Jim Procter [Thu, 7 Jun 2018 15:24:16 +0000 (16:24 +0100)]
JAL-3009 release notes
Jim Procter [Thu, 7 Jun 2018 15:22:37 +0000 (16:22 +0100)]
Merge branch 'bugs/JAL-3009_blockingNetworkThreads' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 7 Jun 2018 15:05:22 +0000 (16:05 +0100)]
JAL-2999 what's new and tweak release notes order
gmungoc [Thu, 7 Jun 2018 08:58:41 +0000 (09:58 +0100)]
JAL-2920 format/comment tidy
gmungoc [Thu, 7 Jun 2018 08:55:54 +0000 (09:55 +0100)]
JAL-2920 wrap description in <html/> if it includes <br/>
gmungoc [Thu, 7 Jun 2018 08:06:16 +0000 (09:06 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' of https://source.jalview.org/git/jalview.git into releases/Release_2_10_4_Branch
gmungoc [Wed, 6 Jun 2018 15:47:55 +0000 (16:47 +0100)]
JAL-2920 unit tests for 3 or more original or variant bases
Jim Procter [Wed, 6 Jun 2018 15:41:49 +0000 (16:41 +0100)]
JAL-2999 refine release notes
Jim Procter [Wed, 6 Jun 2018 15:16:13 +0000 (16:16 +0100)]
JAL-2999 release 2.10.4b1 on Thursday (promise!)
Jim Procter [Wed, 6 Jun 2018 15:15:33 +0000 (16:15 +0100)]
JAL-2920 release notes
Jim Procter [Wed, 6 Jun 2018 15:12:58 +0000 (16:12 +0100)]
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 6 Jun 2018 15:12:17 +0000 (16:12 +0100)]
JAL-2920 revised TODO for JAL-3025
Jim Procter [Wed, 6 Jun 2018 15:06:03 +0000 (16:06 +0100)]
JAL-2920 don’t output variant/original sequence as three-letter codes for more than three bases (pragmatic deviation from HGVC nomenclature)
Jim Procter [Wed, 6 Jun 2018 14:33:19 +0000 (15:33 +0100)]
JAL-2920 JAL-3017 uniprot XML schema included in mappings doc
Jim Procter [Wed, 6 Jun 2018 14:22:53 +0000 (15:22 +0100)]
JAL-1920 JAL-3017 use newline not <br/> in description and update test to cover multi-position variants and newline code
Jim Procter [Wed, 30 May 2018 10:50:19 +0000 (11:50 +0100)]
JAL-3009 news reader thread should be in background. TODO: patch newsreader so it uses GUI thread for displaying itself ?
Jim Procter [Wed, 30 May 2018 10:48:21 +0000 (11:48 +0100)]
JAL-3009 Identifiers.Org retrieval on background thread.
Jim Procter [Sat, 2 Jun 2018 13:17:31 +0000 (14:17 +0100)]
JAL-3017 parse multiple variant elements for uniprot feature
Conflicts:
src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
Merged JAL-3017 into upstream JAL-2920 patches for HGVC nomenclature
note - should properly deal with delins variants http://varnomen.hgvs.org/recommendations/protein/variant/delins/
Jim Procter [Mon, 4 Jun 2018 08:31:41 +0000 (09:31 +0100)]
JAL-2999 update release notes and patch date to 5th June 2018
Jim Procter [Sat, 2 Jun 2018 13:17:31 +0000 (14:17 +0100)]
JAL-3017 parse multiple variant elements for uniprot feature
Jim Procter [Wed, 30 May 2018 10:58:23 +0000 (11:58 +0100)]
JAL-2999 2.10.4b1 release 31st May
Jim Procter [Sat, 26 May 2018 12:36:41 +0000 (13:36 +0100)]
JAL-2999 release date for 2.10.4b1 set for 27th May 2018
Jim Procter [Fri, 25 May 2018 12:58:10 +0000 (13:58 +0100)]
Merge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:58:01 +0000 (13:58 +0100)]
Merge branch 'bug/JAL-2992panelHeight' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:56:34 +0000 (13:56 +0100)]
Merge branch 'bug/JAL-1460_dragndropWindows' into releases/Release_2_10_4_Branch
gmungoc [Fri, 25 May 2018 12:49:33 +0000 (13:49 +0100)]
JAL-2992 simpler heuristic for available height
Jim Procter [Fri, 25 May 2018 10:19:58 +0000 (11:19 +0100)]
Merge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:10:20 +0000 (11:10 +0100)]
Merge branch 'feature/JAL-2994chimeraPath' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:09:33 +0000 (11:09 +0100)]
JAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview
Jim Procter [Fri, 25 May 2018 09:59:51 +0000 (10:59 +0100)]
JAL-2994 add a few future release points for good measure in Chimera path search on Windows
