kjvdheide [Tue, 9 Jan 2018 11:18:07 +0000 (11:18 +0000)]
JAL-2805 added nexus specific parser settings
kjvdheide [Tue, 9 Jan 2018 10:54:54 +0000 (10:54 +0000)]
JAL-2805 broke off the phylogenetic file formats into separate classes
kjvdheide [Tue, 9 Jan 2018 10:53:43 +0000 (10:53 +0000)]
JAL-2805 parser is now File based (instead of FileParse) and source is
now properly set
kjvdheide [Tue, 9 Jan 2018 10:53:01 +0000 (10:53 +0000)]
JAL-2805 Parse returns a TreeI array again
kjvdheide [Tue, 9 Jan 2018 10:52:16 +0000 (10:52 +0000)]
JAL-2805 node sequence is now immediately filled in by the constructor
kjvdheide [Tue, 9 Jan 2018 10:51:36 +0000 (10:51 +0000)]
JAL-2805 added forester --> jalview sequence converter
kjvdheide [Tue, 9 Jan 2018 10:21:01 +0000 (10:21 +0000)]
JAL-2805 added getter in trees for retrieving all node sequences
kjvdheide [Tue, 9 Jan 2018 10:20:04 +0000 (10:20 +0000)]
JAL-1953 moved DataConversions to Forester package
kjvdheide [Mon, 8 Jan 2018 11:10:22 +0000 (11:10 +0000)]
JAL-2844 changed threshold from double to float
kjvdheide [Mon, 8 Jan 2018 11:07:35 +0000 (11:07 +0000)]
JAL-2844 start on moving tree partitioning code into Forester
kjvdheide [Sat, 6 Jan 2018 22:43:52 +0000 (22:43 +0000)]
JAL-2877 added forester as jar once again
kjvdheide [Sat, 6 Jan 2018 22:36:39 +0000 (22:36 +0000)]
JAL-281 first line also checked for PhyloXML identification
kjvdheide [Sat, 6 Jan 2018 22:11:18 +0000 (22:11 +0000)]
JAL-2871 aptx Configuration now created through input stream
kjvdheide [Fri, 5 Jan 2018 04:00:58 +0000 (04:00 +0000)]
JAL-281 ForesterParser now extends from AlignFile
kjvdheide [Thu, 4 Jan 2018 20:18:36 +0000 (20:18 +0000)]
JAL-1953 Moved config to resources folder
kjvdheide [Thu, 4 Jan 2018 20:17:49 +0000 (20:17 +0000)]
JAL-281 ForesterParser factory methods added
kjvdheide [Sun, 31 Dec 2017 18:41:49 +0000 (18:41 +0000)]
JAL-1953 start work on storing nodes in a map per tree object instead of
all together in a static map
kjvdheide [Thu, 21 Dec 2017 16:25:55 +0000 (16:25 +0000)]
JAL-281 added file identify criteria for PhyloXML and Nexus
kjvdheide [Wed, 20 Dec 2017 18:40:31 +0000 (18:40 +0000)]
JAL-2874 made the actionlistener slightly clearer
kjvdheide [Wed, 20 Dec 2017 18:04:25 +0000 (18:04 +0000)]
JAL-2838 JAL-2872 added sorting from the Aptx frame (still misbehaving
with
multiple alignment views)
kjvdheide [Wed, 20 Dec 2017 14:20:29 +0000 (14:20 +0000)]
JAL-281 moved utility methods to .io package
kjvdheide [Wed, 20 Dec 2017 13:24:41 +0000 (13:24 +0000)]
JAL-281 split up TreeParser into separate format parsers
kjvdheide [Tue, 19 Dec 2017 14:34:24 +0000 (14:34 +0000)]
JAL-281 created Nexus and PhyloXML parser classes
kjvdheide [Tue, 19 Dec 2017 14:16:49 +0000 (14:16 +0000)]
JAL-281 cleared out useless tree parser class
kjvdheide [Tue, 19 Dec 2017 14:10:26 +0000 (14:10 +0000)]
JAL-281 added phyloxml and nexus to jalview fileformats
kjvdheide [Mon, 18 Dec 2017 18:30:14 +0000 (18:30 +0000)]
JAL-1953 moved now-generic methods outside of Aptx package
kjvdheide [Mon, 18 Dec 2017 18:21:35 +0000 (18:21 +0000)]
JAL-1953 -External from all interfaces names
kjvdheide [Mon, 18 Dec 2017 18:18:33 +0000 (18:18 +0000)]
