kjvdheide [Sun, 3 Dec 2017 14:56:38 +0000 (14:56 +0000)]
JAL-2844 rearranging code
kjvdheide [Wed, 29 Nov 2017 17:45:42 +0000 (17:45 +0000)]
JAL-2844 check added for clicks left of root node
kjvdheide [Wed, 29 Nov 2017 17:32:12 +0000 (17:32 +0000)]
JAL-2844 entirely X coord based partitioning
kjvdheide [Wed, 29 Nov 2017 13:20:07 +0000 (13:20 +0000)]
JAL-2844 somewhat better repainting
kjvdheide [Wed, 29 Nov 2017 12:07:49 +0000 (12:07 +0000)]
JAL-2844 temporary kludge to draw a line
kjvdheide [Wed, 29 Nov 2017 12:01:17 +0000 (12:01 +0000)]
JAL-2844 added grouping to alignment panel based on partition
kjvdheide [Wed, 29 Nov 2017 03:02:14 +0000 (03:02 +0000)]
JAL-2844 start on colouring back onto the alignment
kjvdheide [Wed, 29 Nov 2017 02:28:54 +0000 (02:28 +0000)]
JAL-2844 added colouring to partition selection
kjvdheide [Tue, 28 Nov 2017 18:06:57 +0000 (18:06 +0000)]
JAL-2844 added offset to x coord to make it equal 0 at the root node
kjvdheide [Tue, 28 Nov 2017 17:47:50 +0000 (17:47 +0000)]
Merge remote-tracking branch 'origin/develop' into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 28 Nov 2017 17:31:28 +0000 (17:31 +0000)]
JAL-2844 first go at partitioning, based on actual tree width
Jim Procter [Tue, 28 Nov 2017 15:06:57 +0000 (15:06 +0000)]
JAL-2740 release notes
Jim Procter [Tue, 28 Nov 2017 14:55:23 +0000 (14:55 +0000)]
Merge branch 'bug/JAL-2740' into develop
Jim Procter [Tue, 28 Nov 2017 14:53:51 +0000 (14:53 +0000)]
JAL-2827 release notes
Jim Procter [Tue, 28 Nov 2017 14:45:15 +0000 (14:45 +0000)]
Merge branch 'bug/JAL-2827' into develop
Jim Procter [Tue, 28 Nov 2017 14:42:00 +0000 (14:42 +0000)]
JAL-2842 release notes
Jim Procter [Tue, 28 Nov 2017 14:24:05 +0000 (14:24 +0000)]
Merge branch 'bug/JAL-2842' into develop
Jim Procter [Mon, 27 Nov 2017 18:46:19 +0000 (18:46 +0000)]
JAL-2851 JAL-2858 release notes for 2.10.3b1
Jim Procter [Mon, 27 Nov 2017 17:18:43 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-2851' into develop
kjvdheide [Mon, 27 Nov 2017 17:08:57 +0000 (17:08 +0000)]
JAL-2852 JAL-2853 forester update
kjvdheide [Mon, 27 Nov 2017 17:07:20 +0000 (17:07 +0000)]
JAL-2844 added selection threshold (non-adjusted calculation for now)
kjvdheide [Mon, 27 Nov 2017 16:25:40 +0000 (16:25 +0000)]
JAL-2799 re-enabled change listener for Aptx's tabs (for future work)
kjvdheide [Mon, 27 Nov 2017 16:20:14 +0000 (16:20 +0000)]
JAL-2844 line drawing at mouse click added on top of Aptx
kjvdheide [Mon, 27 Nov 2017 16:18:17 +0000 (16:18 +0000)]
JAL-2853 colours now enabled by default in Aptx
kjvdheide [Sun, 26 Nov 2017 23:08:21 +0000 (23:08 +0000)]
JAL-2847 first rough attempt at loading in via database ID
kjvdheide [Fri, 24 Nov 2017 19:29:23 +0000 (19:29 +0000)]
JAL-2799 rearranged AptxInit code
kjvdheide [Fri, 24 Nov 2017 19:12:41 +0000 (19:12 +0000)]
