gmungoc [Mon, 16 Apr 2018 09:18:09 +0000 (10:18 +0100)]
JAL-2937 use preferences for presets, simplify some constructors
Mungo Carstairs [Mon, 9 Apr 2018 16:09:32 +0000 (17:09 +0100)]
JAL-2937 Cygwin path preference, method refactoring
Mungo Carstairs [Mon, 9 Apr 2018 16:07:09 +0000 (17:07 +0100)]
JAL-2629 more error checking
Mungo Carstairs [Mon, 9 Apr 2018 16:04:42 +0000 (17:04 +0100)]
JAL-2937 extract reusable utility method
Mungo Carstairs [Mon, 9 Apr 2018 16:03:40 +0000 (17:03 +0100)]
JAL-2069 typo
gmungoc [Fri, 30 Mar 2018 14:50:01 +0000 (15:50 +0100)]
JAL-2599 MapList from HMM nodes to consensus dataset sequence
gmungoc [Fri, 30 Mar 2018 14:47:00 +0000 (15:47 +0100)]
JAL-2629 tidy code, factory methods for param sets
gmungoc [Fri, 30 Mar 2018 14:46:14 +0000 (15:46 +0100)]
JAL-2629 use correct gap character, revised deletion of hmm sequences
gmungoc [Fri, 30 Mar 2018 14:45:00 +0000 (15:45 +0100)]
JAL-2629 Javadoc updates
gmungoc [Fri, 30 Mar 2018 14:44:04 +0000 (15:44 +0100)]
JAL-2629 combine with/without defaults in one method call
gmungoc [Fri, 30 Mar 2018 14:40:18 +0000 (15:40 +0100)]
JAL-2939 field/method naming more consistent
gmungoc [Fri, 30 Mar 2018 14:33:11 +0000 (15:33 +0100)]
JAL-2629 ensure hmm consensus sequence set on alignment output
gmungoc [Fri, 30 Mar 2018 14:32:02 +0000 (15:32 +0100)]
JAL-2941 'map hmm to RF' removed pending clarifications
gmungoc [Fri, 30 Mar 2018 09:53:07 +0000 (10:53 +0100)]
small tidy
gmungoc [Fri, 30 Mar 2018 09:42:33 +0000 (10:42 +0100)]
JAL-2938 revisions to implementation details
gmungoc [Fri, 30 Mar 2018 09:40:44 +0000 (10:40 +0100)]
JAL-2939 remove commented out code
gmungoc [Fri, 30 Mar 2018 09:39:11 +0000 (10:39 +0100)]
JAL-2599 move utility method to MappingUtils
gmungoc [Fri, 30 Mar 2018 09:37:40 +0000 (10:37 +0100)]
JAL-2939 simplified way of getting hmm consensus residue
gmungoc [Fri, 30 Mar 2018 09:36:16 +0000 (10:36 +0100)]
JAL-2629 add title to output alignment window
gmungoc [Fri, 30 Mar 2018 09:35:51 +0000 (10:35 +0100)]
JAL-2629 select HMM selects sequence under cursor
gmungoc [Fri, 30 Mar 2018 08:24:56 +0000 (09:24 +0100)]
JAL-2599 corrected test file name in unit test
gmungoc [Thu, 29 Mar 2018 09:55:23 +0000 (10:55 +0100)]
JAL-2907 test method renamed to match method name change
gmungoc [Thu, 29 Mar 2018 09:47:17 +0000 (10:47 +0100)]
JAL-2907 bug fix redone on HMMER branch
gmungoc [Wed, 28 Mar 2018 14:11:15 +0000 (15:11 +0100)]
JAL-1265 output all dbrefs in Stockholm (+tests) (+some refactoring)
gmungoc [Mon, 26 Mar 2018 11:44:47 +0000 (12:44 +0100)]
JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
gmungoc [Mon, 26 Mar 2018 11:20:44 +0000 (12:20 +0100)]
JAL-2939 unused action handler methods removed
gmungoc [Mon, 26 Mar 2018 11:20:20 +0000 (12:20 +0100)]
JAL-2939 no need to recalc HMM annotation for show/hide logo
gmungoc [Mon, 26 Mar 2018 11:19:01 +0000 (12:19 +0100)]
JAL-2939 always store Information profile
gmungoc [Fri, 23 Mar 2018 12:18:32 +0000 (12:18 +0000)]
JAL-2629 pad gaps when exporting alignment as 'database to search'
gmungoc [Fri, 23 Mar 2018 12:17:13 +0000 (12:17 +0000)]
JAL-2937 unused field removed
gmungoc [Fri, 23 Mar 2018 12:15:49 +0000 (12:15 +0000)]
JAL-2938 update colour schemes enum for class name changes
gmungoc [Fri, 23 Mar 2018 10:28:44 +0000 (10:28 +0000)]
JAL-2938 extracted base class for Hmmer colour schems
gmungoc [Wed, 21 Mar 2018 16:41:17 +0000 (16:41 +0000)]
JAL-2629 tweaks to Information annotation updating
gmungoc [Tue, 20 Mar 2018 16:32:13 +0000 (16:32 +0000)]
JAL-2629 InformationThread.findOrCreateAnnotation and related updates for a more stable recalculation
gmungoc [Tue, 20 Mar 2018 08:23:32 +0000 (08:23 +0000)]