JAL-1953 attempt at changing Aptx's font to Jalview's
kjvdheide [Mon, 18 Dec 2017 18:18:03 +0000 (18:18 +0000)]
JAL-2844 cladogram no longer vertically aligned (was rather confusing)
kjvdheide [Mon, 18 Dec 2017 18:04:15 +0000 (18:04 +0000)]
Merge branch 'kjvdh/features/PhylogenyViewer' of
https://source.jalview.org/git/jalview.git into
kjvdh/features/PhylogenyViewer
kjvdheide [Mon, 18 Dec 2017 15:50:59 +0000 (15:50 +0000)]
JAL-2844 made null tree nodes return null wrappers so partitioning works
kjvdheide [Mon, 18 Dec 2017 15:37:19 +0000 (15:37 +0000)]
Merge branch 'kjvdh/features/PhylogenyViewer' into
kjvdh/features/PhylogenyViewerInterfaces
Conflicts:
src/jalview/ext/archaeopteryx/AptxFrame.java
src/jalview/ext/archaeopteryx/AptxInit.java
src/jalview/ext/archaeopteryx/AptxTreePanel.java
src/jalview/ext/archaeopteryx/JalviewBinding.java
src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java
src/jalview/ext/archaeopteryx/Tree.java
src/jalview/ext/archaeopteryx/TreeNode.java
src/jalview/ext/treeviewer/ExternalTreeParserI.java
src/jalview/ext/treeviewer/ExternalTreeViewerFrameI.java
kjvdheide [Mon, 18 Dec 2017 15:08:51 +0000 (15:08 +0000)]
JAL-1953 redundant tree interface instantiation removed
kjvdheide [Fri, 15 Dec 2017 20:00:30 +0000 (20:00 +0000)]
JAL-2852 EPS saving code ported from TreePanel to Aptx.
kjvdheide [Fri, 15 Dec 2017 16:58:30 +0000 (16:58 +0000)]
JAL-1953 added Y coordinate getter method
kjvdheide [Fri, 15 Dec 2017 16:07:57 +0000 (16:07 +0000)]
JAL-2852 merged the EPS button adding from main branch into interfaces
kjvdheide [Fri, 15 Dec 2017 16:06:57 +0000 (16:06 +0000)]
JAL-1953 node comparing now includes checking node IDs to prevent false
duplicate keys in the node hashmaps
kjvdheide [Fri, 15 Dec 2017 14:54:12 +0000 (14:54 +0000)]
JAL-1953 removed deprecated interfaces
kjvdheide [Fri, 15 Dec 2017 14:53:35 +0000 (14:53 +0000)]
JAL-2852 added EPS export button to File menu
kjvdheide [Thu, 14 Dec 2017 17:00:12 +0000 (17:00 +0000)]
JAL-1953 more progress on interfaces, jalview binding still problematic
kjvdheide [Tue, 12 Dec 2017 18:40:05 +0000 (18:40 +0000)]
JAL-2874 filtering alignment now also works when just zoomed in
kjvdheide [Tue, 12 Dec 2017 18:03:37 +0000 (18:03 +0000)]
JAL-2874 added filtering when a subtree is selected
kjvdheide [Tue, 12 Dec 2017 10:51:13 +0000 (10:51 +0000)]
Merge branch 'kjvdh/features/PhylogenyViewer' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 12 Dec 2017 10:37:19 +0000 (10:37 +0000)]
JAL-2877 disabled Jalview's own viewer for testing
kjvdheide [Mon, 11 Dec 2017 20:58:28 +0000 (20:58 +0000)]
JAL-2872 hide sort button in Aptx unless it's actually possible
kjvdheide [Mon, 11 Dec 2017 20:57:51 +0000 (20:57 +0000)]
JAL-2877 disabled Jalview's default tree viewer when loading files
kjvdheide [Mon, 11 Dec 2017 20:43:08 +0000 (20:43 +0000)]
JAL-1953 fixed interface misnaming
kjvdheide [Mon, 11 Dec 2017 20:34:15 +0000 (20:34 +0000)]
JAL-1953 start on making everything interface based
kjvdheide [Fri, 8 Dec 2017 17:35:06 +0000 (17:35 +0000)]
JAL-1953 renaming of concrete implementation as well
kjvdheide [Fri, 8 Dec 2017 13:47:57 +0000 (13:47 +0000)]
