gmungoc [Tue, 16 May 2017 15:47:40 +0000 (16:47 +0100)]
JAL-2505 unreachable code (for many years) removed
gmungoc [Tue, 16 May 2017 14:38:33 +0000 (15:38 +0100)]
JAL-2505 refactored method removed
gmungoc [Tue, 16 May 2017 14:29:14 +0000 (15:29 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 16 May 2017 14:00:41 +0000 (15:00 +0100)]
JAL-2505 set helix number as feature group in SequenceFeature
constructor
gmungoc [Tue, 16 May 2017 12:40:27 +0000 (13:40 +0100)]
JAL-2403 simplify instantiation / configuration of score model for view
gmungoc [Tue, 16 May 2017 11:18:05 +0000 (12:18 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
kiramt [Tue, 16 May 2017 10:34:09 +0000 (11:34 +0100)]
JAL-2522 Missed fix to applet
gmungoc [Tue, 16 May 2017 10:12:04 +0000 (11:12 +0100)]
JAL-2505 refactor to set type and group in SequenceFeature constructor
gmungoc [Tue, 16 May 2017 10:11:25 +0000 (11:11 +0100)]
JAL-2525 put in missing "transcript" feature type
kiramt [Tue, 16 May 2017 09:37:48 +0000 (10:37 +0100)]
JAL-2388 Rationalised hashCode method in HiddenColumns
gmungoc [Tue, 16 May 2017 09:25:28 +0000 (10:25 +0100)]
JAL-2505 additional tests/asserts prior to refactoring
Jim Procter [Tue, 16 May 2017 08:48:31 +0000 (09:48 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
gmungoc [Tue, 16 May 2017 08:40:39 +0000 (09:40 +0100)]
JAL-2505 set SequenceFeature group in constructor
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
gmungoc [Mon, 15 May 2017 16:02:55 +0000 (17:02 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
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’.
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
gmungoc [Mon, 15 May 2017 10:59:29 +0000 (11:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/gui/OverviewPanel.java
gmungoc [Mon, 15 May 2017 08:43:05 +0000 (09:43 +0100)]
JAL-2490 use findFeatures() for efficient feature overlap lookup
gmungoc [Mon, 15 May 2017 07:46:56 +0000 (08:46 +0100)]
JAL-2480 redundant code (from merge?) removed
gmungoc [Mon, 15 May 2017 07:45:17 +0000 (08:45 +0100)]
JAL-2480 redundant code removed
gmungoc [Fri, 12 May 2017 15:59:19 +0000 (16:59 +0100)]
JAL-2490 performant findFeaturesAtRes
gmungoc [Fri, 12 May 2017 15:29:07 +0000 (16:29 +0100)]
JAL-2483 efficient lookup of feature types and groups - applet
gmungoc [Fri, 12 May 2017 15:00:20 +0000 (16:00 +0100)]
JAL-2525 get sequence features for Ontology term(s), tidy feature sort
methods
gmungoc [Fri, 12 May 2017 14:56:33 +0000 (15:56 +0100)]
JAL-2480 more efficient contains check on add; tidied comparators
gmungoc [Fri, 12 May 2017 14:53:29 +0000 (15:53 +0100)]
JAL-2480 java.util.RangeComparator renamed IntRangeComparator
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
gmungoc [Fri, 12 May 2017 13:32:33 +0000 (14:32 +0100)]
JAL-2480 efficient test for features present on sequence
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
gmungoc [Fri, 12 May 2017 13:22:03 +0000 (14:22 +0100)]
JAL-2480 renamed java.util.RangeComparator to IntRangeComparator
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
gmungoc [Tue, 9 May 2017 08:59:13 +0000 (09:59 +0100)]
JAL-2403 use preferred factory method to create score model
gmungoc [Tue, 9 May 2017 08:52:14 +0000 (09:52 +0100)]
JAL-2480 include sequenceFeatureStore in createDatasetSequence
gmungoc [Tue, 9 May 2017 08:25:49 +0000 (09:25 +0100)]
JAL-2483 JAL-2481 fixed findAllFeatures to handle null group correctly
kiramt [Tue, 9 May 2017 08:09:55 +0000 (09:09 +0100)]
JAL-2388 Added checkbox to toggle hidden columns menu & updated text
gmungoc [Tue, 9 May 2017 07:46:21 +0000 (08:46 +0100)]
JAL-2505 use constructors to set (what will be) final fields in
SequenceFeature
gmungoc [Mon, 8 May 2017 16:45:01 +0000 (17:45 +0100)]
JAL-2505 set type,desc,begin,end,group,score in SequenceFeature
constructor
gmungoc [Mon, 8 May 2017 16:38:18 +0000 (17:38 +0100)]
JAL-2505 refactored SequenceFeature construction so type,begin,end,group
are set in constructor
gmungoc [Mon, 8 May 2017 16:01:31 +0000 (17:01 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/appletgui/IdPanel.java
src/jalview/gui/FeatureRenderer.java
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
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 ()
gmungoc [Thu, 4 May 2017 11:34:21 +0000 (12:34 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Thu, 4 May 2017 11:33:00 +0000 (12:33 +0100)]
JAL-2505 delete and readd amended sequence feature
gmungoc [Thu, 4 May 2017 11:31:36 +0000 (12:31 +0100)]
JAL-2480 JAL-2505 guard against duplicating links
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
git://source.jalview.org / jalview.git / log