kjvdheide [Fri, 17 Nov 2017 15:48:51 +0000 (15:48 +0000)]
JAL-2805 code refactor (actionPerformed cleaned up) & moved tree loading
Jim Procter [Fri, 17 Nov 2017 15:13:58 +0000 (15:13 +0000)]
JAL-2698 source code licencing
Jim Procter [Fri, 17 Nov 2017 14:56:24 +0000 (14:56 +0000)]
JAL-2698 tidy up release notes
kjvdheide [Fri, 17 Nov 2017 14:44:46 +0000 (14:44 +0000)]
JAL-2805 reorganized code, tree building goes through AptxInit for now
kjvdheide [Fri, 17 Nov 2017 14:43:11 +0000 (14:43 +0000)]
JAL-2795 removed unneeded distancematrix length/width check
kjvdheide [Fri, 17 Nov 2017 14:41:40 +0000 (14:41 +0000)]
JAL-2844 changed Aptx config to make all cladogram branches aligned
Jim Procter [Fri, 17 Nov 2017 14:40:37 +0000 (14:40 +0000)]
JAL-2698 Cached PDB Entries -> Cached Structures in UI and help doc
Jim Procter [Fri, 17 Nov 2017 13:52:03 +0000 (13:52 +0000)]
JAL-2466 revised help text for sort by PID
Jim Procter [Fri, 17 Nov 2017 13:51:25 +0000 (13:51 +0000)]
JAL-2698 what’s new and release notes
kjvdheide [Fri, 17 Nov 2017 13:34:22 +0000 (13:34 +0000)]
Merge branch 'kjvdh/features/PhylogenyViewer' of
https://source.jalview.org/git/jalview.git into
kjvdh/features/PhylogenyViewer
Conflicts:
src/jalview/ext/archaeopteryx/AptxBinding.java
src/jalview/ext/forester/io/ExternalTreeParserI.java
src/jalview/ext/forester/io/ForesterTreeParser.java
Jim Procter [Fri, 17 Nov 2017 13:24:33 +0000 (13:24 +0000)]
JAL-2822 known defect for 2.10.3
Jim Procter [Fri, 17 Nov 2017 13:16:10 +0000 (13:16 +0000)]
Merge branch 'bug/JAL-2784' into develop
Jim Procter [Fri, 17 Nov 2017 13:15:20 +0000 (13:15 +0000)]
JAL-2841 JAL-2791 new known defect
Jim Procter [Fri, 17 Nov 2017 13:08:56 +0000 (13:08 +0000)]
JAL-2541 known defect
kjvdheide [Fri, 17 Nov 2017 13:07:27 +0000 (13:07 +0000)]
JAL-2805 couple of method name changes
Jim Procter [Fri, 17 Nov 2017 13:03:05 +0000 (13:03 +0000)]
JAL-2684 clarify release notes
Jim Procter [Fri, 17 Nov 2017 12:31:58 +0000 (12:31 +0000)]
Merge branch 'bug/JAL-2821' into develop
Jim Procter [Fri, 17 Nov 2017 12:26:42 +0000 (12:26 +0000)]
JAL-2840 release notes
Jim Procter [Fri, 17 Nov 2017 12:21:17 +0000 (12:21 +0000)]
Merge branch 'bug/JAL-2837' into develop
kiramt [Fri, 17 Nov 2017 12:14:59 +0000 (12:14 +0000)]
Merge branch 'develop' into bug/JAL-2837
Conflicts:
src/jalview/gui/SeqPanel.java
Jim Procter [Fri, 17 Nov 2017 12:14:21 +0000 (12:14 +0000)]
Merge branch 'doc/JAL-2494_JAL-2828_mergefindAnnotation' into develop
kiramt [Fri, 17 Nov 2017 12:09:20 +0000 (12:09 +0000)]
Merge branch 'develop' into bug/JAL-2837
Jim Procter [Fri, 17 Nov 2017 11:56:59 +0000 (11:56 +0000)]
JAL-2811 release note
Jim Procter [Fri, 17 Nov 2017 11:47:51 +0000 (11:47 +0000)]
JAL-2541 not in 2.10.3, JAL-2831 signed off.
