edu.rit.compbio.phyl

Class MaximumParsimonyBnbSeq

java.lang.Object

edu.rit.compbio.phyl.MaximumParsimonyBnbSeq

public class MaximumParsimonyBnbSeq
extends java.lang.Object

Class MaximumParsimonyBnbSeq provides a sequential algorithm for maximum parsimony phylogenetic tree construction using branch-and-bound search.

To perform a search, the program must:

1. Create an instance of class MaximumParsimonyBnbSeq, passing in a DnaSequenceList of the DNA sequences in the tree, the initial bound for branch-and-bound search, 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 MaximumParsimonyBnbSeq is not multiple thread safe; it is intended to be used in a single-threaded program.

Constructor Summary

Constructors

Constructor and Description
MaximumParsimonyBnbSeq(DnaSequenceList seqList, int initialBound, 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

MaximumParsimonyBnbSeq

public MaximumParsimonyBnbSeq(DnaSequenceList seqList,
                              int initialBound,
                              MaximumParsimonyResults results)

Construct a new maximum parsimony phylogenetic tree construction algorithm object.

Parameters:

seqList - DNA sequence list.

initialBound - Initial bound for branch-and-bound search.

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. The findTrees() method will only find trees whose parsimony scores are less than or equal to the initialBound specified to the constructor or the best bound found thereafter, whichever is smaller.