gmungoc [Fri, 26 May 2017 07:33:28 +0000 (08:33 +0100)]
JAL-2480 move ContiguousI and Range to jalview.datamodel
gmungoc [Thu, 25 May 2017 16:52:12 +0000 (17:52 +0100)]
JAL-2557 removal of Sequence.sequenceFeatures
Jim Procter [Thu, 25 May 2017 16:16:27 +0000 (17:16 +0100)]
Merge branch 'develop' into features/JAL-1648_cache_user_inputs
bugfixes in finder for feature creation and minimum window size merged to topic
kiramt [Thu, 25 May 2017 13:31:51 +0000 (14:31 +0100)]
JAl-2034 Ported to applet
kiramt [Thu, 25 May 2017 13:06:38 +0000 (14:06 +0100)]
JAL-2034 don't update overview after click without drag on group
gmungoc [Thu, 25 May 2017 10:54:39 +0000 (11:54 +0100)]
JAL-2050 make SequenceFeature.score final, adjust constructor calls
gmungoc [Thu, 25 May 2017 09:35:08 +0000 (10:35 +0100)]
JAL-2505 simplifying number of SequenceFeature constructors JAL-2060
constant for NO_SCORE defined in SequenceFeature
gmungoc [Thu, 25 May 2017 09:16:49 +0000 (10:16 +0100)]
JAL-2505 removed SequenceFeature constructor JAL-1641 include
description, otherDetails in feature roundtrip verification
gmungoc [Thu, 25 May 2017 08:30:53 +0000 (09:30 +0100)]
JAL-2490 test coverage of empty and null feature group in Jalview format
export
kiramt [Thu, 25 May 2017 07:49:08 +0000 (08:49 +0100)]
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
gmungoc [Wed, 24 May 2017 15:42:50 +0000 (16:42 +0100)]
JAL-2505 make SequenceFeature type, begin, end, featureGroup final
gmungoc [Wed, 24 May 2017 15:42:06 +0000 (16:42 +0100)]
JAL-2506 relocate Uniprot binding classes, bind to UniprotFeature not
SequenceFeature
gmungoc [Wed, 24 May 2017 14:55:19 +0000 (15:55 +0100)]
JAL-2505 remove setters for SequenceFeature.begin,end,type,featureGroup
gmungoc [Wed, 24 May 2017 14:45:16 +0000 (15:45 +0100)]
JAL-2529 add object_type=cdna to EnsemblCdna parameters
gmungoc [Wed, 24 May 2017 14:21:43 +0000 (15:21 +0100)]
Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList
gmungoc [Wed, 24 May 2017 13:47:36 +0000 (14:47 +0100)]
JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional
features
kiramt [Wed, 24 May 2017 12:47:58 +0000 (13:47 +0100)]
JAL-2551 Fix to group colouring when group extent is reduced
gmungoc [Wed, 24 May 2017 10:26:11 +0000 (11:26 +0100)]
JAL-2542 correct adjustment of sequence features for flanking sequence
kiramt [Wed, 24 May 2017 09:44:47 +0000 (10:44 +0100)]
JAL-2034 Added isDefined flag to SequenceGroup
gmungoc [Wed, 24 May 2017 08:17:07 +0000 (09:17 +0100)]
JAL-2505 delete and readd modified feature after Cut or Paste
Jim Procter [Tue, 23 May 2017 19:39:17 +0000 (20:39 +0100)]
JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation
Jim Procter [Tue, 23 May 2017 19:35:59 +0000 (20:35 +0100)]
JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list
Jim Procter [Tue, 23 May 2017 19:35:23 +0000 (20:35 +0100)]
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests
gmungoc [Tue, 23 May 2017 16:10:23 +0000 (17:10 +0100)]
JAL-2490 find features for export as GFF, JAL-2548 respect group
visibility
gmungoc [Tue, 23 May 2017 13:50:28 +0000 (14:50 +0100)]
JAL-2490 test coverage for printGffFormat before refactoring
gmungoc [Tue, 23 May 2017 12:52:39 +0000 (13:52 +0100)]
JAL-2490 unit tests for getFeaturesForGroup
gmungoc [Tue, 23 May 2017 11:55:08 +0000 (12:55 +0100)]
JAL-2547 don't show features in tooltip over a gap
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
gmungoc [Thu, 18 May 2017 13:15:32 +0000 (14:15 +0100)]
JAL-2541 initial unit tests for edit cut relocate features
gmungoc [Thu, 18 May 2017 13:15:04 +0000 (14:15 +0100)]
JAL-2541 fix to initSeqFrom (and minor code tidy); more tests for
deleteChars
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
kiramt [Tue, 16 May 2017 15:10:07 +0000 (16:10 +0100)]
JAL-2536 Overview window sizing not subject to min size restrictions
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
gmungoc [Tue, 16 May 2017 13:10:40 +0000 (14:10 +0100)]
JAL-2517 restore complex colour scheme on Cancel in User Defined Colours
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
kiramt [Tue, 16 May 2017 09:15:40 +0000 (10:15 +0100)]
Merge branch 'develop' into bug/JAL-2491
kiramt [Tue, 16 May 2017 09:10:03 +0000 (10:10 +0100)]
JAL-2491 Better merge
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
git://source.jalview.org / jalview.git / log