Jim Procter [Mon, 7 May 2018 17:08:11 +0000 (18:08 +0100)]
JAL-2321 ensure default is ‘parseImmediately=true’
Jim Procter [Mon, 7 May 2018 16:43:56 +0000 (17:43 +0100)]
JAL-2321 use configured values for structure derived annotation
Jim Procter [Mon, 7 May 2018 16:39:17 +0000 (17:39 +0100)]
JAL-2321 add secondary structure & temp factor if not already present on mapped sequences
Jim Procter [Mon, 7 May 2018 16:38:29 +0000 (17:38 +0100)]
JAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() called from constructor
Jim Procter [Mon, 7 May 2018 16:36:28 +0000 (17:36 +0100)]
JAL-2321 isParseImmediately() allows the parse() method to determine if it was called by the constructor or after construction
Jim Procter [Mon, 7 May 2018 16:35:18 +0000 (17:35 +0100)]
JAL-2321 allow JmolParser to be configured before parsing data
gmungoc [Mon, 7 May 2018 14:16:42 +0000 (15:16 +0100)]
JAL-2808 ensure test setUp/tearDown alwaysRun
gmungoc [Mon, 7 May 2018 13:59:27 +0000 (14:59 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Conflicts:
.classpath
Jim Procter [Mon, 7 May 2018 13:23:05 +0000 (14:23 +0100)]
JAL-2906 apply GPLv3 license source
Jim Procter [Mon, 7 May 2018 08:53:05 +0000 (09:53 +0100)]
JAL-2960 don’t override a swing method and create infinite recursion ;) toFront now raiseViewer !
Jim Procter [Mon, 7 May 2018 08:29:54 +0000 (09:29 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_4_Branch
gmungoc [Fri, 4 May 2018 15:35:02 +0000 (16:35 +0100)]
JAL-2906 small tweaks to release notes
Jim Procter [Fri, 4 May 2018 14:24:49 +0000 (15:24 +0100)]
JAL-2906 2.10.4 release for 8th May 2018
Jim Procter [Fri, 4 May 2018 14:15:16 +0000 (15:15 +0100)]
Merge branch 'bug/JAL-2899' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 4 May 2018 14:05:41 +0000 (15:05 +0100)]
JAL-2906 removed mention of experimental features, updated what’s new for 2.10.4 release, and help TOC.
Jim Procter [Fri, 4 May 2018 13:37:59 +0000 (14:37 +0100)]
JAL-2976 patch NPE when trying to open Uniprot FTS
Jim Procter [Fri, 4 May 2018 13:15:45 +0000 (14:15 +0100)]
JAL-2929 JAL-2922 release notes
Jim Procter [Fri, 4 May 2018 12:55:06 +0000 (13:55 +0100)]
JAL-2976 typo in installAnywhere build for VAqua dependency
Jim Procter [Fri, 4 May 2018 12:26:37 +0000 (13:26 +0100)]
JAL-2960 release notes
Jim Procter [Fri, 4 May 2018 12:26:20 +0000 (13:26 +0100)]
JAL-2948 transfer features/annotation is now available for all users
Jim Procter [Fri, 4 May 2018 12:11:48 +0000 (13:11 +0100)]
JAL-2960 raise the structure view after adding structures to it
Jim Procter [Fri, 4 May 2018 09:35:33 +0000 (10:35 +0100)]
JAL-2976 Vaqua fallback release notes JAL-2906
Jim Procter [Fri, 4 May 2018 07:41:23 +0000 (08:41 +0100)]
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 2 May 2018 14:41:51 +0000 (15:41 +0100)]
JAL-2976 fallback to Vaqua for Macs that don’t work for Quaqua
Jim Procter [Wed, 2 May 2018 14:41:15 +0000 (15:41 +0100)]
JAL-2976 Vaqua(4) as a dependency
Jim Procter [Tue, 1 May 2018 15:59:48 +0000 (16:59 +0100)]
JAL-2899 release notes
Jim Procter [Tue, 1 May 2018 11:31:15 +0000 (12:31 +0100)]
JAL-2973 JAL-2974 known defects for 2.10.4 (JAL-2906)
Jim Procter [Tue, 1 May 2018 11:30:48 +0000 (12:30 +0100)]
JAL-2925 release notes
Jim Procter [Tue, 1 May 2018 10:58:40 +0000 (11:58 +0100)]
