jalview.git
2018-01-09 kjvdheideJAL-2805 added nexus specific parser settings
2018-01-09 kjvdheideJAL-2805 broke off the phylogenetic file formats into...
2018-01-09 kjvdheideJAL-2805 parser is now File based (instead of FileParse...
2018-01-09 kjvdheideJAL-2805 Parse returns a TreeI array again
2018-01-09 kjvdheideJAL-2805 node sequence is now immediately filled in...
2018-01-09 kjvdheideJAL-2805 added forester --> jalview sequence converter
2018-01-09 kjvdheideJAL-2805 added getter in trees for retrieving all node...
2018-01-09 kjvdheideJAL-1953 moved DataConversions to Forester package
2018-01-08 kjvdheideJAL-2844 changed threshold from double to float
2018-01-08 kjvdheideJAL-2844 start on moving tree partitioning code into...
2018-01-06 kjvdheideJAL-2877 added forester as jar once again
2018-01-06 kjvdheideJAL-281 first line also checked for PhyloXML identification
2018-01-06 kjvdheideJAL-2871 aptx Configuration now created through input...
2018-01-05 kjvdheideJAL-281 ForesterParser now extends from AlignFile
2018-01-04 kjvdheideJAL-1953 Moved config to resources folder
2018-01-04 kjvdheideJAL-281 ForesterParser factory methods added
2018-01-02 kjvdheideJAL-1953 start work on storing nodes in a map per tree...
2017-12-21 kjvdheideJAL-281 added file identify criteria for PhyloXML and...
2017-12-20 kjvdheideJAL-2874 made the actionlistener slightly clearer
2017-12-20 kjvdheideJAL-2838 JAL-2872 added sorting from the Aptx frame...
2017-12-20 kjvdheideJAL-281 moved utility methods to .io package
2017-12-20 kjvdheideJAL-281 split up TreeParser into separate format parsers
2017-12-19 kjvdheideJAL-281 created Nexus and PhyloXML parser classes
2017-12-19 kjvdheideJAL-281 cleared out useless tree parser class
2017-12-19 kjvdheideJAL-281 added phyloxml and nexus to jalview fileformats
2017-12-18 kjvdheideJAL-1953 moved now-generic methods outside of Aptx...
2017-12-18 kjvdheideJAL-1953 -External from all interfaces names
2017-12-18 kjvdheideJAL-1953 attempt at changing Aptx's font to Jalview's
2017-12-18 kjvdheideJAL-2844 cladogram no longer vertically aligned (was...
2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of
2017-12-18 kjvdheideJAL-2844 made null tree nodes return null wrappers...
2017-12-18 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' into
2017-12-18 kjvdheideJAL-1953 redundant tree interface instantiation removed
2017-12-15 kjvdheideJAL-2852 EPS saving code ported from TreePanel to Aptx.
2017-12-15 kjvdheideJAL-1953 added Y coordinate getter method
2017-12-15 kjvdheideJAL-2852 merged the EPS button adding from main branch...
2017-12-15 kjvdheideJAL-1953 node comparing now includes checking node...
2017-12-15 kjvdheideJAL-1953 removed deprecated interfaces
2017-12-15 kjvdheideJAL-2852 added EPS export button to File menu
2017-12-14 kjvdheideJAL-1953 more progress on interfaces, jalview binding...
2017-12-12 kjvdheideJAL-2874 filtering alignment now also works when just...
2017-12-12 kjvdheideJAL-2874 added filtering when a subtree is selected
2017-12-12 kjvdheideMerge branch 'kjvdh/features/PhylogenyViewer' of https...
2017-12-12 kjvdheideJAL-2877 disabled Jalview's own viewer for testing spikes/thomas
2017-12-11 kjvdheideJAL-2872 hide sort button in Aptx unless it's actually...
2017-12-11 kjvdheideJAL-2877 disabled Jalview's default tree viewer when...
2017-12-11 kjvdheideJAL-1953 fixed interface misnaming
2017-12-11 kjvdheideJAL-1953 start on making everything interface based
2017-12-08 kjvdheideJAL-1953 renaming of concrete implementation as well
2017-12-08 kjvdheideJAL-2844 reallow clicks to the left of the root (groups...
