0000 (15:41 +0100)]
JAL-2435 mirror antiAlias setting between cDNA and Protein
Jim Procter [Fri, 12 May 2017 14:09:45 +0000 (15:09 +0100)]
Merge branch 'features/JAL-2388OverviewWindow' into develop
Jim Procter [Fri, 12 May 2017 14:01:17 +0000 (15:01 +0100)]
JAL-2388 mention overview popup in documentation
Jim Procter [Fri, 12 May 2017 13:56:21 +0000 (14:56 +0100)]
JAL-2388 checkbox in overview popup for applet
Jim Procter [Fri, 12 May 2017 13:29:46 +0000 (14:29 +0100)]
Merge branch 'features/JAL-2228_efficient_featurecounts' into develop
Jim Procter [Fri, 12 May 2017 13:29:28 +0000 (14:29 +0100)]
JAL-2228 updated script in help docs, renamed docs, and added note about non-backwards compatibility of feature counter script
Jim Procter [Thu, 11 May 2017 15:21:14 +0000 (16:21 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
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
kiramt [Wed, 10 May 2017 13:29:07 +0000 (14:29 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Wed, 10 May 2017 13:28:50 +0000 (14:28 +0100)]
JAL-2522 Fix to cursor scrolling
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
kiramt [Tue, 9 May 2017 08:09:55 +0000 (09:09 +0100)]
JAL-2388 Added checkbox to toggle hidden columns menu & updated text
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 [Fri, 5 May 2017 15:21:02 +0000 (16:21 +0100)]
Merge branch 'develop' into features/JAL-2435splitScreenFont
gmungoc [Fri, 5 May 2017 15:14:36 +0000 (16:14 +0100)]
JAL-964 JAL-2510 update Feature Settings from Amend Features, warn if
hidden type or group
kiramt [Fri, 5 May 2017 11:05:50 +0000 (12:05 +0100)]
Merge remote-tracking branch
'origin/features/JAL-2388hiddencolumnschanges' into
features/JAL-2388OverviewWindow
Conflicts:
resources/lang/Messages.properties
kiramt [Fri, 5 May 2017 09:50:22 +0000 (10:50 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
Conflicts:
src/jalview/appletgui/TreePanel.java
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/TreePanel.java
kiramt [Fri, 5 May 2017 09:35:48 +0000 (10:35 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
Conflicts:
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/io/AnnotationFile.java
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 14:00:58 +0000 (15:00 +0100)]
Merge branch 'develop' into features/JAL-2228_efficient_featurecounts
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
git://source.jalview.org / jalview.git / log