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2017-11-13	kjvdheide	JAL-2805 more name changes for clarity	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 more interface name changing	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 name changed of interfaces for consistency	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 Jalview sequence binding interface expanded	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 TreeParser now interface based	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 Added tree building interface	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 name change	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 deleted old Aptx class for loading just Newick...	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 more interface work	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2794 removed unused interface	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 undid accidental double (buggy) binding, more...	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 warning messages added if Forester detects...	commit \| commitdiff \| tree
2017-11-13	kjvdheide	JAL-2805 First try at loading tree through Forester...	commit \| commitdiff \| tree
2017-11-10	kjvdheide	JAL-2794 reorganized node select code, added subtree...	commit \| commitdiff \| tree
2017-11-10	kjvdheide	JAL-2794 comments comments comments	commit \| commitdiff \| tree
2017-11-10	kjvdheide	JAL-2794 most method parameters/class variables made...	commit \| commitdiff \| tree
2017-11-10	kjvdheide	JAL-2794 comments, selected node now doesn't have to...	commit \| commitdiff \| tree
2017-11-09	kjvdheide	JAL-2794 PaintRefresher support, Aptx node selection...	commit \| commitdiff \| tree
2017-11-09	kjvdheide	JAL-2794 interface comment	commit \| commitdiff \| tree
2017-11-09	kjvdheide	JAL-2794 Made HashMap with Nodes as keys and sequences...	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 Aptx instances get their parent alignment...	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 Cleaning up tree conversion, sequences are...	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 getters and setters for finding nodes in forester...	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2795 created static class for forester conversions	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 Interface name change (oops)	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 made JalviewTreeViewerBinding an interface	commit \| commitdiff \| tree
2017-11-08	kjvdheide	JAL-2794 Added getter for AlignmentViewport to TreeBuilder	commit \| commitdiff \| tree
2017-11-06	kjvdheide	JAL-2794 simplified/clarified associating leaves to...	commit \| commitdiff \| tree
2017-11-03	kjvdheide	JAL-2794 created tree viewer binding class	commit \| commitdiff \| tree
2017-11-03	kjvdheide	JAL-2795 bunch of cleanup and comments	commit \| commitdiff \| tree
2017-11-02	kjvdheide	JAL-2795 added back test loop for Aptx tree naming...	commit \| commitdiff \| tree
2017-11-02	kjvdheide	JAL-2795 Reverted code changes needed to cluster from...	commit \| commitdiff \| tree
2017-11-02	kjvdheide	JAL-2795 Forester now NJ-clusters the DistanceMatrix...	commit \| commitdiff \| tree
2017-11-02	kjvdheide	JAL-2795 moved matrix conversion to the ForesterMatrix...	commit \| commitdiff \| tree
2017-11-01	kjvdheide	JAL-2795 Sequence[] references now as SequenceI[] ...	commit \| commitdiff \| tree
2017-11-01	kjvdheide	JAL-2795 removed sequences[] class variable, more comments	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 neater error message	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 added error catching for invalid identifier	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 changed getting index of identifier to Stream...	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 rebuilt MatrixConverter to be purely static	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 finalized method arguments; commited forester...	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 removed unneeded for loop (woops) and initialized...	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 implemented getting/setting identifiers	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 added comments links from ForesterMatrix to...	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 removed now unneeded values variable in ForesterMatrix	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 add get for all matrix values to MatrixI ...	commit \| commitdiff \| tree
2017-10-30	kjvdheide	JAL-2795 foresterMatrix now stores distance values...	commit \| commitdiff \| tree
2017-10-29	kjvdheide	JAL-2795 more matrix implementations	commit \| commitdiff \| tree
2017-10-28	kjvdheide	JAL-2795 moved ForesterMatrix to ext.forester	commit \| commitdiff \| tree
2017-10-28	kjvdheide	JAL-2795 Added get and set values to the converted...	commit \| commitdiff \| tree
2017-10-27	kjvdheide	JAL-2795 start of Jalview's Matrix conversion	commit \| commitdiff \| tree
2017-10-27	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Start of matrix converter	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Added proper title to aptx trees	commit \| commitdiff \| tree
2017-10-26	kjvdheide	test name change	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Made FreeUpMemoryTest compatible with modified CalculationCh...	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Added getters for scoremodel & scoreparams in TreeBuilder	commit \| commitdiff \| tree
2017-10-26	kjvdheide	TreeBuilder now stores the used ScoreModel and ScoreParams	commit \| commitdiff \| tree
2017-10-26	kjvdheide	small name fixes in TreeBuilder	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Added TreeBuilder as parameter to the converter constructor	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Name changed of aptx treebuilder to treeconverter	commit \| commitdiff \| tree
2017-10-26	kjvdheide	added getSeqData to TreeBuilder	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Added full names to the tree algorithm enum	commit \| commitdiff \| tree
2017-10-26	kjvdheide	added abbreviations	commit \| commitdiff \| tree
2017-10-26	kjvdheide	added enum for the different tree algorithms	commit \| commitdiff \| tree
2017-10-26	kjvdheide	Couple more thread names	commit \| commitdiff \| tree
2017-10-26	kjvdheide	named most Jalview threads	commit \| commitdiff \| tree
2017-10-26	kjvdheide	removed accidental added enters, commented out broken...	commit \| commitdiff \| tree
2017-10-25	kjvdheide	finished up tests for trees made from jalview data	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Implemented distance tests	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Implemented tree title test for tree made from Jalview	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Added tree title test	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Removed redundant annotations	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Added branch name tests	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-25	kjvdheide	Added abstract class for tree viewer testing, rearranged...	commit \| commitdiff \| tree
2017-10-24	kjvdheide	Tests for Aptx tree created from a Phylogeny object...	commit \| commitdiff \| tree
2017-10-24	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-13	kjvdheide	basic tests for Aptx	commit \| commitdiff \| tree
2017-10-13	kjvdheide	ArchaeopteryxInit is now static	commit \| commitdiff \| tree
2017-10-13	kjvdheide	simplified aptx frame creation code	commit \| commitdiff \| tree
2017-10-13	kjvdheide	forester added as submodule	commit \| commitdiff \| tree
2017-10-13	kjvdheide	Slight Aptx colour change	commit \| commitdiff \| tree
2017-10-12	kjvdheide	Custom aptx configuration added	commit \| commitdiff \| tree
2017-10-12	kjvdheide	moved Aptx creation from CalculationChooser to separate...	commit \| commitdiff \| tree
2017-10-12	kjvdheide	Created test class for Archaeopteryx tree viewing	commit \| commitdiff \| tree
2017-10-11	kjvdheide	forester as submodule with InternalFrame + start of...	commit \| commitdiff \| tree
2017-10-11	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-11	kjvdheide	just a comment	commit \| commitdiff \| tree
2017-10-11	kjvdheide	Added tree building (without distances yet)	commit \| commitdiff \| tree
2017-10-10	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-10-10	kjvdheide	Start of programmatically creating Aptx trees	commit \| commitdiff \| tree
2017-10-09	kjvdheide	fixed incorrect panel title	commit \| commitdiff \| tree
2017-10-09	kjvdheide	Start of creating tree nodes for Aptx	commit \| commitdiff \| tree
2017-10-09	kjvdheide	Fully separated tree GUI from calculation	commit \| commitdiff \| tree
2017-10-07	kjvdheide	Renaming	commit \| commitdiff \| tree
2017-10-06	kjvdheide	Start of creating the objects Archaeopteryx needs	commit \| commitdiff \| tree
2017-10-05	kjvdheide	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
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