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2018-01-09	kjvdheide	JAL-2805 allow for non-xsd validating phyloxml parsing	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 check no longer errors if the sequence is...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added check for sequences already being present...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 put the sequence setting in if statement ...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added Aptx factory method reading directly...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added nexus specific parser settings	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 broke off the phylogenetic file formats into...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 parser is now File based (instead of FileParse...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 Parse returns a TreeI array again	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 node sequence is now immediately filled in...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added forester --> jalview sequence converter	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added getter in trees for retrieving all node...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-1953 moved DataConversions to Forester package	commit \| commitdiff \| tree
2018-01-08	kjvdheide	JAL-2844 changed threshold from double to float	commit \| commitdiff \| tree
2018-01-08	kjvdheide	JAL-2844 start on moving tree partitioning code into...	commit \| commitdiff \| tree
2018-01-06	kjvdheide	JAL-2877 added forester as jar once again	commit \| commitdiff \| tree
2018-01-06	kjvdheide	JAL-281 first line also checked for PhyloXML identification	commit \| commitdiff \| tree
2018-01-06	kjvdheide	JAL-2871 aptx Configuration now created through input...	commit \| commitdiff \| tree
2018-01-05	kjvdheide	JAL-281 ForesterParser now extends from AlignFile	commit \| commitdiff \| tree
2018-01-04	kjvdheide	JAL-1953 Moved config to resources folder	commit \| commitdiff \| tree
2018-01-04	kjvdheide	JAL-281 ForesterParser factory methods added	commit \| commitdiff \| tree
2018-01-02	kjvdheide	JAL-1953 start work on storing nodes in a map per tree...	commit \| commitdiff \| tree
2017-12-21	kjvdheide	JAL-281 added file identify criteria for PhyloXML and...	commit \| commitdiff \| tree
2017-12-20	kjvdheide	JAL-2874 made the actionlistener slightly clearer	commit \| commitdiff \| tree
2017-12-20	kjvdheide	JAL-2838 JAL-2872 added sorting from the Aptx frame...	commit \| commitdiff \| tree
2017-12-20	kjvdheide	JAL-281 moved utility methods to .io package	commit \| commitdiff \| tree
2017-12-20	kjvdheide	JAL-281 split up TreeParser into separate format parsers	commit \| commitdiff \| tree
2017-12-19	kjvdheide	JAL-281 created Nexus and PhyloXML parser classes	commit \| commitdiff \| tree
2017-12-19	kjvdheide	JAL-281 cleared out useless tree parser class	commit \| commitdiff \| tree
2017-12-19	kjvdheide	JAL-281 added phyloxml and nexus to jalview fileformats	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-1953 moved now-generic methods outside of Aptx...	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-1953 -External from all interfaces names	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-1953 attempt at changing Aptx's font to Jalview's	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-2844 cladogram no longer vertically aligned (was...	commit \| commitdiff \| tree
2017-12-18	kjvdheide	Merge branch 'kjvdh/features/PhylogenyViewer' of	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-2844 made null tree nodes return null wrappers...	commit \| commitdiff \| tree
2017-12-18	kjvdheide	Merge branch 'kjvdh/features/PhylogenyViewer' into	commit \| commitdiff \| tree
2017-12-18	kjvdheide	JAL-1953 redundant tree interface instantiation removed	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-2852 EPS saving code ported from TreePanel to Aptx.	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-1953 added Y coordinate getter method	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-2852 merged the EPS button adding from main branch...	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-1953 node comparing now includes checking node...	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-1953 removed deprecated interfaces	commit \| commitdiff \| tree
2017-12-15	kjvdheide	JAL-2852 added EPS export button to File menu	commit \| commitdiff \| tree
2017-12-14	kjvdheide	JAL-1953 more progress on interfaces, jalview binding...	commit \| commitdiff \| tree
2017-12-12	kjvdheide	JAL-2874 filtering alignment now also works when just...	commit \| commitdiff \| tree
2017-12-12	kjvdheide	JAL-2874 added filtering when a subtree is selected	commit \| commitdiff \| tree
2017-12-12	kjvdheide	Merge branch 'kjvdh/features/PhylogenyViewer' of https...	commit \| commitdiff \| tree
2017-12-12	kjvdheide	JAL-2877 disabled Jalview's own viewer for testing	commit \| commitdiff \| tree
2017-12-11	kjvdheide	JAL-2872 hide sort button in Aptx unless it's actually...	commit \| commitdiff \| tree
