gmungoc [Wed, 13 Dec 2017 16:54:31 +0000 (16:54 +0000)]
JAL-2843 add isByAttribute to interface for convenience
gmungoc [Mon, 11 Dec 2017 15:16:05 +0000 (15:16 +0000)]
JAL-2843 add colour by attribute, and no value colour, to features file
gmungoc [Fri, 8 Dec 2017 15:44:34 +0000 (15:44 +0000)]
JAL-2843 example filters added
gmungoc [Fri, 8 Dec 2017 15:21:04 +0000 (15:21 +0000)]
JAL-2843 read/write feature filters from/to Jalview features file
gmungoc [Fri, 8 Dec 2017 15:20:23 +0000 (15:20 +0000)]
JAL-2843 refactor / tidy for feature filter input/output
gmungoc [Fri, 8 Dec 2017 15:17:25 +0000 (15:17 +0000)]
JAL-2843 methods relocated
gmungoc [Fri, 8 Dec 2017 15:13:41 +0000 (15:13 +0000)]
JAL-2843 toStableString, fromString for Jalview features file format
gmungoc [Fri, 8 Dec 2017 15:10:59 +0000 (15:10 +0000)]
JAL-2843 FeatureRenderer.getFeatureFilters returns the map, not a copy
gmungoc [Tue, 5 Dec 2017 09:25:37 +0000 (09:25 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Mon, 4 Dec 2017 15:53:44 +0000 (15:53 +0000)]
Merge branch 'spikes/mungo' into features/JAL-1793VCF
Conflicts:
src/jalview/ext/htsjdk/HtsContigDb.java
src/jalview/io/vcf/VCFLoader.java
test/jalview/ext/htsjdk/TestHtsContigDb.java
test/jalview/io/vcf/VCFLoaderTest.java
gmungoc [Mon, 4 Dec 2017 15:21:25 +0000 (15:21 +0000)]
JAL-2850 JAL-1766 option to load contig sequence referenced by VCF
gmungoc [Mon, 4 Dec 2017 11:31:41 +0000 (11:31 +0000)]
JAL-2845 locate reverse strand insertion as complement insertion at a preceding position
gmungoc [Mon, 4 Dec 2017 09:21:09 +0000 (09:21 +0000)]
JAL-2835 small refactor to only extract transcript consequence once
gmungoc [Fri, 1 Dec 2017 17:03:17 +0000 (17:03 +0000)]
JAL-2835 spike updated to latest (use specific SO term for feature)
gmungoc [Fri, 1 Dec 2017 17:01:36 +0000 (17:01 +0000)]
JAL-2835 refactored to extract specific consequence term per transcript and allele
gmungoc [Fri, 1 Dec 2017 15:52:58 +0000 (15:52 +0000)]
JAL-2792 sort feature attributes for output, not for storage
gmungoc [Fri, 1 Dec 2017 15:51:29 +0000 (15:51 +0000)]
JAL-2835 additional sub-terms of sequence_variant added
gmungoc [Thu, 30 Nov 2017 15:20:19 +0000 (15:20 +0000)]
JAL-2850 improved use of htsjdk api to read contig info
gmungoc [Thu, 30 Nov 2017 15:19:40 +0000 (15:19 +0000)]
JAL-1766 additional tests for stub htsjdk wrapper
Jim Procter [Thu, 30 Nov 2017 12:04:15 +0000 (12:04 +0000)]
JAL-2849 release notes
Jim Procter [Thu, 30 Nov 2017 11:34:22 +0000 (11:34 +0000)]
Merge branch 'bug/JAL-2849' into develop
Jim Procter [Thu, 30 Nov 2017 11:34:02 +0000 (11:34 +0000)]
JAL-2849 JAL-2863 file format preferences TODO
Jim Procter [Thu, 30 Nov 2017 11:28:36 +0000 (11:28 +0000)]
JAL-2849 fix
Jim Procter [Tue, 28 Nov 2017 15:18:14 +0000 (15:18 +0000)]
Merge branch 'bug/JAL-2859_uniprottowrongpdbid' into develop
Jim Procter [Tue, 28 Nov 2017 15:06:57 +0000 (15:06 +0000)]
JAL-2740 release notes
Jim Procter [Tue, 28 Nov 2017 14:55:23 +0000 (14:55 +0000)]
Merge branch 'bug/JAL-2740' into develop
