ee.ut.ga.business
Class GeneticAlgorithm

java.lang.Object
  ee.ut.ga.business.GeneticAlgorithm

public class GeneticAlgorithm

extends java.lang.Object

Field Summary

private static int	BEST_TO_LEAVE
private java.util.Map	data
private static java.lang.String	FITNESS_FUNCTION
private static int	GOOD_ALL
private static java.lang.String	INITIAL_PATH
static org.apache.log4j.Logger	log
private static java.lang.String	LOGGING_PATH
private java.util.List	population
private static int	POPULATION_SIZE
private java.util.Map	priors
private static int	PWM_MIN_LENGTH

Constructor Summary

GeneticAlgorithm(java.lang.String propPath)

Method Summary

private void	evaluate() First step of GA: evaluation - calculate fitness value for each PWM in population.
void	generation() GA generation change.
private java.lang.String	getFormattedDate()
private boolean	isUniquePWM(PWM childPWM, java.util.List children)
private void	logPopulation()
private void	readProperties(java.lang.String propPath)
private void	reproduct() Third step of GA: reproduction - full population of parents by children.
private void	select() Second step of GA: selection - get the best PWMs.

Methods inherited from class java.lang.Object

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

Field Detail

log

public static org.apache.log4j.Logger log

data

private java.util.Map data

priors

private java.util.Map priors

population

private java.util.List population

GOOD_ALL

private static int GOOD_ALL

BEST_TO_LEAVE

private static int BEST_TO_LEAVE

POPULATION_SIZE

private static int POPULATION_SIZE

PWM_MIN_LENGTH

private static int PWM_MIN_LENGTH

FITNESS_FUNCTION

private static java.lang.String FITNESS_FUNCTION

INITIAL_PATH

private static java.lang.String INITIAL_PATH

LOGGING_PATH

private static java.lang.String LOGGING_PATH

Constructor Detail

GeneticAlgorithm

public GeneticAlgorithm(java.lang.String propPath)
                 throws java.lang.Exception

Method Detail

readProperties

private void readProperties(java.lang.String propPath)
                     throws java.lang.Exception

Throws:

java.lang.Exception

generation

public void generation()
                throws java.lang.Exception

GA generation change.

Throws:

java.lang.Exception

evaluate

private void evaluate()

First step of GA: evaluation - calculate fitness value for each PWM in population.

select

private void select()

Second step of GA: selection - get the best PWMs.

reproduct

private void reproduct()
                throws java.lang.Exception

Third step of GA: reproduction - full population of parents by children.

Throws:

java.lang.Exception

isUniquePWM

private boolean isUniquePWM(PWM childPWM,
                            java.util.List children)

logPopulation

private void logPopulation()

getFormattedDate

private java.lang.String getFormattedDate()