Jim Procter [Fri, 17 Nov 2017 11:47:25 +0000 (11:47 +0000)]
JAL-2698 11th hour release today
Jim Procter [Fri, 17 Nov 2017 11:28:43 +0000 (11:28 +0000)]
Merge branch 'bug/JAL-2831' into develop
kjvdheide [Fri, 17 Nov 2017 02:24:58 +0000 (02:24 +0000)]
JAL-281 added menu items and listeners to load from URL/Db
kjvdheide [Fri, 17 Nov 2017 01:49:47 +0000 (01:49 +0000)]
JAL-281 changed load associated tree GUI item to menu selection
Jim Procter [Thu, 16 Nov 2017 16:50:03 +0000 (16:50 +0000)]
JAL-2541 JAL-2829 JAL-2830 JAL-2822 catch all release note entry for sequence feature relocation
Jim Procter [Thu, 16 Nov 2017 16:45:35 +0000 (16:45 +0000)]
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into develop
kiramt [Thu, 16 Nov 2017 11:57:15 +0000 (11:57 +0000)]
JAL-2831 Removed unwanted hidden sequences checks
kjvdheide [Thu, 16 Nov 2017 11:38:47 +0000 (11:38 +0000)]
JAL-2805 expanded tree and treenode interfaces
kjvdheide [Thu, 16 Nov 2017 11:30:08 +0000 (11:30 +0000)]
JAL-2805 loads of file reorganizing, interfaces expanded
kiramt [Thu, 16 Nov 2017 09:12:06 +0000 (09:12 +0000)]
JAL-2842 remove infinite loop in cursor move
kiramt [Wed, 15 Nov 2017 16:22:21 +0000 (16:22 +0000)]
JAL-2831 Don't show cursor if position in hidden region
kiramt [Wed, 15 Nov 2017 16:05:18 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Wed, 15 Nov 2017 13:23:00 +0000 (13:23 +0000)]
JAL-2811 Updated following review
kiramt [Wed, 15 Nov 2017 11:44:44 +0000 (11:44 +0000)]
JAL-2840 fix wrapped scrolling when using cursor at a hidden region
kiramt [Wed, 15 Nov 2017 11:17:41 +0000 (11:17 +0000)]
JAL-2834 JAL-2836 temporarily disabled wrapped mode fastpaint
kjvdheide [Wed, 15 Nov 2017 10:39:47 +0000 (10:39 +0000)]
JAL-2805 functional binding on loading associated trees
kiramt [Wed, 15 Nov 2017 08:47:47 +0000 (08:47 +0000)]
JAL-2831 ported to applet
kiramt [Tue, 14 Nov 2017 19:36:53 +0000 (19:36 +0000)]
JAL-2831 tidies and tests
kjvdheide [Tue, 14 Nov 2017 17:17:50 +0000 (17:17 +0000)]
JAL-2805 viewport is passed along to the tree parser
kjvdheide [Tue, 14 Nov 2017 17:17:04 +0000 (17:17 +0000)]
JAL-2795 added duplication check when calculated nodes are bound to seqs
kjvdheide [Tue, 14 Nov 2017 17:15:54 +0000 (17:15 +0000)]
JAL-2805 added getters for hashmaps filled with associated seqs/nodes
kjvdheide [Tue, 14 Nov 2017 16:57:36 +0000 (16:57 +0000)]
JAL-2805 added static method for logging duplications when using map.put
kjvdheide [Tue, 14 Nov 2017 16:56:50 +0000 (16:56 +0000)]
JAL-2805 more sensible interface method params
kiramt [Tue, 14 Nov 2017 16:03:47 +0000 (16:03 +0000)]
JAL-2831 tidy
kjvdheide [Tue, 14 Nov 2017 16:00:29 +0000 (16:00 +0000)]
JAL-2805 finished up interface comments
kjvdheide [Tue, 14 Nov 2017 15:31:49 +0000 (15:31 +0000)]
JAL-2805 re-enabled one2many checks
kjvdheide [Tue, 14 Nov 2017 15:28:56 +0000 (15:28 +0000)]
JAL-2805 interface comments, progress on associating leaves
kiramt [Tue, 14 Nov 2017 14:59:52 +0000 (14:59 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 14:56:37 +0000 (14:56 +0000)]
