Jim Procter [Mon, 9 Apr 2018 09:17:12 +0000 (10:17 +0100)]
JAL-2944 ’new view’ and ‘add to view’ button rather than selecting from combo box to make it easier to successively add structures to existing view (which is the default action when return is pressed)
Jim Procter [Mon, 9 Apr 2018 09:14:57 +0000 (10:14 +0100)]
JAL-1847 superpose checkbox in structure chooser
Jim Procter [Mon, 9 Apr 2018 09:09:58 +0000 (10:09 +0100)]
JAL-1847 JAL-2944 make superposition step a configurable property when opening/adding data to a structure viewer
Jim Procter [Fri, 6 Apr 2018 10:00:02 +0000 (11:00 +0100)]
failing test for JAL-2223
Jim Procter [Thu, 5 Apr 2018 21:04:13 +0000 (22:04 +0100)]
JAL-2945 resolve model as PDB file. Need to verify behaviour with multiple model PDB/mmCIF files
Jim Procter [Thu, 5 Apr 2018 20:49:38 +0000 (21:49 +0100)]
JAL-2945 failing test for structure mapping
Jim Procter [Thu, 5 Apr 2018 20:49:16 +0000 (21:49 +0100)]
JAL-2945 formatting
Jim Procter [Thu, 5 Apr 2018 20:47:46 +0000 (21:47 +0100)]
JAL-2945 provide access to last highlighted results
Jim Procter [Thu, 5 Apr 2018 13:31:56 +0000 (14:31 +0100)]
JAL-2944 open selected structures in existing or a new view, and by default offer last opened/selected structure view as target view
Jim Procter [Thu, 5 Apr 2018 13:28:10 +0000 (14:28 +0100)]
JAL-2944 combo box to pick which viewer to load structures into
Jim Procter [Thu, 5 Apr 2018 13:27:29 +0000 (14:27 +0100)]
JAL-2944 methods to check existence and get a title for existing or to-be-created StructureViewer
Jim Procter [Thu, 5 Apr 2018 13:26:26 +0000 (14:26 +0100)]
JAL-2944 allow StructureViewer proxy to be created for an existing view in order to add structures to it
Jim Procter [Thu, 5 Apr 2018 13:24:08 +0000 (14:24 +0100)]
JAL-2944 get viewer’s title via toString()
Jim Procter [Thu, 5 Apr 2018 13:23:02 +0000 (14:23 +0100)]
JAL-2944 expose UI update methods in api
Jim Procter [Thu, 5 Apr 2018 13:17:01 +0000 (14:17 +0100)]
JAL-2944 remove modal prompt logic and expose methods for adding structure data to a view via the StructureDisplay API
Jim Procter [Thu, 5 Apr 2018 13:06:47 +0000 (14:06 +0100)]
JAL-2944 pull up structure viewer discovery routine to Desktop
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
git://source.jalview.org / jalview.git / log