phylonet.recomp.comparator
Class PAUPParsDiffComparator

java.lang.Object
  phylonet.recomp.comparator.PAUPWindowComparator
      phylonet.recomp.comparator.PAUPParsDiffComparator

All Implemented Interfaces:

WindowComparator

public class PAUPParsDiffComparator
extends PAUPWindowComparator

This class implements a Parsimony difference window comparator that uses PAUP's implementation of maximum parsimony.

Author:

Derek Ruths

Nested Class Summary

Nested classes/interfaces inherited from class phylonet.recomp.comparator.PAUPWindowComparator

PAUPWindowComparator.DistanceMeasure

Constructor Summary

PAUPParsDiffComparator(java.io.File paup_path, int pop_size, int num_iterations, int num_levels)
Construct a comparator that uses the top num_levels of the parsimony trees for a window.

Method Summary

double	compare(int window1_coord, int window2_coord, char[][] window1, char[][] window2) This method compares two adjacent windows.
java.lang.String	toString()

Methods inherited from class phylonet.recomp.comparator.PAUPWindowComparator

invertNormalizedScore

Methods inherited from class java.lang.Object

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

Constructor Detail

PAUPParsDiffComparator

public PAUPParsDiffComparator(java.io.File paup_path,
                              int pop_size,
                              int num_iterations,
                              int num_levels)
                       throws java.io.FileNotFoundException

Construct a comparator that uses the top num_levels of the parsimony trees for a window.

Parameters:

paup_path - is the path to the PAUP executable on this system.

num_levels - the number of top levels to incorporate in the score computation.

num_iterations - the number of iterations the MP heuristic should use to find the optimal trees.

pop_size - the number of trees used in the MP search to find the optimal trees.

Throws:

java.io.FileNotFoundException - if paup_path does not specify a valid paup file

Method Detail

compare

public double compare(int window1_coord,
                      int window2_coord,
                      char[][] window1,
                      char[][] window2)

Description copied from interface: WindowComparator

This method compares two adjacent windows. window1 preceeds window2. The comparison score does not have to be normalized.

Parameters:

window1_coord - is the starting coordinate of window 1

window2_coord - is the starting coordinate of window 2

window1 - is the subsequence of each sequence within the first window

window2 - is the subsequence of each sequence within the second window

Returns:

the comparison score.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object