edu.rit.compbio.phyl

Class MaximumParsimonyExhSeq

java.lang.Object

edu.rit.compbio.phyl.MaximumParsimonyExhSeq

public class MaximumParsimonyExhSeq
extends java.lang.Object

Class MaximumParsimonyExhSeq provides a sequential algorithm for maximum parsimony phylogenetic tree construction using exhaustive search.

To perform a search, the program must:

1. Create an instance of class MaximumParsimonyExhSeq, passing in a DnaSequenceList of the DNA sequences in the tree and a MaximumParsimonyResults object to hold the search results.

2. Call the findTrees() method. The results of the search are returned in the MaximumParsimonyResults object specified to the constructor.

Note: Class MaximumParsimonyExhSeq is not multiple thread safe; it is intended to be used in a single-threaded program.

Constructor Summary

Constructors

Constructor and Description
MaximumParsimonyExhSeq(DnaSequenceList seqList, MaximumParsimonyResults results) Construct a new maximum parsimony phylogenetic tree construction algorithm object.

Method Summary

Modifier and Type	Method and Description
void	findTrees() Find the maximum parsimony phylogenetic tree(s) in the search graph.

Methods inherited from class java.lang.Object

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

Constructor Detail

MaximumParsimonyExhSeq

public MaximumParsimonyExhSeq(DnaSequenceList seqList,
                              MaximumParsimonyResults results)

Construct a new maximum parsimony phylogenetic tree construction algorithm object.

Parameters:

seqList - DNA sequence list.

results - Object in which to store the results.

Method Detail

findTrees

public void findTrees()

Find the maximum parsimony phylogenetic tree(s) in the search graph. The DNA sequence list was specified to the constructor. The results are stored in the MaximumParsimonyResults object specified to the constructor.