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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/
analysis
/ NJTree.java
2023-02-23
James Procter
JAL-4134 - refactor tree calculation code to work with...
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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2017-04-11
gmungoc
JAL-2428 Javadoc
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2017-04-09
gmungoc
JAL-2393 remove unused commented code
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commitdiff
2017-03-06
gmungoc
JAL-2428 separate TreeModel from TreeBuilder/NJTree...
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commitdiff
2017-03-03
gmungoc
JAL-2428 use BitSet for clusters and done flags
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commitdiff
2017-02-27
gmungoc
JAL-1632 similarity options on TreeChooser panel affect...
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commitdiff
2017-02-27
gmungoc
JAL-1632 refactored NJTree constructor to include Simil...
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commitdiff
2017-02-27
gmungoc
JAL-2403 JAL-838 remove unused methods and unneeded...
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2017-02-24
gmungoc
JAL-838 added 'SeqSpace' PID mode, added parameters...
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2017-02-24
gmungoc
JAL-2403 code tidy
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commitdiff
2017-02-24
gmungoc
JAL-2403 JAL-1483 push 'reverseRange' inside Matrix
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2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
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2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
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commitdiff
2017-02-17
gmungoc
JAL-2423 refactored method to build panel title for...
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2017-02-17
gmungoc
JAL-2403 constants for "NJ", "AV"
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commitdiff
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
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2016-09-01
gmungoc
JAL-1421 add generics to NJTree, refactor recursive...
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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commitdiff
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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commitdiff
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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2015-01-07
Jim Procter
JAL-1483 source formatting
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2015-01-07
Jim Procter
JAL-1483 refactor NJTree constructor to allow preconfig...
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commitdiff
2015-01-07
Jim Procter
JAL-1483 organise imports
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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commitdiff
2014-06-06
Jim Procter
JAL-1517 source formatting
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commitdiff
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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commitdiff
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
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commitdiff
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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commitdiff
2014-04-21
Jim Procter
JAL-1473 refactor score matrices and tree score calcula...
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commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
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commitdiff
2012-10-03
jprocter
formatting
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commitdiff
2012-08-03
jprocter
JAL-1115 reference to List<SequenceI> passed in 'alignm...
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commitdiff
2011-10-10
jprocter
update author list in license for (JAL-826)
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2011-09-27
jprocter
apply version 2.7 copyright
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2011-05-30
jprocter
bug for clients using NJTree directly - pwtype should...
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2011-04-07
jprocter
resolves JAL-804
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commitdiff
2010-11-14
jprocter
node rename for deuniquifying trees from web service...
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commitdiff
2010-09-23
jprocter
apply jalview code style
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commitdiff
2010-09-23
jprocter
Jalview 2.6 source licence
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commitdiff
2010-04-30
jprocter
jalview 2.5 release banner
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2009-08-21
jprocter
commented debug lines indicating calculation progress
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2009-06-08
jprocter
apply gpl development license
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commitdiff
2009-06-01
jprocter
apply method for a NodeTransform to nodes in a tree
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2008-09-04
jprocter
merge from 2_4_Release branch
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2007-07-13
jprocter
comments for future viz/detection of internal sequence...
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2007-06-17
jprocter
javadoc
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2007-02-07
amwaterhouse
Formatting
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commitdiff
2006-12-06
jprocter
general pairwise substitution score models for pairwise...
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2006-12-05
amwaterhouse
sequence is char []
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2006-11-21
jprocter
fix unselectable tree leaf nodes when node mapping...
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2006-10-12
amwaterhouse
Comment out debug to compile applet
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2006-10-10
jprocter
debug message bugfix on duplicate tree leaf names.
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2006-10-10
jprocter
bugfix for dodgy trees which contain the same leafname...
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2006-10-09
jprocter
imported Vamsas bindings and alpha vamsas client code...
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2006-08-21
amwaterhouse
header updated
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2006-08-04
jprocter
recover original data for tree and pca as alignment...
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2006-07-27
amwaterhouse
Sends gapChar to seqData
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commitdiff
2006-07-26
jprocter
Implemented CIGAR representation of an Alignment view...
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2006-07-21
amwaterhouse
this.seqs = seqs
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2006-07-21
amwaterhouse
Load tree from file constructor fixed
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2006-07-19
amwaterhouse
Original tree data output in PFAM format
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2006-07-18
amwaterhouse
Works on strings, not seqs
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commitdiff
2005-12-06
amwaterhouse
hasDistances added
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2005-12-06
amwaterhouse
after merge
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commitdiff
2005-11-18
jprocter
Fixed bug dragonfly.compbio.dundee.ac.uk/mantis/view...
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2005-10-03
amwaterhouse
Remove redundancy from eclipse
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commitdiff
2005-09-30
amwaterhouse
Restore file before eclipse changes
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commitdiff
2005-09-30
amwaterhouse
Remove redundancy in Eclipse
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commitdiff
2005-06-30
amwaterhouse
Formatting changes
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commitdiff
2005-06-08
amwaterhouse
Formatted source
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commitdiff
2005-06-08
amwaterhouse
GPL license added
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commitdiff
2005-06-03
jprocter
Reinstated 'create tree from selected region only'...
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2005-05-25
jprocter
tidied up system.out messages and moved many to stderr.
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2005-05-24
jprocter
extended the UpdatePlaceholders to check for any new...
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2005-05-24
jprocter
added PropertyChangeListeners for alignviewport.alignme...
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2005-05-20
jprocter
added tree node property for sequence placeholders.
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2005-05-19
amwaterhouse
toString () method added
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2005-05-05
jprocter
Moved tree leafname to alignment set matching into...
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2005-05-03
amwaterhouse
1.1 compatible
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2005-03-18
jprocter
New constructors for turning NewickFile objects into...
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commitdiff
2005-03-08
jprocter
fixed so that alignment percentage ID is used for dista...
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2004-11-02
amwaterhouse
Jalview Imported Sources
start
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