Merge branch 'develop' into features/mchmmer
gmungoc [Fri, 16 Mar 2018 15:15:49 +0000 (15:15 +0000)]
JAL-2679 getGeneId() now uses the same pattern as getGeneLoci, getSpecies
gmungoc [Fri, 16 Mar 2018 15:03:11 +0000 (15:03 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop
Conflicts:
src/jalview/ext/ensembl/EnsemblLookup.java
gmungoc [Fri, 16 Mar 2018 14:47:12 +0000 (14:47 +0000)]
JAL-2922 update FeatureRenderer and repaint feature settings after Invert Selection
gmungoc [Fri, 16 Mar 2018 09:59:59 +0000 (09:59 +0000)]
Merge branch 'develop' into features/mchmmer
gmungoc [Fri, 16 Mar 2018 09:59:01 +0000 (09:59 +0000)]
Merge branch 'bug/JAL-2865removeGC' into develop
gmungoc [Fri, 16 Mar 2018 09:56:56 +0000 (09:56 +0000)]
Merge branch 'develop' into trialMerge
Conflicts:
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
gmungoc [Thu, 15 Mar 2018 16:24:06 +0000 (16:24 +0000)]
JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
gmungoc [Wed, 14 Mar 2018 16:36:29 +0000 (16:36 +0000)]
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db source'
gmungoc [Wed, 14 Mar 2018 14:41:14 +0000 (14:41 +0000)]
JAL-2679 reinstating changes lost in VCF merge
Conflicts:
src/jalview/ext/ensembl/EnsemblLookup.java
gmungoc [Wed, 14 Mar 2018 14:41:14 +0000 (14:41 +0000)]
JAL-2679 reinstating changes lost in VCF merge
Jim Procter [Wed, 14 Mar 2018 08:53:17 +0000 (08:53 +0000)]
JAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4 release notes
gmungoc [Tue, 13 Mar 2018 16:22:55 +0000 (16:22 +0000)]
JAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH)
gmungoc [Thu, 8 Mar 2018 14:06:44 +0000 (14:06 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges/JAL-2906_update2_11_from_2_10_4
gmungoc [Thu, 8 Mar 2018 14:05:51 +0000 (14:05 +0000)]
JAL-2885 tests updated for code changes
gmungoc [Thu, 8 Mar 2018 11:29:11 +0000 (11:29 +0000)]
JAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation
Jim Procter [Wed, 7 Mar 2018 14:40:59 +0000 (14:40 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
check carefully that JAL-2885 (configurable Ensembl/Genomes Endpoints) functionality is still present
gmungoc [Wed, 7 Mar 2018 12:05:23 +0000 (12:05 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 12:04:58 +0000 (12:04 +0000)]
JAL-2922 [2] not [1] for Boolean column of table
gmungoc [Wed, 7 Mar 2018 11:53:57 +0000 (11:53 +0000)]
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:53:26 +0000 (11:53 +0000)]
JAL-2922 i18n and bespoke handler for Invert Selection
gmungoc [Wed, 7 Mar 2018 11:30:09 +0000 (11:30 +0000)]
Merge branch 'bug/JAL-2924nullTooltip' into releases/Release_2_10_4_Branch
gmungoc [Wed, 7 Mar 2018 11:27:57 +0000 (11:27 +0000)]
JAL-2926 fix copy group consensus (and paste sequence with space in name)
gmungoc [Wed, 7 Mar 2018 11:27:20 +0000 (11:27 +0000)]
JAL-2925 handle empty annotation when copying group consensus
gmungoc [Wed, 7 Mar 2018 11:04:42 +0000 (11:04 +0000)]
JAL-2913 use FIGURE_USERIDWIDTH for fixed id width property
gmungoc [Wed, 7 Mar 2018 10:35:12 +0000 (10:35 +0000)]
JAL-2629 storage and lifecycle of alignment/group HMM annotations revised
gmungoc [Fri, 2 Mar 2018 16:07:27 +0000 (16:07 +0000)]
JAL-2729 draft help pages for HMMER menu
gmungoc [Thu, 1 Mar 2018 10:07:46 +0000 (10:07 +0000)]
JAL-2629 revising hmmer annotation updating (wip)
gmungoc [Wed, 28 Feb 2018 17:54:15 +0000 (17:54 +0000)]
JAL-2924 no tooltip over null annotation positions
gmungoc [Wed, 28 Feb 2018 17:50:03 +0000 (17:50 +0000)]
JAL-2629 some tidying of Hmmer commands (wip)
Jim Procter [Wed, 28 Feb 2018 10:32:14 +0000 (10:32 +0000)]
Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2_10_4_Branch
Jim Procter [Tue, 27 Feb 2018 16:18:59 +0000 (16:18 +0000)]
