source.jalview.org Git - jalview.git/history - src/jalview/analysis/NJTree.java

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[jalview.git] / src / jalview / analysis / NJTree.java

2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-04-11	gmungoc	JAL-2428 Javadoc	blob \| commitdiff \| diff to current
2017-04-09	gmungoc	JAL-2393 remove unused commented code	blob \| commitdiff \| diff to current
2017-03-06	gmungoc	JAL-2428 separate TreeModel from TreeBuilder/NJTree...	blob \| commitdiff \| diff to current
2017-03-03	gmungoc	JAL-2428 use BitSet for clusters and done flags	blob \| commitdiff \| diff to current
2017-02-27	gmungoc	JAL-1632 similarity options on TreeChooser panel affect...	blob \| commitdiff \| diff to current
2017-02-27	gmungoc	JAL-1632 refactored NJTree constructor to include Simil...	blob \| commitdiff \| diff to current
2017-02-27	gmungoc	JAL-2403 JAL-838 remove unused methods and unneeded...	blob \| commitdiff \| diff to current
2017-02-24	gmungoc	JAL-838 added 'SeqSpace' PID mode, added parameters...	blob \| commitdiff \| diff to current
2017-02-24	gmungoc	JAL-2403 code tidy	blob \| commitdiff \| diff to current
2017-02-24	gmungoc	JAL-2403 JAL-1483 push 'reverseRange' inside Matrix	blob \| commitdiff \| diff to current
2017-02-23	gmungoc	JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...	blob \| commitdiff \| diff to current
2017-02-20	gmungoc	JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2423 refactored method to build panel title for...	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2403 constants for "NJ", "AV"	blob \| commitdiff \| diff to current
2017-02-13	gmungoc	JAL-1632 JAL-2416 load score matrices from file, as...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-09-01	gmungoc	JAL-1421 add generics to NJTree, refactor recursive...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-07	Jim Procter	JAL-1483 source formatting	blob \| commitdiff \| diff to current
2015-01-07	Jim Procter	JAL-1483 refactor NJTree constructor to allow preconfig...	blob \| commitdiff \| diff to current
2015-01-07	Jim Procter	JAL-1483 organise imports	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-1473 refactor score matrices and tree score calcula...	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-03	jprocter	JAL-1115 reference to List<SequenceI> passed in 'alignm...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-05-30	jprocter	bug for clients using NJTree directly - pwtype should...	blob \| commitdiff \| diff to current
2011-04-07	jprocter	resolves JAL-804	blob \| commitdiff \| diff to current
2010-11-14	jprocter	node rename for deuniquifying trees from web service...	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-08-21	jprocter	commented debug lines indicating calculation progress	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2009-06-01	jprocter	apply method for a NodeTransform to nodes in a tree	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2007-07-13	jprocter	comments for future viz/detection of internal sequence...	blob \| commitdiff \| diff to current
2007-06-17	jprocter	javadoc	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2006-12-06	jprocter	general pairwise substitution score models for pairwise...	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	sequence is char []	blob \| commitdiff \| diff to current
2006-11-21	jprocter	fix unselectable tree leaf nodes when node mapping...	blob \| commitdiff \| diff to current
2006-10-12	amwaterhouse	Comment out debug to compile applet	blob \| commitdiff \| diff to current
2006-10-10	jprocter	debug message bugfix on duplicate tree leaf names.	blob \| commitdiff \| diff to current
2006-10-10	jprocter	bugfix for dodgy trees which contain the same leafname...	blob \| commitdiff \| diff to current
2006-10-09	jprocter	imported Vamsas bindings and alpha vamsas client code...	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-08-04	jprocter	recover original data for tree and pca as alignment...	blob \| commitdiff \| diff to current
2006-07-27	amwaterhouse	Sends gapChar to seqData	blob \| commitdiff \| diff to current
2006-07-26	jprocter	Implemented CIGAR representation of an Alignment view...	blob \| commitdiff \| diff to current
2006-07-21	amwaterhouse	this.seqs = seqs	blob \| commitdiff \| diff to current
2006-07-21	amwaterhouse	Load tree from file constructor fixed	blob \| commitdiff \| diff to current
2006-07-19	amwaterhouse	Original tree data output in PFAM format	blob \| commitdiff \| diff to current
2006-07-18	amwaterhouse	Works on strings, not seqs	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	hasDistances added	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	after merge	blob \| commitdiff \| diff to current
2005-11-18	jprocter	Fixed bug dragonfly.compbio.dundee.ac.uk/mantis/view...	blob \| commitdiff \| diff to current
2005-10-03	amwaterhouse	Remove redundancy from eclipse	blob \| commitdiff \| diff to current
2005-09-30	amwaterhouse	Restore file before eclipse changes	blob \| commitdiff \| diff to current
2005-09-30	amwaterhouse	Remove redundancy in Eclipse	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Formatted source	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	GPL license added	blob \| commitdiff \| diff to current
2005-06-03	jprocter	Reinstated 'create tree from selected region only'...	blob \| commitdiff \| diff to current
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	blob \| commitdiff \| diff to current
2005-05-24	jprocter	extended the UpdatePlaceholders to check for any new...	blob \| commitdiff \| diff to current
2005-05-24	jprocter	added PropertyChangeListeners for alignviewport.alignme...	blob \| commitdiff \| diff to current
2005-05-20	jprocter	added tree node property for sequence placeholders.	blob \| commitdiff \| diff to current
2005-05-19	amwaterhouse	toString () method added	blob \| commitdiff \| diff to current
2005-05-05	jprocter	Moved tree leafname to alignment set matching into...	blob \| commitdiff \| diff to current
2005-05-03	amwaterhouse	1.1 compatible	blob \| commitdiff \| diff to current
2005-03-18	jprocter	New constructors for turning NewickFile objects into...	blob \| commitdiff \| diff to current
2005-03-08	jprocter	fixed so that alignment percentage ID is used for dista...	blob \| commitdiff \| diff to current
2004-11-02	amwaterhouse	Jalview Imported Sources start	blob \| commitdiff \| diff to current

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