Jim Procter [Fri, 25 May 2018 09:47:32 +0000 (10:47 +0100)]
JAL-1460 temp variable for clearer conditional and some extra brackets for readability only
Jim Procter [Fri, 25 May 2018 09:47:11 +0000 (10:47 +0100)]
JAL-1460 javadoc
gmungoc [Fri, 25 May 2018 08:13:35 +0000 (09:13 +0100)]
JAL-2995 tooltip on fields with double-click to browse for file
gmungoc [Fri, 25 May 2018 08:13:00 +0000 (09:13 +0100)]
JAL-2994 temporary patch with paths to Chimera for Windows
Jim Procter [Thu, 24 May 2018 15:34:34 +0000 (16:34 +0100)]
JAL-2999 issues resolved (or nearly so) for 2.10.4b1
gmungoc [Thu, 24 May 2018 14:59:49 +0000 (15:59 +0100)]
JAL-2997 additional tests
Jim Procter [Thu, 24 May 2018 13:38:59 +0000 (14:38 +0100)]
JAL-1460 tidied up the use of windows link file parser
Jim Procter [Thu, 24 May 2018 12:52:32 +0000 (13:52 +0100)]
JAL-1460 more complete drag'n'drop debugging info and bugfixes
Jim Procter [Thu, 24 May 2018 10:56:32 +0000 (11:56 +0100)]
JAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutHandler class (thanks to StackOverFlow post..)
Jim Procter [Thu, 24 May 2018 10:54:26 +0000 (11:54 +0100)]
JAL-1460 new data flavor for URLs added belt-and-braces URL drop code found in Marinacci and Adamson’s ’Swing Hacks’ (https://books.google.co.uk/books?id=oNbFfcyAtv4C&lpg=PA336&ots=hflsI561Dv&dq=java%20drag%20and%20drop%20url&pg=PA337#v=onepage&q=java%20drag%20and%20drop%20url&f=false ) plus OS X bug workaround.
gmungoc [Wed, 23 May 2018 16:14:17 +0000 (17:14 +0100)]
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel
gmungoc [Wed, 23 May 2018 15:49:53 +0000 (16:49 +0100)]
JAL-2997 unit test
Jim Procter [Wed, 23 May 2018 15:19:56 +0000 (16:19 +0100)]
fix for JAL-2991 - we could do better :/
gmungoc [Wed, 23 May 2018 14:33:08 +0000 (15:33 +0100)]
JAL-2997 handle tab-delimited trailing column number when parsing
Jim Procter [Wed, 23 May 2018 14:18:52 +0000 (15:18 +0100)]
JAL-2999 release notes and version bump for jalview 2.10.4b1
Jim Procter [Wed, 23 May 2018 14:17:45 +0000 (15:17 +0100)]
JAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing built in help pages
gmungoc [Mon, 21 May 2018 11:17:01 +0000 (12:17 +0100)]
JAL-2920 use HGVS notation for protein variant feature
Jim Procter [Thu, 10 May 2018 10:49:14 +0000 (11:49 +0100)]
JAL-2920 release notes
Jim Procter [Thu, 10 May 2018 10:35:44 +0000 (11:35 +0100)]
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 10 May 2018 10:35:11 +0000 (11:35 +0100)]
JAL-2920 basic test for Description from features with/out description, variation and original attributes
Jim Procter [Thu, 10 May 2018 10:34:23 +0000 (11:34 +0100)]
JAL-2920 simplified logic and added corner cases for missing attributes (probably not needed but..)
Jim Procter [Wed, 9 May 2018 19:46:50 +0000 (20:46 +0100)]
JAL-2906 update release date and release notes
Jim Procter [Wed, 9 May 2018 19:46:04 +0000 (20:46 +0100)]
JAL-2931 patch IA paths for new build box
gmungoc [Wed, 9 May 2018 13:59:14 +0000 (14:59 +0100)]
JAL-2984 add pdb as sequence(s) if associate structure is declined
Jim Procter [Wed, 9 May 2018 09:39:51 +0000 (10:39 +0100)]
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 9 May 2018 09:39:19 +0000 (10:39 +0100)]
JAL-2976 fixed bad equivalence check and implemented belt-and-braces check for quaqua in class name string of look and feel to decide when to fallback to violetlib-Aqua.
Jim Procter [Tue, 8 May 2018 09:59:37 +0000 (10:59 +0100)]
JAL-2321 release notes
Jim Procter [Tue, 8 May 2018 09:57:35 +0000 (10:57 +0100)]
Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 7 May 2018 17:08:38 +0000 (18:08 +0100)]
JAL-2321 patch test to ensure structures are actually annotated when loaded directly to desktop
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
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
git://source.jalview.org / jalview.git / log