JAL-2799 ALL trees are now loaded in as separate Aptx instances
kjvdheide [Fri, 24 Nov 2017 18:46:59 +0000 (18:46 +0000)]
JAL-2794 binding now exclusively supports single tab Aptx views
kjvdheide [Fri, 24 Nov 2017 16:37:00 +0000 (16:37 +0000)]
Merge branch 'kjvdh/features/PhylogenyViewer' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Fri, 24 Nov 2017 16:36:35 +0000 (16:36 +0000)]
JAL-2838 start on sorting
kjvdheide [Fri, 24 Nov 2017 11:39:37 +0000 (11:39 +0000)]
JAL-2838 made getAssociatedPanels public
kiramt [Thu, 23 Nov 2017 11:52:01 +0000 (11:52 +0000)]
Merge branch 'develop' into bug/JAL-2851
kiramt [Thu, 23 Nov 2017 11:50:39 +0000 (11:50 +0000)]
JAL-2851 Fix merge error breaking vertical scrolling
kjvdheide [Wed, 22 Nov 2017 19:04:54 +0000 (19:04 +0000)]
JAL-2794 reworked, everything routes via avport.sendselection now
kjvdheide [Wed, 22 Nov 2017 18:01:13 +0000 (18:01 +0000)]
JAL-2794 removed several redundancies in the binding code
kjvdheide [Wed, 22 Nov 2017 14:06:57 +0000 (14:06 +0000)]
JAL-281 fixed misplaced quote in example text
kjvdheide [Wed, 22 Nov 2017 14:06:25 +0000 (14:06 +0000)]
JAL-2844 mouse press code rearranged to prepare for tree partitioning
kjvdheide [Wed, 22 Nov 2017 13:21:37 +0000 (13:21 +0000)]
JAL-2847 small things, filled in actionperformeds
kjvdheide [Wed, 22 Nov 2017 10:52:10 +0000 (10:52 +0000)]
JAL-2799 fixed selections not carrying over to tabs with invokeLater
kjvdheide [Tue, 21 Nov 2017 15:37:56 +0000 (15:37 +0000)]
JAL-2847 added database menu items and listeners
kjvdheide [Tue, 21 Nov 2017 13:12:14 +0000 (13:12 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_3_Branch' into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 21 Nov 2017 13:09:35 +0000 (13:09 +0000)]
JAL-281 added string label for loading from database
Jim Procter [Mon, 20 Nov 2017 16:17:26 +0000 (16:17 +0000)]
JAL-2698 only allow InstallAnywhere launches with version 1.8.* of java - java 9 JVM args not yet working for 2.10.3
kjvdheide [Mon, 20 Nov 2017 15:32:02 +0000 (15:32 +0000)]
Merge remote-tracking branch 'origin/releases/Release_2_10_3_Branch'
into kjvdh/features/PhylogenyViewer
Conflicts:
.classpath
Jim Procter [Mon, 20 Nov 2017 14:44:16 +0000 (14:44 +0000)]
JAL-2698 patch path for InstallAnywhere build. Webstart and source builds unchanged
kjvdheide [Mon, 20 Nov 2017 11:13:36 +0000 (11:13 +0000)]
JAL-2799 JAL-2805 JAL-281 multiple trees can now be loaded in
kjvdheide [Mon, 20 Nov 2017 09:35:38 +0000 (09:35 +0000)]
JAL-281 added history box to tree url input window
kjvdheide [Fri, 17 Nov 2017 17:57:31 +0000 (17:57 +0000)]
JAL-281 option pane with error handling for selecting an URL
Jim Procter [Fri, 17 Nov 2017 21:29:19 +0000 (21:29 +0000)]
JAL-2698 tidy release notes and whats new
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
git://source.jalview.org / jalview.git / log