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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis / NJTree.java
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-04-11 gmungocJAL-2428 Javadoc commit | commitdiff
2017-04-09 gmungocJAL-2393 remove unused commented code commit | commitdiff
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... commit | commitdiff
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags commit | commitdiff
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... commit | commitdiff
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... commit | commitdiff
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded... commit | commitdiff
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... commit | commitdiff
2017-02-24 gmungocJAL-2403 code tidy commit | commitdiff
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix commit | commitdiff
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... commit | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... commit | commitdiff
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... commit | commitdiff
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" commit | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... commit | commitdiff
2015-01-07 Jim ProcterJAL-1483 source formatting commit | commitdiff
2015-01-07 Jim ProcterJAL-1483 refactor NJTree constructor to allow preconfig... commit | commitdiff
2015-01-07 Jim ProcterJAL-1483 organise imports commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula... commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-08-03 jprocterJAL-1115 reference to List<SequenceI> passed in 'alignm... commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-05-30 jprocterbug for clients using NJTree directly - pwtype should... commit | commitdiff
2011-04-07 jprocterresolves JAL-804 commit | commitdiff
2010-11-14 jprocternode rename for deuniquifying trees from web service... commit | commitdiff
2010-09-23 jprocterapply jalview code style commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-08-21 jproctercommented debug lines indicating calculation progress commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2009-06-01 jprocterapply method for a NodeTransform to nodes in a tree commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2007-07-13 jproctercomments for future viz/detection of internal sequence... commit | commitdiff
2007-06-17 jprocterjavadoc commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2006-12-06 jproctergeneral pairwise substitution score models for pairwise... commit | commitdiff
2006-12-05 amwaterhousesequence is char [] commit | commitdiff
2006-11-21 jprocterfix unselectable tree leaf nodes when node mapping... commit | commitdiff
2006-10-12 amwaterhouseComment out debug to compile applet commit | commitdiff
2006-10-10 jprocterdebug message bugfix on duplicate tree leaf names. commit | commitdiff
2006-10-10 jprocterbugfix for dodgy trees which contain the same leafname... commit | commitdiff
2006-10-09 jprocterimported Vamsas bindings and alpha vamsas client code... commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2006-08-04 jprocterrecover original data for tree and pca as alignment... commit | commitdiff
2006-07-27 amwaterhouseSends gapChar to seqData commit | commitdiff
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view... commit | commitdiff
2006-07-21 amwaterhousethis.seqs = seqs commit | commitdiff
2006-07-21 amwaterhouseLoad tree from file constructor fixed commit | commitdiff
2006-07-19 amwaterhouseOriginal tree data output in PFAM format commit | commitdiff
2006-07-18 amwaterhouseWorks on strings, not seqs commit | commitdiff
2005-12-06 amwaterhousehasDistances added commit | commitdiff
2005-12-06 amwaterhouseafter merge commit | commitdiff
2005-11-18 jprocterFixed bug dragonfly.compbio.dundee.ac.uk/mantis/view... commit | commitdiff
2005-10-03 amwaterhouseRemove redundancy from eclipse commit | commitdiff
2005-09-30 amwaterhouseRestore file before eclipse changes commit | commitdiff
2005-09-30 amwaterhouseRemove redundancy in Eclipse commit | commitdiff
2005-06-30 amwaterhouseFormatting changes commit | commitdiff
2005-06-08 amwaterhouseFormatted source commit | commitdiff
2005-06-08 amwaterhouseGPL license added commit | commitdiff
2005-06-03 jprocterReinstated 'create tree from selected region only'... commit | commitdiff
2005-05-25 jproctertidied up system.out messages and moved many to stderr. commit | commitdiff
2005-05-24 jprocterextended the UpdatePlaceholders to check for any new... commit | commitdiff
2005-05-24 jprocteradded PropertyChangeListeners for alignviewport.alignme... commit | commitdiff
2005-05-20 jprocteradded tree node property for sequence placeholders. commit | commitdiff
2005-05-19 amwaterhousetoString () method added commit | commitdiff
2005-05-05 jprocterMoved tree leafname to alignment set matching into... commit | commitdiff
2005-05-03 amwaterhouse1.1 compatible commit | commitdiff
2005-03-18 jprocterNew constructors for turning NewickFile objects into... commit | commitdiff
2005-03-08 jprocterfixed so that alignment percentage ID is used for dista... commit | commitdiff
2004-11-02 amwaterhouseJalview Imported Sources start commit | commitdiff