Jim Procter [Tue, 28 Nov 2017 14:53:51 +0000 (14:53 +0000)]
JAL-2827 release notes
Jim Procter [Tue, 28 Nov 2017 14:45:15 +0000 (14:45 +0000)]
Merge branch 'bug/JAL-2827' into develop
Jim Procter [Tue, 28 Nov 2017 14:42:00 +0000 (14:42 +0000)]
JAL-2842 release notes
Jim Procter [Tue, 28 Nov 2017 14:24:05 +0000 (14:24 +0000)]
Merge branch 'bug/JAL-2842' into develop
gmungoc [Tue, 28 Nov 2017 10:25:22 +0000 (10:25 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Tue, 28 Nov 2017 09:07:51 +0000 (09:07 +0000)]
JAL-2850 MapList.isToForwardStrand added
Jim Procter [Mon, 27 Nov 2017 22:09:45 +0000 (22:09 +0000)]
JAL-2859 disambiguate with PDB ID if no file path
Jim Procter [Mon, 27 Nov 2017 22:07:07 +0000 (22:07 +0000)]
JAL-2859 failing test demonstrating sequences with pdb without a local file map all get mapped together
Jim Procter [Mon, 27 Nov 2017 18:46:19 +0000 (18:46 +0000)]
JAL-2851 JAL-2858 release notes for 2.10.3b1
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
gmungoc [Mon, 27 Nov 2017 15:21:33 +0000 (15:21 +0000)]
JAL-2850 VCFLoader refactored to load VCF to contig sequences
gmungoc [Fri, 24 Nov 2017 14:50:45 +0000 (14:50 +0000)]
JAL-2808 update spike to latest
gmungoc [Fri, 24 Nov 2017 14:46:42 +0000 (14:46 +0000)]
JAL-2808 refactoring to better handler filter by Score or Label etc
gmungoc [Fri, 24 Nov 2017 14:42:08 +0000 (14:42 +0000)]
JAL-2808 relocate constants for compiler, add COLUMN_COUNT constant
gmungoc [Fri, 24 Nov 2017 14:40:21 +0000 (14:40 +0000)]
JAL-2808 refine FeatureMatcher interface and matcher toString methods
gmungoc [Fri, 24 Nov 2017 14:38:17 +0000 (14:38 +0000)]
JAL-2808 don't cache i18n - MessageManager already does that
gmungoc [Thu, 23 Nov 2017 16:21:26 +0000 (16:21 +0000)]
JAL-2808 update spike to latest (filter range tooltip, Present condition)
gmungoc [Thu, 23 Nov 2017 16:20:03 +0000 (16:20 +0000)]
JAL-2808 refactor KeyedMatcher as FeatureMatcher with byLabel, byScore, byAttribute factory methods
gmungoc [Thu, 23 Nov 2017 12:52:45 +0000 (12:52 +0000)]
JAL-2808 update spike to latest (filter range, Present option)
gmungoc [Thu, 23 Nov 2017 12:51:15 +0000 (12:51 +0000)]
JAL-2808 removed field filters; sort CSQ data by key
gmungoc [Thu, 23 Nov 2017 12:50:43 +0000 (12:50 +0000)]
JAL-2808 added conditions Present, NotPresent as options
kiramt [Thu, 23 Nov 2017 11:52:01 +0000 (11:52 +0000)]
Merge branch 'develop' into bug/JAL-2851
kiramt [Thu, 23 Nov 2017 11:50:39 +0000 (11:50 +0000)]
JAL-2851 Fix merge error breaking vertical scrolling
gmungoc [Thu, 23 Nov 2017 10:38:20 +0000 (10:38 +0000)]
JAL-2808 refactor conversion of table data to beans for controller
gmungoc [Thu, 23 Nov 2017 10:05:32 +0000 (10:05 +0000)]
JAL-2808 pass FeatureSettings to controller as array of data bean
gmungoc [Wed, 22 Nov 2017 16:56:35 +0000 (16:56 +0000)]
JAL-2808 update conditions list on change of attribute (safely)
gmungoc [Wed, 22 Nov 2017 15:36:06 +0000 (15:36 +0000)]
JAL-2069 spike updated with latest (FeatureTypeSettings)