JAL-2844 reallow clicks to the left of the root (groups whole tree as 1)
kjvdheide [Thu, 7 Dec 2017 16:22:08 +0000 (16:22 +0000)]
JAL-2866 and .jar removed again
kjvdheide [Thu, 7 Dec 2017 15:40:54 +0000 (15:40 +0000)]
JAL-2866 forester .jar added to lib
kjvdheide [Thu, 7 Dec 2017 14:24:14 +0000 (14:24 +0000)]
JAL-2872 Redundant Aptx GUI menu items hidden, sorting item added
kjvdheide [Wed, 6 Dec 2017 16:07:42 +0000 (16:07 +0000)]
JAL-2794 disabled branch colors on selection for now
kjvdheide [Wed, 6 Dec 2017 16:03:34 +0000 (16:03 +0000)]
JAL-2871 Added check whether configuration has been loaded in
kjvdheide [Tue, 5 Dec 2017 16:08:42 +0000 (16:08 +0000)]
JAL-2838 Sorting from the alignment view menu now functional
kjvdheide [Tue, 5 Dec 2017 16:07:05 +0000 (16:07 +0000)]
JAL-2847 Rearranging and cleaning up of database query code
kjvdheide [Tue, 5 Dec 2017 15:25:02 +0000 (15:25 +0000)]
JAL-2794 associate leaves now iterates through ALL nodes (also internal)
kjvdheide [Tue, 5 Dec 2017 14:21:04 +0000 (14:21 +0000)]
JAL-2847 various error popups for db querying now have formatted strings
kjvdheide [Tue, 5 Dec 2017 13:45:24 +0000 (13:45 +0000)]
JAL-2847 Strings for the various tree databases added
kjvdheide [Tue, 5 Dec 2017 13:02:07 +0000 (13:02 +0000)]
JAL-2847 if pfam id is detected in first sequence its shown in db query
kjvdheide [Tue, 5 Dec 2017 12:39:23 +0000 (12:39 +0000)]
JAL-2847 added pfam to DBRef source name lookup
kjvdheide [Tue, 5 Dec 2017 11:29:52 +0000 (11:29 +0000)]
JAL-2805 JAL-2847 JAL-281 added file path to Aptx frame title
kjvdheide [Tue, 5 Dec 2017 10:07:27 +0000 (10:07 +0000)]
JAL-2838 tree viewer interface expanded to include sorting
kjvdheide [Tue, 5 Dec 2017 10:06:24 +0000 (10:06 +0000)]
Merge remote-tracking branch 'origin/develop' into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 5 Dec 2017 03:50:27 +0000 (03:50 +0000)]
JAL-2838 filled in actionPerformed of the tree sort menu items
kjvdheide [Tue, 5 Dec 2017 03:29:43 +0000 (03:29 +0000)]
JAL-2838 Aptx frames now appear in the alignment sorting menu
kjvdheide [Sun, 3 Dec 2017 16:30:05 +0000 (16:30 +0000)]
JAL-2847 start of cleaning up db loading code
kjvdheide [Sun, 3 Dec 2017 14:56:38 +0000 (14:56 +0000)]
JAL-2844 rearranging code
Jim Procter [Thu, 30 Nov 2017 12:04:15 +0000 (12:04 +0000)]
JAL-2849 release notes
Jim Procter [Thu, 30 Nov 2017 11:34:22 +0000 (11:34 +0000)]
Merge branch 'bug/JAL-2849' into develop
Jim Procter [Thu, 30 Nov 2017 11:34:02 +0000 (11:34 +0000)]
JAL-2849 JAL-2863 file format preferences TODO
Jim Procter [Thu, 30 Nov 2017 11:28:36 +0000 (11:28 +0000)]
JAL-2849 fix
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 15:18:14 +0000 (15:18 +0000)]
Merge branch 'bug/JAL-2859_uniprottowrongpdbid' into develop
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 22:09:45 +0000 (22:09 +0000)]
JAL-2859 disambiguate with PDB ID if no file path
Jim Procter [Mon, 27 Nov 2017 22:07:07 +0000 (22:07 +0000)]
JAL-2859 failing test demonstrating sequences with pdb without a local file map all get mapped together
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
git://source.jalview.org / jalview.git / log