ee.ut.ga.business
Class FitnessFunction

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

public class FitnessFunction

extends java.lang.Object

Field Summary

static org.apache.log4j.Logger

log

Constructor Summary

FitnessFunction()

Method Summary

private static int	calculate(java.util.List weights, double threshold) Calculates quantity of DNA sequencies where maximum weight is not less than threshold.
static java.util.List	calculateAllWeights(java.util.Map data, PWM pwm) Calculates all weights for specified Position-Weight-Matrix in given data.
private static void	calculateOptimalPValue(java.util.List weights, PWM pwm) Calculates optimal pValue.
private static void	calculateOptimalPValue(java.util.List weights, PWM pwm, int goodAll) Calculates optimal pValue.
private static void	getOptimalPValue(java.util.List weights, PWM pwm, int GOOD_ALL)
private static void	getOptimalRocArea(java.util.List weights, PWM pwm, int GOOD_ALL)
private static java.math.BigDecimal	getRocArea(java.util.List weights, int GOOD_ALL)
private static void	logCalculatingProcess(int k)
private static java.math.BigDecimal	pValue(int goodInt, int goodAllInt, int badInt, int badAllInt) Calculates pValue.
private static boolean	pValueIsPoositiveTrue(int good, int goodAll, int bad, int badAll, java.math.BigDecimal tempValue)
private static void	setBestValue(PWM pwm, int good, int goodAll, int bad, int badAll, double threshold)
static void	setFitnessValue(java.util.Map data, PWM pwm, int GOOD_ALL, java.lang.String FITNESS_FUNCTION) Counts fitness value of specified PWM in given data.

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

Constructor Detail

FitnessFunction

public FitnessFunction()

Method Detail

setFitnessValue

public static void setFitnessValue(java.util.Map data,
                                   PWM pwm,
                                   int GOOD_ALL,
                                   java.lang.String FITNESS_FUNCTION)

Counts fitness value of specified PWM in given data. Fitness value counts with the help of pValue. Larger result means that PWM suits better to the final result of the project.

calculateAllWeights

public static java.util.List calculateAllWeights(java.util.Map data,
                                                 PWM pwm)

Calculates all weights for specified Position-Weight-Matrix in given data.

Returns:

List of Weight

logCalculatingProcess

private static void logCalculatingProcess(int k)

getOptimalRocArea

private static void getOptimalRocArea(java.util.List weights,
                                      PWM pwm,
                                      int GOOD_ALL)

getRocArea

private static java.math.BigDecimal getRocArea(java.util.List weights,
                                               int GOOD_ALL)

getOptimalPValue

private static void getOptimalPValue(java.util.List weights,
                                     PWM pwm,
                                     int GOOD_ALL)

calculateOptimalPValue

private static void calculateOptimalPValue(java.util.List weights,
                                           PWM pwm)

Calculates optimal pValue.

calculateOptimalPValue

private static void calculateOptimalPValue(java.util.List weights,
                                           PWM pwm,
                                           int goodAll)

Calculates optimal pValue.

calculate

private static int calculate(java.util.List weights,
                             double threshold)

Calculates quantity of DNA sequencies where maximum weight is not less than threshold.

setBestValue

private static void setBestValue(PWM pwm,
                                 int good,
                                 int goodAll,
                                 int bad,
                                 int badAll,
                                 double threshold)

pValueIsPoositiveTrue

private static boolean pValueIsPoositiveTrue(int good,
                                             int goodAll,
                                             int bad,
                                             int badAll,
                                             java.math.BigDecimal tempValue)

pValue

private static java.math.BigDecimal pValue(int goodInt,
                                           int goodAllInt,
                                           int badInt,
                                           int badAllInt)

Calculates pValue.