JAL-2811 Changed to overlay on via graphics context, not separate image
kiramt [Tue, 14 Nov 2017 14:10:30 +0000 (14:10 +0000)]
JAL-2811 Missed commit
kiramt [Tue, 14 Nov 2017 13:43:40 +0000 (13:43 +0000)]
JAL-2811 Made it work for hidden columns/seqs too
kiramt [Tue, 14 Nov 2017 12:11:21 +0000 (12:11 +0000)]
JAL-2831 Attempt at cursor fix for wrapped mode
Jim Procter [Tue, 14 Nov 2017 12:11:04 +0000 (12:11 +0000)]
JAL-2758 update uniprot retrieval test
kiramt [Tue, 14 Nov 2017 11:12:55 +0000 (11:12 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 10:33:33 +0000 (10:33 +0000)]
JAL-2831 deal with hidden cols and seqs in new cursor code
kiramt [Tue, 14 Nov 2017 10:15:46 +0000 (10:15 +0000)]
JAL-2831 Added move viewport event and set up cursor code to use it
kiramt [Tue, 14 Nov 2017 09:30:31 +0000 (09:30 +0000)]
Merge branch 'imp/JAL-2774' into bug/JAL-2831
Jim Procter [Mon, 13 Nov 2017 20:25:06 +0000 (20:25 +0000)]
JAL-2758 release notes
Jim Procter [Mon, 13 Nov 2017 20:22:01 +0000 (20:22 +0000)]
JAL-2698 formatting
kjvdheide [Mon, 13 Nov 2017 20:19:43 +0000 (20:19 +0000)]
JAL-2805 interface comments
kjvdheide [Mon, 13 Nov 2017 20:07:06 +0000 (20:07 +0000)]
JAL-2805 some more name changes
kjvdheide [Mon, 13 Nov 2017 20:03:31 +0000 (20:03 +0000)]
JAL-2805 more name changes for clarity
kjvdheide [Mon, 13 Nov 2017 19:56:05 +0000 (19:56 +0000)]
JAL-2805 more interface name changing
kjvdheide [Mon, 13 Nov 2017 19:55:14 +0000 (19:55 +0000)]
JAL-2805 name changed of interfaces for consistency
kjvdheide [Mon, 13 Nov 2017 19:47:19 +0000 (19:47 +0000)]
JAL-2805 Jalview sequence binding interface expanded
kjvdheide [Mon, 13 Nov 2017 19:46:17 +0000 (19:46 +0000)]
JAL-2805 TreeParser now interface based
kiramt [Mon, 13 Nov 2017 19:40:06 +0000 (19:40 +0000)]
JAL-2811 Tidy
kjvdheide [Mon, 13 Nov 2017 19:34:25 +0000 (19:34 +0000)]
JAL-2805 Added tree building interface
kjvdheide [Mon, 13 Nov 2017 19:22:02 +0000 (19:22 +0000)]
JAL-2805 name change
kjvdheide [Mon, 13 Nov 2017 19:19:10 +0000 (19:19 +0000)]
JAL-2805 deleted old Aptx class for loading just Newick files
kjvdheide [Mon, 13 Nov 2017 19:16:43 +0000 (19:16 +0000)]
JAL-2805 more interface work
kjvdheide [Mon, 13 Nov 2017 19:03:58 +0000 (19:03 +0000)]
JAL-2794 removed unused interface
kjvdheide [Mon, 13 Nov 2017 19:02:16 +0000 (19:02 +0000)]
JAL-2805 undid accidental double (buggy) binding, more interface support
Jim Procter [Mon, 13 Nov 2017 18:59:59 +0000 (18:59 +0000)]
Merge branch 'features/JAL-2758_shorteruniprot' into develop
Jim Procter [Mon, 13 Nov 2017 18:57:10 +0000 (18:57 +0000)]
JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name
Jim Procter [Mon, 13 Nov 2017 18:56:22 +0000 (18:56 +0000)]
JAL-2758 typo
kiramt [Mon, 13 Nov 2017 16:42:20 +0000 (16:42 +0000)]
JAl-2811 Working for wrapped panels too
gmungoc [Mon, 13 Nov 2017 16:23:12 +0000 (16:23 +0000)]
JAL-2662 tweak README, format code
Jim Procter [Mon, 13 Nov 2017 16:05:37 +0000 (16:05 +0000)]
JAL-2698 what's new...
