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
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 [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 [Wed, 18 Apr 2018 11:28:37 +0000 (12:28 +0100)]
JAL-2593 render 'duplicate' features if transparency is applied
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
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 [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 17:13:49 +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 16:46:37 +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!
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 [Fri, 16 Mar 2018 14:47:12 +0000 (14:47 +0000)]
JAL-2922 update FeatureRenderer and repaint feature settings after Invert Selection
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
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 14:05:51 +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
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, 28 Feb 2018 17:54:15 +0000 (17:54 +0000)]
JAL-2924 no tooltip over null annotation positions
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
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
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
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
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
git://source.jalview.org / jalview.git / log