org.aisb.bio.tools
Class PSSSMFitnessFunction

java.lang.Object
  org.aisb.bio.tools.PSSSMFitnessFunction

All Implemented Interfaces:

FitnessFunction

public class PSSSMFitnessFunction

extends java.lang.Object

implements FitnessFunction

This class implements a fitness function based on a PSSM.

Author:

Doug DeJulio

Constructor Summary

PSSSMFitnessFunction()

Method Summary

int	fitness(Sequence seq) Calculate the fitness of this sequence.
void	loadFromFile(java.lang.String pssmFileName) Load the PSSM from a file.

Methods inherited from class java.lang.Object

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

Constructor Detail

PSSSMFitnessFunction

public PSSSMFitnessFunction()

Method Detail

fitness

public int fitness(Sequence seq)

Description copied from interface: FitnessFunction

Calculate the fitness of this sequence.

Specified by:

fitness in interface FitnessFunction

Parameters:

seq - The sequence under consideration.

Returns:

An integer representing the fitness.

loadFromFile

public void loadFromFile(java.lang.String pssmFileName)

Load the PSSM from a file.

Parameters:

pssmFileName -