org.aisb.bio.tools
Class SimilarityMatrixComparator

java.lang.Object
  org.aisb.bio.tools.MonomerComparator
      org.aisb.bio.tools.SimilarityMatrixComparator

public class SimilarityMatrixComparator

extends MonomerComparator

This is a simple implementation of a similarity matrix for comparing monomers. Today, it only works for amino acids.

Author:

Doug DeJulio

Field Summary

int[][]

value

Constructor Summary

SimilarityMatrixComparator()

Method Summary

int	compare(Monomer m1, Monomer m2)
void	loadFromFile(File file) Initialize the matrix from a given file.
void	loadFromFile(String fileName) For convenience, initialize the matrix from a file with the given name.

Methods inherited from class java.lang.Object

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

Field Detail

value

public int[][] value

Constructor Detail

SimilarityMatrixComparator

public SimilarityMatrixComparator()

Method Detail

loadFromFile

public void loadFromFile(File file)
                  throws IOException

Initialize the matrix from a given file.

Parameters:

file - The file from which to load.

Throws:

IOException

loadFromFile

public void loadFromFile(String fileName)
                  throws IOException

For convenience, initialize the matrix from a file with the given name.

Parameters:

fileName - The name of the file from which to load.

Throws:

IOException

compare

public int compare(Monomer m1,
                   Monomer m2)

Specified by:

compare in class MonomerComparator