gmungoc [Wed, 22 Nov 2017 15:33:17 +0000 (15:33 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Wed, 22 Nov 2017 15:24:52 +0000 (15:24 +0000)]
JAL-2808 JAL-2069 FeatureTypeSettings (with new Filters tab) replaces FeatureColourChooser (not applet)
gmungoc [Wed, 22 Nov 2017 12:29:47 +0000 (12:29 +0000)]
JAL-2069 renamed helper method better
gmungoc [Wed, 22 Nov 2017 12:27:33 +0000 (12:27 +0000)]
JAL-2808 defer dispose to allow screen location to be captured
gmungoc [Wed, 22 Nov 2017 12:26:19 +0000 (12:26 +0000)]
JAL-2069 Javadoc added only
gmungoc [Wed, 22 Nov 2017 12:25:13 +0000 (12:25 +0000)]
JAL-1424 enhanced to report dynamic keys separately
gmungoc [Wed, 22 Nov 2017 09:34:58 +0000 (09:34 +0000)]
JAL-2808 capture feature attributes datatype (Character/Number/Mixed) for more intelligent filter conditions
Jim Procter [Mon, 20 Nov 2017 16:17:26 +0000 (16:17 +0000)]
JAL-2698 only allow InstallAnywhere launches with version 1.8.* of java - java 9 JVM args not yet working for 2.10.3
Jim Procter [Mon, 20 Nov 2017 14:44:16 +0000 (14:44 +0000)]
JAL-2698 patch path for InstallAnywhere build. Webstart and source builds unchanged
Jim Procter [Fri, 17 Nov 2017 21:29:19 +0000 (21:29 +0000)]
JAL-2698 tidy release notes and whats new
Jim Procter [Fri, 17 Nov 2017 15:13:58 +0000 (15:13 +0000)]
JAL-2698 source code licencing
Jim Procter [Fri, 17 Nov 2017 14:56:24 +0000 (14:56 +0000)]
JAL-2698 tidy up release notes
Jim Procter [Fri, 17 Nov 2017 14:40:37 +0000 (14:40 +0000)]
JAL-2698 Cached PDB Entries -> Cached Structures in UI and help doc
Jim Procter [Fri, 17 Nov 2017 13:52:03 +0000 (13:52 +0000)]
JAL-2466 revised help text for sort by PID
Jim Procter [Fri, 17 Nov 2017 13:51:25 +0000 (13:51 +0000)]
JAL-2698 what’s new and release notes
Jim Procter [Fri, 17 Nov 2017 13:24:33 +0000 (13:24 +0000)]
JAL-2822 known defect for 2.10.3
Jim Procter [Fri, 17 Nov 2017 13:16:10 +0000 (13:16 +0000)]
Merge branch 'bug/JAL-2784' into develop
Jim Procter [Fri, 17 Nov 2017 13:15:20 +0000 (13:15 +0000)]
JAL-2841 JAL-2791 new known defect
Jim Procter [Fri, 17 Nov 2017 13:08:56 +0000 (13:08 +0000)]
JAL-2541 known defect
Jim Procter [Fri, 17 Nov 2017 13:03:05 +0000 (13:03 +0000)]
JAL-2684 clarify release notes
Jim Procter [Fri, 17 Nov 2017 12:31:58 +0000 (12:31 +0000)]
Merge branch 'bug/JAL-2821' into develop
Jim Procter [Fri, 17 Nov 2017 12:26:42 +0000 (12:26 +0000)]
JAL-2840 release notes
Jim Procter [Fri, 17 Nov 2017 12:21:17 +0000 (12:21 +0000)]
Merge branch 'bug/JAL-2837' into develop
kiramt [Fri, 17 Nov 2017 12:14:59 +0000 (12:14 +0000)]
Merge branch 'develop' into bug/JAL-2837
Conflicts:
src/jalview/gui/SeqPanel.java
Jim Procter [Fri, 17 Nov 2017 12:14:21 +0000 (12:14 +0000)]
Merge branch 'doc/JAL-2494_JAL-2828_mergefindAnnotation' into develop
kiramt [Fri, 17 Nov 2017 12:09:20 +0000 (12:09 +0000)]
Merge branch 'develop' into bug/JAL-2837
Jim Procter [Fri, 17 Nov 2017 11:56:59 +0000 (11:56 +0000)]
JAL-2811 release note
Jim Procter [Fri, 17 Nov 2017 11:47:51 +0000 (11:47 +0000)]
JAL-2541 not in 2.10.3, JAL-2831 signed off.
