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 [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
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
git://source.jalview.org / jalview.git / log