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2018-01-29	kjvdheide	JAL-1953 some more comments, moved JalviewBinding	commit \| commitdiff \| tree
2018-01-28	kjvdheide	JAL-1953 more javadoc comments	commit \| commitdiff \| tree
2018-01-26	kjvdheide	JAL-1953 first pass of adding javadoc, some methods...	commit \| commitdiff \| tree
2018-01-26	kjvdheide	JAL-2856 added refreshing of Aptx view when tree frame...	commit \| commitdiff \| tree
2018-01-26	kjvdheide	JAL-2798 label name changed	commit \| commitdiff \| tree
2018-01-25	kjvdheide	JAL-2844 allow clicks outside of the tree range again...	commit \| commitdiff \| tree
2018-01-25	kjvdheide	JAL-2844 updated forester.jar for drawing partitioning...	commit \| commitdiff \| tree
2018-01-25	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2018-01-25	kjvdheide	JAL-2844 branch colour setter improved	commit \| commitdiff \| tree
2018-01-24	kjvdheide	JAL-2866 remove forester's submodule folder	commit \| commitdiff \| tree
2018-01-24	kjvdheide	JAL-2866 remove forester from .gitmodules	commit \| commitdiff \| tree
2018-01-24	kjvdheide	JAL-2872 added setters for GUI sizes	commit \| commitdiff \| tree
2018-01-24	kjvdheide	JAL-2798 added != null check for Aptx trees	commit \| commitdiff \| tree
2018-01-22	kjvdheide	Revert "JAL-2890 added CIPRES client .jar"	commit \| commitdiff \| tree
2018-01-22	kjvdheide	Revert "JAL-2890 proper .jar this time and copied cipres...	commit \| commitdiff \| tree
2018-01-22	kjvdheide	Revert "JAL-2890 added CIPRES' javadoc .jar to Jalview...	commit \| commitdiff \| tree
2018-01-19	kjvdheide	JAL-2805 small redundant method call fix	commit \| commitdiff \| tree
2018-01-19	kjvdheide	JAL-2890 added CIPRES' javadoc .jar to Jalview lib	commit \| commitdiff \| tree
2018-01-19	kjvdheide	JAL-2890 proper .jar this time and copied cipres' example...	commit \| commitdiff \| tree
2018-01-19	kjvdheide	JAL-2890 added CIPRES client .jar	commit \| commitdiff \| tree
2018-01-18	kjvdheide	JAL-2805 disabled Nexus file identification(as its...	commit \| commitdiff \| tree
2018-01-17	kjvdheide	JAL-1951 added comment to NexusFile clarifying Forester...	commit \| commitdiff \| tree
2018-01-17	kjvdheide	JAL-2794 tree viewer frame now has its binding object...	commit \| commitdiff \| tree
2018-01-17	kjvdheide	JAL-2798 now added to active views when associated...	commit \| commitdiff \| tree
2018-01-17	kjvdheide	JAL-281 added initialising trees to FileLoader if fileformat...	commit \| commitdiff \| tree
2018-01-17	kjvdheide	JAL-281 added isTreeFile() boolean	commit \| commitdiff \| tree
2018-01-16	kjvdheide	JAL-2798 rough saving/loading a single Aptx view functionali...	commit \| commitdiff \| tree
2018-01-16	kjvdheide	JAL-2798 comments	commit \| commitdiff \| tree
2018-01-16	kjvdheide	JAL-2798 tree frame is now added to active views when...	commit \| commitdiff \| tree
2018-01-16	kjvdheide	JAL-2798 added methods for getting/adding external...	commit \| commitdiff \| tree
2018-01-16	kjvdheide	JAL-2798 added method to tree for writing to jalview...	commit \| commitdiff \| tree
2018-01-12	kjvdheide	JAL-2805 check actually works now	commit \| commitdiff \| tree
2018-01-12	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2018-01-12	kjvdheide	JAL-2798 Aptx is now saved to the project	commit \| commitdiff \| tree
2018-01-12	kjvdheide	JAL-2805 removed unused Aptx instance creation code	commit \| commitdiff \| tree
2018-01-12	kjvdheide	JAL-2805 added getter and setter for jalview association...	commit \| commitdiff \| tree
2018-01-11	kjvdheide	JAL-2884 old Newick trees are now loaded in as Aptx...	commit \| commitdiff \| tree
2018-01-11	kjvdheide	JAL-2795 simplified instance creation from calculation	commit \| commitdiff \| tree
2018-01-11	kjvdheide	JAL-2798 alignmentviewport's current external tree...	commit \| commitdiff \| tree
2018-01-10	kjvdheide	JAL-1953 named various threads	commit \| commitdiff \| tree
2018-01-10	kjvdheide	JAL-2795 calculated trees are now passed along as Newick...	commit \| commitdiff \| tree
2018-01-10	kjvdheide	JAL-2795 disabled most tests for now	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 file identifying lines are turned to lowercase...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 correct nexus parser is now created	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 Creating jalview sequence now requires the...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added derive sequence when creating jalview...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 getNodeSequences returns a list now instead...	commit \| commitdiff \| tree
2018-01-09	kjvdheide	JAL-2805 added check for null node sequences during...	commit \| commitdiff \| tree
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
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