statalign.base
Class TreeAlgo

java.lang.Object
  statalign.base.thread.Stoppable
      statalign.base.TreeAlgo

public class TreeAlgo
extends Stoppable

Field Summary

double	BIGNUM
int	GAPEXT
int	GAPOPEN
static double	MINEDGELEN

Constructor Summary

TreeAlgo()

TreeAlgo(int gapOpen, int gapExt)

Method Summary

void	addAlignSeqsToTree(Tree tree, java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)
Tree	buildNJTree(java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)
Tree	rearrangeTree(Tree tree, java.lang.String[] names)

Methods inherited from class statalign.base.thread.Stoppable

pausable, stoppable

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GAPOPEN

public int GAPOPEN

GAPEXT

public int GAPEXT

BIGNUM

public double BIGNUM

MINEDGELEN

public static double MINEDGELEN

Constructor Detail

TreeAlgo

public TreeAlgo()

TreeAlgo

public TreeAlgo(int gapOpen,
                int gapExt)

Method Detail

buildNJTree

public Tree buildNJTree(java.lang.String[] sequences,
                        java.lang.String[] names,
                        SubstitutionModel model,
                        java.lang.String filename)
                 throws StoppedException

Throws:

StoppedException

rearrangeTree

public Tree rearrangeTree(Tree tree,
                          java.lang.String[] names)

addAlignSeqsToTree

public void addAlignSeqsToTree(Tree tree,
                               java.lang.String[] sequences,
                               java.lang.String[] names,
                               SubstitutionModel model,
                               java.lang.String filename)
                        throws StoppedException

Throws:

StoppedException