JAL-2759 release notes for 2.10.4
gmungoc [Tue, 27 Feb 2018 16:18:31 +0000 (16:18 +0000)]
JAL-2668 method name change for clarity
gmungoc [Tue, 27 Feb 2018 15:56:53 +0000 (15:56 +0000)]
JAL-2668 fix broken factory method for colour scheme
gmungoc [Tue, 27 Feb 2018 15:48:51 +0000 (15:48 +0000)]
JAL-2717 JAL-2668 fixes to HMMER colour scheme display names, enabled state, test coverage
Jim Procter [Tue, 27 Feb 2018 11:16:41 +0000 (11:16 +0000)]
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
Jim Procter [Tue, 27 Feb 2018 11:07:48 +0000 (11:07 +0000)]
fix for JAL-2922 - update states all at once and then refresh
gmungoc [Mon, 26 Feb 2018 11:10:48 +0000 (11:10 +0000)]
JAL-2599 test coverage and bug fixes for 'minimal file' parsing
Jim Procter [Mon, 26 Feb 2018 10:13:30 +0000 (10:13 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 26 Feb 2018 10:12:45 +0000 (10:12 +0000)]
JAL-984 remove all references to idwidth.gif - in build.xml too :)
Jim Procter [Fri, 23 Feb 2018 16:54:28 +0000 (16:54 +0000)]
JAL-2885 release notes
gmungoc [Fri, 23 Feb 2018 16:12:16 +0000 (16:12 +0000)]
JAL-2599 corrected case-insensitive symbol indexing
Jim Procter [Fri, 23 Feb 2018 16:01:42 +0000 (16:01 +0000)]
Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch
gmungoc [Fri, 23 Feb 2018 15:52:36 +0000 (15:52 +0000)]
JAL-2599 parser and datamodel use primitive double[] not List<Double>
Jim Procter [Fri, 23 Feb 2018 11:40:15 +0000 (11:40 +0000)]
JAL-2885 xfam https
Jim Procter [Fri, 23 Feb 2018 11:39:34 +0000 (11:39 +0000)]
JAL-2885 XFAM_DOMAIN->XFAM_BASEURL
Jim Procter [Fri, 23 Feb 2018 11:35:43 +0000 (11:35 +0000)]
JAL-2885 Ensembl* -> https
Jim Procter [Fri, 23 Feb 2018 11:33:41 +0000 (11:33 +0000)]
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
Jim Procter [Fri, 23 Feb 2018 11:24:03 +0000 (11:24 +0000)]
JAL-2885 renamed base URL getter from getDomain..
gmungoc [Thu, 22 Feb 2018 16:05:43 +0000 (16:05 +0000)]
JAL-2629 tidy tests, refactor hmmer node mapping slightly
Jim Procter [Thu, 22 Feb 2018 15:15:35 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 15:14:46 +0000 (15:14 +0000)]
JAL-984 ID width adjuster needs to be white !
Jim Procter [Thu, 22 Feb 2018 15:05:36 +0000 (15:05 +0000)]
JAL-2666 release notes
Jim Procter [Thu, 22 Feb 2018 14:48:58 +0000 (14:48 +0000)]
Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:34:44 +0000 (14:34 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:34:23 +0000 (14:34 +0000)]
JAL-984 remove all references to idwidth.gif and use int constants in place of width/height of image when switching between margin adjustment active/inactive mouse cursor
Jim Procter [Thu, 22 Feb 2018 14:16:26 +0000 (14:16 +0000)]
JAL-2906 typo fixes
Jim Procter [Thu, 22 Feb 2018 14:15:19 +0000 (14:15 +0000)]
JAL-984 release notes
Jim Procter [Thu, 22 Feb 2018 14:08:47 +0000 (14:08 +0000)]
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 22 Feb 2018 14:08:15 +0000 (14:08 +0000)]
JAL-294 remove unneeded paint() method
Jim Procter [Thu, 22 Feb 2018 14:07:58 +0000 (14:07 +0000)]
JAL-984 remove commented/unnecessary if clause
gmungoc [Thu, 22 Feb 2018 13:43:32 +0000 (13:43 +0000)]
JAL-2629 tidy unit tests, constants etc
Jim Procter [Wed, 21 Feb 2018 17:40:04 +0000 (17:40 +0000)]
JAL-2906 release notes for 2.10.4
Jim Procter [Wed, 21 Feb 2018 17:19:01 +0000 (17:19 +0000)]
Merge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Feb 2018 16:28:31 +0000 (16:28 +0000)]
JAL-2778 reinstate transparent windows to avoid ugly borders on OSX
gmungoc [Wed, 21 Feb 2018 16:18:29 +0000 (16:18 +0000)]
JAL-2629 simplifying method signatures in Hmmer command classes
git://source.jalview.org / jalview.git / log