gmungoc [Tue, 23 May 2017 11:37:10 +0000 (12:37 +0100)]
JAL-2490 tidy code and tests for feature export in Jalview format
gmungoc [Tue, 23 May 2017 09:54:57 +0000 (10:54 +0100)]
JAL-2490 improved lookup of features for Export Features (Jalview
format)
gmungoc [Tue, 23 May 2017 09:54:15 +0000 (10:54 +0100)]
JAL-2480 methods to get features for group
gmungoc [Mon, 22 May 2017 15:40:48 +0000 (16:40 +0100)]
JAL-2505 use setter not direct access to sf.description
gmungoc [Mon, 22 May 2017 15:40:14 +0000 (16:40 +0100)]
JAL-2505 updates after conflicting merge of JAL-2504
gmungoc [Mon, 22 May 2017 14:55:53 +0000 (15:55 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/gui/FeatureRenderer.java
gmungoc [Mon, 22 May 2017 14:37:32 +0000 (15:37 +0100)]
JAL-2504 update the right feature colour when creating a new feature
gmungoc [Mon, 22 May 2017 14:16:40 +0000 (15:16 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/analysis/AlignmentSorter.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/analysis/AlignmentSorterTest.java
gmungoc [Mon, 22 May 2017 13:39:57 +0000 (14:39 +0100)]
JAL-2544 unit tests for sort by feature score
gmungoc [Mon, 22 May 2017 13:33:07 +0000 (14:33 +0100)]
JAL-2544 check feature overlaps selection region
gmungoc [Mon, 22 May 2017 13:13:23 +0000 (14:13 +0100)]
JAL-2543 identify as JSON before HTML
gmungoc [Mon, 22 May 2017 13:06:19 +0000 (14:06 +0100)]
JAL-2546 JAL-2490 efficient lookup of features, correct handling of
non-positional features
gmungoc [Mon, 22 May 2017 12:02:47 +0000 (13:02 +0100)]
JAL-2490 add non-positional feature case to test prior to refactoring
gmungoc [Mon, 22 May 2017 11:24:56 +0000 (12:24 +0100)]
JAL-2480 always include all non-positional features in getAllFeatures()
kiramt [Mon, 22 May 2017 10:57:47 +0000 (11:57 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2256' into develop
Jim Procter [Mon, 22 May 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2418 patch build - broken htsjdk import
gmungoc [Fri, 19 May 2017 15:59:48 +0000 (16:59 +0100)]
JAL-2526 removed redundant call to Sequence.findPosition()
gmungoc [Fri, 19 May 2017 15:46:41 +0000 (16:46 +0100)]
JAL-2490 refactored test for 'hasFeatures'
gmungoc [Fri, 19 May 2017 10:48:11 +0000 (11:48 +0100)]
JAL-2544 only include features in selected columns for sort
gmungoc [Fri, 19 May 2017 10:47:16 +0000 (11:47 +0100)]
JAL-2490 performant lookup of features for sorting
gmungoc [Fri, 19 May 2017 07:38:35 +0000 (08:38 +0100)]
JAL-2490 only count sequences where feature overlap is confirmed
gmungoc [Fri, 19 May 2017 07:21:54 +0000 (08:21 +0100)]
JAL-2505 unit test for sort by feature density, Javadoc
gmungoc [Thu, 18 May 2017 16:01:44 +0000 (17:01 +0100)]
JAL-2490 initial unit tests prior to refactoring
Jim Procter [Thu, 18 May 2017 15:33:00 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop
Jim Procter [Thu, 18 May 2017 15:31:27 +0000 (16:31 +0100)]
JAL-2388 return empty hidden columns for fully visible alignment view
gmungoc [Thu, 18 May 2017 14:56:25 +0000 (15:56 +0100)]
JAL-2490 lookup sequence features for "labelClass"
gmungoc [Thu, 18 May 2017 14:51:10 +0000 (15:51 +0100)]
JAL-2490 lookup features at each column position
gmungoc [Thu, 18 May 2017 14:28:54 +0000 (15:28 +0100)]
JAL-2543 html-encode quote characters in feature description
gmungoc [Thu, 18 May 2017 13:57:37 +0000 (14:57 +0100)]
JAL-2490 retrieve visible features only
gmungoc [Thu, 18 May 2017 13:28:18 +0000 (14:28 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
kiramt [Thu, 18 May 2017 13:09:21 +0000 (14:09 +0100)]
JAL-2256 Corrected AllCols/Rows iterator behaviour for single element
Jim Procter [Thu, 18 May 2017 11:18:14 +0000 (12:18 +0100)]
JAL-2418 remove explicit test suite stats
Jim Procter [Wed, 17 May 2017 15:26:52 +0000 (16:26 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
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 14:50:14 +0000 (15:50 +0100)]
JAL-2447 add links to issues.jalview.org for experimental features
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
gmungoc [Tue, 16 May 2017 15:47:40 +0000 (16:47 +0100)]
JAL-2505 unreachable code (for many years) removed
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
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
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
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
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
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
git://source.jalview.org / jalview.git / log