org.aisb.bio.tools
Class PSSMFitnessFunction

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

All Implemented Interfaces:

FitnessFunction

public class PSSMFitnessFunction

extends java.lang.Object

implements FitnessFunction

This class implements a fitness function based on a PSSM.

The PSSM must be in a plain text file formatted as discussed in assignment B3.

Author:

Doug DeJulio

Constructor Summary

PSSMFitnessFunction()

Method Summary

int	fitness(Sequence inputSequence) Calculate the fitness of this sequence.
int	getMaximumScore() Calculate and return the maximum score.
void	loadFromFile(java.io.File pssmFile)
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

PSSMFitnessFunction

public PSSMFitnessFunction()

Method Detail

fitness

public int fitness(Sequence inputSequence)

Description copied from interface: FitnessFunction

Calculate the fitness of this sequence.

Specified by:

fitness in interface FitnessFunction

Parameters:

inputSequence - The sequence under consideration.

Returns:

An integer representing the fitness.

getMaximumScore

public int getMaximumScore()

Calculate and return the maximum score.

Returns:

The maximum score.

loadFromFile

public void loadFromFile(java.lang.String pssmFileName)
                  throws java.io.IOException

Load the PSSM from a file.

Parameters:

pssmFileName - The name of the PSSM file.

Throws:

java.io.IOException

loadFromFile

public void loadFromFile(java.io.File pssmFile)
                  throws java.io.IOException

Throws:

java.io.IOException