2017-12-07 kjvdheideJAL-2866 and .jar removed again
2017-12-07 kjvdheideJAL-2866 forester .jar added to lib
2017-12-07 kjvdheideJAL-2872 Redundant Aptx GUI menu items hidden, sorting...
2017-12-06 kjvdheideJAL-2794 disabled branch colors on selection for now
2017-12-06 kjvdheideJAL-2871 Added check whether configuration has been...
2017-12-05 kjvdheideJAL-2838 Sorting from the alignment view menu now funct...
2017-12-05 kjvdheideJAL-2847 Rearranging and cleaning up of database query...
2017-12-05 kjvdheideJAL-2794 associate leaves now iterates through ALL...
2017-12-05 kjvdheideJAL-2847 various error popups for db querying now have...
2017-12-05 kjvdheideJAL-2847 Strings for the various tree databases added
2017-12-05 kjvdheideJAL-2847 if pfam id is detected in first sequence its...
2017-12-05 kjvdheideJAL-2847 added pfam to DBRef source name lookup
2017-12-05 kjvdheideJAL-2805 JAL-2847 JAL-281 added file path to Aptx frame...
2017-12-05 kjvdheideJAL-2838 tree viewer interface expanded to include...
2017-12-05 kjvdheideMerge remote-tracking branch 'origin/develop' into...
2017-12-05 kjvdheideJAL-2838 filled in actionPerformed of the tree sort...
2017-12-05 kjvdheideJAL-2838 Aptx frames now appear in the alignment sortin...
2017-12-03 kjvdheideJAL-2847 start of cleaning up db loading code
2017-12-03 kjvdheideJAL-2844 rearranging code
2017-11-30 Jim ProcterJAL-2849 release notes
2017-11-30 Jim ProcterMerge branch 'bug/JAL-2849' into develop
2017-11-30 Jim ProcterJAL-2849 JAL-2863 file format preferences TODO

2017-11-30 Jim ProcterJAL-2849 fix
2017-11-29 kjvdheideJAL-2844 check added for clicks left of root node
2017-11-29 kjvdheideJAL-2844 entirely X coord based partitioning
2017-11-29 kjvdheideJAL-2844 somewhat better repainting
2017-11-29 kjvdheideJAL-2844 temporary kludge to draw a line
2017-11-29 kjvdheideJAL-2844 added grouping to alignment panel based on...
2017-11-29 kjvdheideJAL-2844 start on colouring back onto the alignment
2017-11-29 kjvdheideJAL-2844 added colouring to partition selection
2017-11-28 kjvdheideJAL-2844 added offset to x coord to make it equal 0...
2017-11-28 kjvdheideMerge remote-tracking branch 'origin/develop' into...
2017-11-28 kjvdheideJAL-2844 first go at partitioning, based on actual...
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2859_uniprottowrongpdbid' into...
2017-11-28 Jim ProcterJAL-2740 release notes
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2740' into develop
2017-11-28 Jim ProcterJAL-2827 release notes
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2827' into develop
2017-11-28 Jim ProcterJAL-2842 release notes
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2842' into develop
2017-11-27 Jim ProcterJAL-2859 disambiguate with PDB ID if no file path bug/JAL-2859_uniprottowrongpdbid
2017-11-27 Jim ProcterJAL-2859 failing test demonstrating sequences with...
2017-11-27 Jim ProcterJAL-2851 JAL-2858 release notes for 2.10.3b1
2017-11-27 Jim ProcterMerge branch 'bug/JAL-2851' into develop
2017-11-27 kjvdheideJAL-2852 JAL-2853 forester update
2017-11-27 kjvdheideJAL-2844 added selection threshold (non-adjusted calcul...
2017-11-27 kjvdheideJAL-2799 re-enabled change listener for Aptx's tabs...
2017-11-27 kjvdheideJAL-2844 line drawing at mouse click added on top of...
2017-11-27 kjvdheideJAL-2853 colours now enabled by default in Aptx
2017-11-26 kjvdheideJAL-2847 first rough attempt at loading in via database ID
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