Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...
[jalview.git] / src / jalview / analysis / NJTree.java
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-04-11 gmungocJAL-2428 Javadoc
2017-04-09 gmungocJAL-2393 remove unused commented code
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree...
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect...
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil...
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded...
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters...
2017-02-24 gmungocJAL-2403 code tidy
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
2017-02-17 gmungocJAL-2423 refactored method to build panel title for...
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV"
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-01-07 Jim ProcterJAL-1483 source formatting
2015-01-07 Jim ProcterJAL-1483 refactor NJTree constructor to allow preconfig...
2015-01-07 Jim ProcterJAL-1483 organise imports
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula...
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-08-03 jprocterJAL-1115 reference to List<SequenceI> passed in 'alignm...
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-05-30 jprocterbug for clients using NJTree directly - pwtype should...
2011-04-07 jprocterresolves JAL-804
2010-11-14 jprocternode rename for deuniquifying trees from web service...
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2009-08-21 jproctercommented debug lines indicating calculation progress
2009-06-08 jprocterapply gpl development license
2009-06-01 jprocterapply method for a NodeTransform to nodes in a tree
2008-09-04 jproctermerge from 2_4_Release branch
2007-07-13 jproctercomments for future viz/detection of internal sequence...
2007-06-17 jprocterjavadoc
2007-02-07 amwaterhouseFormatting
2006-12-06 jproctergeneral pairwise substitution score models for pairwise...
2006-12-05 amwaterhousesequence is char []
2006-11-21 jprocterfix unselectable tree leaf nodes when node mapping...
2006-10-12 amwaterhouseComment out debug to compile applet
2006-10-10 jprocterdebug message bugfix on duplicate tree leaf names.
2006-10-10 jprocterbugfix for dodgy trees which contain the same leafname...
2006-10-09 jprocterimported Vamsas bindings and alpha vamsas client code...
2006-08-21 amwaterhouseheader updated
2006-08-04 jprocterrecover original data for tree and pca as alignment...
2006-07-27 amwaterhouseSends gapChar to seqData
2006-07-26 jprocterImplemented CIGAR representation of an Alignment view...
2006-07-21 amwaterhousethis.seqs = seqs
2006-07-21 amwaterhouseLoad tree from file constructor fixed
2006-07-19 amwaterhouseOriginal tree data output in PFAM format
2006-07-18 amwaterhouseWorks on strings, not seqs
2005-12-06 amwaterhousehasDistances added
2005-12-06 amwaterhouseafter merge
2005-11-18 jprocterFixed bug dragonfly.compbio.dundee.ac.uk/mantis/view...
2005-10-03 amwaterhouseRemove redundancy from eclipse
2005-09-30 amwaterhouseRestore file before eclipse changes
2005-09-30 amwaterhouseRemove redundancy in Eclipse
2005-06-30 amwaterhouseFormatting changes
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-06-03 jprocterReinstated 'create tree from selected region only'...
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-24 jprocterextended the UpdatePlaceholders to check for any new...
2005-05-24 jprocteradded PropertyChangeListeners for alignviewport.alignme...
2005-05-20 jprocteradded tree node property for sequence placeholders.
2005-05-19 amwaterhousetoString () method added
2005-05-05 jprocterMoved tree leafname to alignment set matching into...
2005-05-03 amwaterhouse1.1 compatible
2005-03-18 jprocterNew constructors for turning NewickFile objects into...
2005-03-08 jprocterfixed so that alignment percentage ID is used for dista...
2004-11-02 amwaterhouseJalview Imported Sources start