calhoun.analysis.crf.features.supporting.phylogenetic
Class RootedBinaryPhylogeneticTree

java.lang.Object
  calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree

All Implemented Interfaces:

java.io.Serializable

public class RootedBinaryPhylogeneticTree
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

java.util.ArrayList<BinaryTreeNode>

T

Constructor Summary

RootedBinaryPhylogeneticTree(java.lang.String ss)

Method Summary

PhylogeneticTreeFelsensteinOrder	getFelsensteinOrder(java.lang.String[] msaOrder) Given an ordering of species in a multiple alignment file, determine an order for computations by which Felsenstein's algorithm can be performed, and the branch lengths involved at each step.
int	getNumSpecies()
java.util.Set<java.lang.String>	getSpeciesSet()
double	longest_branch_length()
java.lang.String	newick()
int	nSpecies()
RootedBinaryPhylogeneticTree	subtree(java.lang.String[] sn)
void	summarize_tree()
double	total_branch_length()

Methods inherited from class java.lang.Object

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

Field Detail

T

public java.util.ArrayList<BinaryTreeNode> T

Constructor Detail

RootedBinaryPhylogeneticTree

public RootedBinaryPhylogeneticTree(java.lang.String ss)

Method Detail

newick

public java.lang.String newick()

summarize_tree

public void summarize_tree()

total_branch_length

public double total_branch_length()

longest_branch_length

public double longest_branch_length()

getNumSpecies

public int getNumSpecies()

getFelsensteinOrder

public PhylogeneticTreeFelsensteinOrder getFelsensteinOrder(java.lang.String[] msaOrder)

Given an ordering of species in a multiple alignment file, determine an order for computations by which Felsenstein's algorithm can be performed, and the branch lengths involved at each step. For example, for the phylogenetic tree

(((cnDT,cnDS),cnAB),(cnBB,cnBV)) and the MSA in the order (0=cnDT,1=cnDS,2=cnAB,3=cnBB,4=cnBV), can compute in this order:

5 = combine(0,1)

6 = combine(2,5)

7 = combine(3,4)

8 = combine(6,7)

and the final answer is at node 8.

The computation for nodes 5-8 can be represented by

ileft = new int[]{0,5,3,6};

iright = new int[]{1,2,4,7};

Parameters:

msaOrder - the (n) species presented in a multiple alignment, in order of their listing in the file

Returns:

an ordering in which the (n-1) recursive calculations for Felsenstein's algorithm can be performed.

subtree

public RootedBinaryPhylogeneticTree subtree(java.lang.String[] sn)

getSpeciesSet

public java.util.Set<java.lang.String> getSpeciesSet()

nSpecies

public int nSpecies()