cs195z.phylogeny
Class PStudentTreeAlgorithms

java.lang.Object
  cs195z.phylogeny.PStudentTreeAlgorithms

All Implemented Interfaces:

PTreeAlgorithms

public class PStudentTreeAlgorithms
extends Object
implements PTreeAlgorithms

Field Summary

Fields inherited from interface cs195z.support.PTreeAlgorithms

INFINITY

Constructor Summary

PStudentTreeAlgorithms()
Please do not add arguments to the constructor.

Method Summary

void	felsenstein(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, double[][] transitionProb, int sequenceLength) Implements the Felsenstein max likelihood algorithm and makes changes to the PSpeciesNodes.
void	sankoff(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree, HashMap<ZCharacter,Integer> stateIndices, int[][] costMatrix, int sequenceLength) Implements the Sankoff algorithm and makes changes to the PSpeciesNodes.

Methods inherited from class java.lang.Object

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

Constructor Detail

PStudentTreeAlgorithms

public PStudentTreeAlgorithms()

Please do not add arguments to the constructor. If you wish, you can initialize the class (with private variables) but this is not required.

Method Detail

felsenstein

public void felsenstein(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree,
                        HashMap<ZCharacter,Integer> stateIndices,
                        double[][] transitionProb,
                        int sequenceLength)

Description copied from interface: PTreeAlgorithms

Implements the Felsenstein max likelihood algorithm and makes changes to the PSpeciesNodes. See docs, especially for the probability specification.

Specified by:

felsenstein in interface PTreeAlgorithms

Parameters:

tree - a binary tree with the constraint that it is complete

stateIndices - the indices for transitionProb, by ZCharacter

sequenceLength - we conveniently provide the length in characters

sankoff

public void sankoff(net.datastructures.LinkedBinaryTree<PSpeciesNode> tree,
                    HashMap<ZCharacter,Integer> stateIndices,
                    int[][] costMatrix,
                    int sequenceLength)

Description copied from interface: PTreeAlgorithms

Implements the Sankoff algorithm and makes changes to the PSpeciesNodes. See docs.

Specified by:

sankoff in interface PTreeAlgorithms

Parameters:

tree - a binary tree with the constraint that it is complete

stateIndices - the indices for costMatrix, by ZCharacter

costMatrix - the scoring matrix from [parent][child]

sequenceLength - we conveniently provide the length in characters