gmungoc [Thu, 19 Apr 2018 15:32:01 +0000 (16:32 +0100)]
JAL-591 utility method renamed and slightly generalised
gmungoc [Wed, 18 Apr 2018 13:22:41 +0000 (14:22 +0100)]
Merge branch 'develop' into features/mchmmer
Conflicts:
.classpath
gmungoc [Wed, 18 Apr 2018 11:41:08 +0000 (12:41 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Conflicts:
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/renderer/seqfeatures/FeatureRendererTest.java
gmungoc [Wed, 18 Apr 2018 11:28:37 +0000 (12:28 +0100)]
JAL-2593 render 'duplicate' features if transparency is applied
gmungoc [Wed, 18 Apr 2018 11:13:23 +0000 (12:13 +0100)]
JAL-2629 corrected cutoff parameter passing to hmmsearch
gmungoc [Tue, 17 Apr 2018 17:44:41 +0000 (18:44 +0100)]
Merge branch 'features/mchmmer' of https://source.jalview.org/git/jalview.git into features/mchmmer
Conflicts:
src/jalview/hmmer/HmmerCommand.java
gmungoc [Tue, 17 Apr 2018 17:38:54 +0000 (18:38 +0100)]
JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified
Mungo Carstairs [Tue, 17 Apr 2018 15:01:30 +0000 (16:01 +0100)]
JAL-2937 working Cygwin bash execution of hmmbuild on Windows
gmungoc [Mon, 16 Apr 2018 09:19:31 +0000 (10:19 +0100)]
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence
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 [Thu, 22 Mar 2018 09:50:46 +0000 (09:50 +0000)]
JAL-2929 unit test, tidy unused/unneeded fields/parameters
Jim Procter [Wed, 21 Mar 2018 17:22:17 +0000 (17:22 +0000)]
JAL-2754 reinstate PA import from bad conflict merge
Jim Procter [Wed, 21 Mar 2018 17:21:21 +0000 (17:21 +0000)]
JAL-2754 remove duplicate classpath entry again
Jim Procter [Wed, 21 Mar 2018 17:15:42 +0000 (17:15 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Jim Procter [Wed, 21 Mar 2018 17:13:49 +0000 (17:13 +0000)]
Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Mar 2018 17:13:04 +0000 (17:13 +0000)]
JAL-2754 don’t use deprecated api for getting font metrics
Jim Procter [Wed, 21 Mar 2018 17:12:17 +0000 (17:12 +0000)]
JAL-2754 fix eclipse compilation error about referencing deprecated API via @see
gmungoc [Wed, 21 Mar 2018 17:05:58 +0000 (17:05 +0000)]
JAL-2929 use configure Overview gap colour instead of white past end of sequence
Jim Procter [Wed, 21 Mar 2018 16:46:55 +0000 (16:46 +0000)]
Merge branch 'patch/JAL-2754_patch2104forJava8' into develop
Jim Procter [Wed, 21 Mar 2018 16:46:37 +0000 (16:46 +0000)]
Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Mar 2018 16:45:44 +0000 (16:45 +0000)]
JAL-2754 dont put '<>' in <echo> text!
gmungoc [Wed, 21 Mar 2018 16:41:17 +0000 (16:41 +0000)]
JAL-2629 tweaks to Information annotation updating
Jim Procter [Wed, 21 Mar 2018 16:35:39 +0000 (16:35 +0000)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Jim Procter [Wed, 21 Mar 2018 16:32:59 +0000 (16:32 +0000)]
Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 21 Mar 2018 16:32:34 +0000 (16:32 +0000)]
JAL-2754 clean up proguard path spec and config variables
gmungoc [Fri, 27 Oct 2017 11:20:28 +0000 (12:20 +0100)]
JAL-2754 renamed proguard.jar to include version number
gmungoc [Fri, 27 Oct 2017 11:03:22 +0000 (12:03 +0100)]
JAL-2754 5.3.3 update of proguard.jar
gmungoc [Fri, 27 Oct 2017 09:52:05 +0000 (10:52 +0100)]
JAL-2754 update to specify Java 1.8(+)
gmungoc [Fri, 6 Oct 2017 08:39:02 +0000 (09:39 +0100)]
JAL-2754 update to Java 1.8
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
git://source.jalview.org / jalview.git / log