2017-12-11	kjvdheide	JAL-2877 disabled Jalview's default tree viewer when...	commit \| commitdiff \| tree
2017-12-11	kjvdheide	JAL-1953 fixed interface misnaming	commit \| commitdiff \| tree
2017-12-11	kjvdheide	JAL-1953 start on making everything interface based	commit \| commitdiff \| tree
2017-12-08	kjvdheide	JAL-1953 renaming of concrete implementation as well	commit \| commitdiff \| tree
2017-12-08	kjvdheide	JAL-2844 reallow clicks to the left of the root (groups...	commit \| commitdiff \| tree
2017-12-07	kjvdheide	JAL-2866 and .jar removed again	commit \| commitdiff \| tree
2017-12-07	kjvdheide	JAL-2866 forester .jar added to lib	commit \| commitdiff \| tree
2017-12-07	kjvdheide	JAL-2872 Redundant Aptx GUI menu items hidden, sorting...	commit \| commitdiff \| tree
2017-12-06	kjvdheide	JAL-2794 disabled branch colors on selection for now	commit \| commitdiff \| tree
2017-12-06	kjvdheide	JAL-2871 Added check whether configuration has been...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2838 Sorting from the alignment view menu now functional	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2847 Rearranging and cleaning up of database query...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2794 associate leaves now iterates through ALL...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2847 various error popups for db querying now have...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2847 Strings for the various tree databases added	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2847 if pfam id is detected in first sequence its...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2847 added pfam to DBRef source name lookup	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2805 JAL-2847 JAL-281 added file path to Aptx frame...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2838 tree viewer interface expanded to include...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	Merge remote-tracking branch 'origin/develop' into...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2838 filled in actionPerformed of the tree sort...	commit \| commitdiff \| tree
2017-12-05	kjvdheide	JAL-2838 Aptx frames now appear in the alignment sorting...	commit \| commitdiff \| tree
2017-12-03	kjvdheide	JAL-2847 start of cleaning up db loading code	commit \| commitdiff \| tree
2017-12-03	kjvdheide	JAL-2844 rearranging code	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 check added for clicks left of root node	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 entirely X coord based partitioning	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 somewhat better repainting	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 temporary kludge to draw a line	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 added grouping to alignment panel based on...	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 start on colouring back onto the alignment	commit \| commitdiff \| tree
2017-11-29	kjvdheide	JAL-2844 added colouring to partition selection	commit \| commitdiff \| tree
2017-11-28	kjvdheide	JAL-2844 added offset to x coord to make it equal 0...	commit \| commitdiff \| tree
2017-11-28	kjvdheide	Merge remote-tracking branch 'origin/develop' into...	commit \| commitdiff \| tree
2017-11-28	kjvdheide	JAL-2844 first go at partitioning, based on actual...	commit \| commitdiff \| tree
2017-11-27	kjvdheide	JAL-2852 JAL-2853 forester update	commit \| commitdiff \| tree
2017-11-27	kjvdheide	JAL-2844 added selection threshold (non-adjusted calculation...	commit \| commitdiff \| tree
2017-11-27	kjvdheide	JAL-2799 re-enabled change listener for Aptx's tabs...	commit \| commitdiff \| tree
2017-11-27	kjvdheide	JAL-2844 line drawing at mouse click added on top of...	commit \| commitdiff \| tree
2017-11-27	kjvdheide	JAL-2853 colours now enabled by default in Aptx	commit \| commitdiff \| tree
2017-11-26	kjvdheide	JAL-2847 first rough attempt at loading in via database ID	commit \| commitdiff \| tree
2017-11-24	kjvdheide	JAL-2799 rearranged AptxInit code	commit \| commitdiff \| tree
2017-11-24	kjvdheide	JAL-2799 ALL trees are now loaded in as separate Aptx...	commit \| commitdiff \| tree
2017-11-24	kjvdheide	JAL-2794 binding now exclusively supports single tab...	commit \| commitdiff \| tree
2017-11-24	kjvdheide	Merge branch 'kjvdh/features/PhylogenyViewer' of https...	commit \| commitdiff \| tree
2017-11-24	kjvdheide	JAL-2838 start on sorting	commit \| commitdiff \| tree
2017-11-24	kjvdheide	JAL-2838 made getAssociatedPanels public	commit \| commitdiff \| tree
2017-11-22	kjvdheide	JAL-2794 reworked, everything routes via avport.sendselectio...	commit \| commitdiff \| tree
2017-11-22	kjvdheide	JAL-2794 removed several redundancies in the binding...	commit \| commitdiff \| tree
2017-11-22	kjvdheide	JAL-281 fixed misplaced quote in example text	commit \| commitdiff \| tree
2017-11-22	kjvdheide	JAL-2844 mouse press code rearranged to prepare for...	commit \| commitdiff \| tree
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