kiramt [Mon, 13 Nov 2017 15:53:12 +0000 (15:53 +0000)]
JAL-2811 Add layer for cursor in SeqCanvas
kjvdheide [Mon, 13 Nov 2017 15:43:56 +0000 (15:43 +0000)]
JAL-2805 warning messages added if Forester detects file loading issues
Jim Procter [Mon, 13 Nov 2017 15:41:10 +0000 (15:41 +0000)]
JAL-2810 release notes
Jim Procter [Mon, 13 Nov 2017 15:38:34 +0000 (15:38 +0000)]
Merge branch 'imp/JAL-2810_ftsIDtab' into develop
kjvdheide [Mon, 13 Nov 2017 14:22:27 +0000 (14:22 +0000)]
JAL-2805 First try at loading tree through Forester by calling Aptx main
Added file filters for Forester supported tree formats to the file
chooser window and Forester tree parser in the ActionPerformed of
loading an associated tree, also see Forester commits for more details
Jim Procter [Mon, 13 Nov 2017 15:32:05 +0000 (15:32 +0000)]
JAL-2698 stub for 2.10.3 new known issues entries
Jim Procter [Mon, 13 Nov 2017 15:31:05 +0000 (15:31 +0000)]
JAL-2702 groovy interpreter update and java 9 jnlp release notes
Jim Procter [Mon, 13 Nov 2017 15:03:27 +0000 (15:03 +0000)]
Merge branch 'bug/JAL-2702_groovyconsoleJava9' into develop
Jim Procter [Mon, 13 Nov 2017 14:33:06 +0000 (14:33 +0000)]
JAL-2702 --illegal-access=warn for JVM launch
gmungoc [Mon, 13 Nov 2017 14:11:08 +0000 (14:11 +0000)]
JAL-2176 removed unused Sequence.index
Jim Procter [Mon, 13 Nov 2017 13:52:48 +0000 (13:52 +0000)]
JAL-2702 update to groovy 2.4.12
Jim Procter [Mon, 13 Nov 2017 13:00:17 +0000 (13:00 +0000)]
JAL-2810 updated help docs for auto search checkbox and retrieve IDs tab
kiramt [Mon, 13 Nov 2017 12:46:37 +0000 (12:46 +0000)]
JAL-2784 new checks for gg==null
Jim Procter [Mon, 13 Nov 2017 12:44:08 +0000 (12:44 +0000)]
JAL-2810 updated screenshots in documentation
Jim Procter [Mon, 13 Nov 2017 12:43:38 +0000 (12:43 +0000)]
JAL-2810 auto search checkbox state stored as user preference. Enabled by default.
gmungoc [Mon, 13 Nov 2017 12:02:43 +0000 (12:02 +0000)]
JAL-2679 example accession changed to
CAD01290
Jim Procter [Mon, 13 Nov 2017 11:53:27 +0000 (11:53 +0000)]
JAL-2810 mainFramTabs -> tabs
git://source.jalview.org / jalview.git / log