Jim Procter [Fri, 17 Nov 2017 11:47:25 +0000 (11:47 +0000)]
JAL-2698 11th hour release today
Jim Procter [Fri, 17 Nov 2017 11:28:43 +0000 (11:28 +0000)]
Merge branch 'bug/JAL-2831' into develop
gmungoc [Fri, 17 Nov 2017 09:49:04 +0000 (09:49 +0000)]
JAL-2808 set (read-only) condition text field as disabled
Jim Procter [Thu, 16 Nov 2017 16:50:03 +0000 (16:50 +0000)]
JAL-2541 JAL-2829 JAL-2830 JAL-2822 catch all release note entry for sequence feature relocation
Jim Procter [Thu, 16 Nov 2017 16:45:35 +0000 (16:45 +0000)]
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into develop
gmungoc [Thu, 16 Nov 2017 14:23:00 +0000 (14:23 +0000)]
JAL-2069 fix minor bugs in variable setting
gmungoc [Thu, 16 Nov 2017 12:20:04 +0000 (12:20 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
kiramt [Thu, 16 Nov 2017 11:57:15 +0000 (11:57 +0000)]
JAL-2831 Removed unwanted hidden sequences checks
gmungoc [Thu, 16 Nov 2017 09:15:21 +0000 (09:15 +0000)]
JAL-2069 removed unused and redundant thresholdIsMinMax
gmungoc [Thu, 16 Nov 2017 09:13:00 +0000 (09:13 +0000)]
JAL-2816 JAL-2835 additional tests to include colour/filter by attribute
kiramt [Thu, 16 Nov 2017 09:12:06 +0000 (09:12 +0000)]
JAL-2842 remove infinite loop in cursor move
gmungoc [Thu, 16 Nov 2017 09:05:03 +0000 (09:05 +0000)]
JAL-2835 update test for array-valued attribute name
gmungoc [Thu, 16 Nov 2017 09:03:49 +0000 (09:03 +0000)]
JAL-2835 update test for CSQ data held as a Map
gmungoc [Thu, 16 Nov 2017 08:18:10 +0000 (08:18 +0000)]
JAL-2835 test updated for colour by 'nested attribute'
gmungoc [Thu, 16 Nov 2017 08:13:52 +0000 (08:13 +0000)]
JAL-2816 tests for findFeaturesAtColumn
kiramt [Wed, 15 Nov 2017 16:22:21 +0000 (16:22 +0000)]
JAL-2831 Don't show cursor if position in hidden region
kiramt [Wed, 15 Nov 2017 16:05:18 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
gmungoc [Wed, 15 Nov 2017 15:47:41 +0000 (15:47 +0000)]
JAL-2816 exclude filtered / thresholded out features when finding
kiramt [Wed, 15 Nov 2017 13:23:00 +0000 (13:23 +0000)]
JAL-2811 Updated following review
git://source.jalview.org / jalview.git / log