JAL-2593 JAL-2945 JAL-2952 JAL-2954 release notes for 2.10.4 JAL-2906
Jim Procter [Tue, 1 May 2018 10:15:50 +0000 (11:15 +0100)]
JAL-2223 JAL-2781 JAL-2780 JAL-2946 JAL-2906 release notes
Jim Procter [Tue, 1 May 2018 09:30:03 +0000 (10:30 +0100)]
JAL-2906 reformat release notes
Jim Procter [Tue, 1 May 2018 09:29:46 +0000 (10:29 +0100)]
JAL-2906 typo
Jim Procter [Tue, 1 May 2018 09:29:19 +0000 (10:29 +0100)]
JAL-2944 revised docs and structure chooser screen shots
Jim Procter [Tue, 1 May 2018 08:21:39 +0000 (09:21 +0100)]
JAL-2899 colouring moved from SwingWorker to a background thread
Jim Procter [Mon, 30 Apr 2018 15:49:41 +0000 (16:49 +0100)]
Merge branch 'bug/JAL-2899' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 30 Apr 2018 09:50:14 +0000 (10:50 +0100)]
JAL-2906 release 2.10.4 on 1st May 2018
Jim Procter [Wed, 25 Apr 2018 11:03:17 +0000 (12:03 +0100)]
Merge branch 'features/JAL-2944_openStructuresInSelectedView' into releases/Release_2_10_4_Branch
gmungoc [Tue, 24 Apr 2018 14:27:36 +0000 (15:27 +0100)]
JAL-2959 no Print dialog shown if Page Format is Cancelled
gmungoc [Tue, 24 Apr 2018 14:08:26 +0000 (15:08 +0100)]
JAL-2939 exit calc thread if no HMM in alignment
gmungoc [Tue, 24 Apr 2018 14:07:25 +0000 (15:07 +0100)]
JAL-591 use constant for Preferences key
gmungoc [Tue, 24 Apr 2018 14:06:05 +0000 (15:06 +0100)]
JAL-2616 unused field removed
gmungoc [Tue, 24 Apr 2018 07:06:03 +0000 (08:06 +0100)]
JAL-2956 unit test
gmungoc [Mon, 23 Apr 2018 14:59:47 +0000 (15:59 +0100)]
JAL-2956 save/restore HMMER profile to/from Jalview project
gmungoc [Mon, 23 Apr 2018 11:27:51 +0000 (12:27 +0100)]
JAL-2954 more efficient SearchResults.markColumns
gmungoc [Mon, 23 Apr 2018 10:26:58 +0000 (11:26 +0100)]
JAL-2952 set negative TempFactor values as AlignmentAnnotation.graphMin
gmungoc [Mon, 23 Apr 2018 08:43:16 +0000 (09:43 +0100)]
JAL-2957 don't validate input on arrow keys
gmungoc [Mon, 23 Apr 2018 08:41:59 +0000 (09:41 +0100)]
JAL-591 ensure slider hidden if text input field only
gmungoc [Fri, 20 Apr 2018 20:59:16 +0000 (21:59 +0100)]
JAL-591 slider scale factor now derived from min-max range
gmungoc [Fri, 20 Apr 2018 17:04:53 +0000 (18:04 +0100)]
JAL-591 tidy and comment code
gmungoc [Fri, 20 Apr 2018 09:05:30 +0000 (10:05 +0100)]
JAL-2629 tweaks to text
gmungoc [Fri, 20 Apr 2018 09:05:08 +0000 (10:05 +0100)]
JAL-591 OptionBox FlowLayout, tweaks to wrapping of options and params
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
gmungoc [Fri, 13 Apr 2018 07:21:00 +0000 (08:21 +0100)]
Merge branch 'features/JAL-2944_openStructuresInSelectedView' of https://source.jalview.org/git/jalview.git into features/JAL-2944_openStructuresInSelectedView
gmungoc [Thu, 12 Apr 2018 15:28:41 +0000 (16:28 +0100)]
JAL-2223 don't add duplicate mappings to StructureSelectionManager
gmungoc [Thu, 12 Apr 2018 13:28:25 +0000 (14:28 +0100)]
JAL-1847 minor post-review updates
gmungoc [Thu, 12 Apr 2018 13:01:26 +0000 (14:01 +0100)]
JAL-2944 tidies for review comments
Jim Procter [Wed, 11 Apr 2018 15:42:02 +0000 (16:42 +0100)]
JAL-2946 catch unexpected SIFTS mapping exceptions and failover to Needleman and Wunsch mapping
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
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
git://source.jalview.org / jalview.git / log