Uses of Class
ee.ut.ga.model.PWM

Packages that use PWM

ee.ut.ga.business

Uses of PWM in ee.ut.ga.business

Methods in ee.ut.ga.business that return PWM

static PWM	ReproductionMethods.reproduct(java.util.List parents, java.util.Map priors, int PWM_MIN_LENGTH) Reproducts new PWM using random parent and random reproduction method.
private static PWM	ReproductionMethods.reproduct(PWM parentPWM, int mutationTimes, java.util.Map priors, int PWM_MIN_LENGTH) Randomly chooses one of reproduction methods.
private static PWM	ReproductionMethods.reproduct(PWM parentPWM, java.util.Map priors, int PWM_MIN_LENGTH) Randomly chooses one of reproduction methods.
private static PWM	ReproductionMethods.deleteColumn(PWM parentPWM, int position, java.util.Map priors) Deletes column in PWM at the specified position.
private static PWM	ReproductionMethods.deleteColumn(PWM parentPWM, java.util.Map priors) Deletes random column in PWM.
private static PWM	ReproductionMethods.addColumn(PWM parentPWM, int position, java.util.Map priors) Adds column into PWM at the specified position.
private static PWM	ReproductionMethods.addColumn(PWM parentPWM, java.util.Map priors) Adds column into PWM at random position.

Methods in ee.ut.ga.business with parameters of type PWM

private static PWM	ReproductionMethods.reproduct(PWM parentPWM, int mutationTimes, java.util.Map priors, int PWM_MIN_LENGTH) Randomly chooses one of reproduction methods.
private static PWM	ReproductionMethods.reproduct(PWM parentPWM, java.util.Map priors, int PWM_MIN_LENGTH) Randomly chooses one of reproduction methods.
private static PWM	ReproductionMethods.deleteColumn(PWM parentPWM, int position, java.util.Map priors) Deletes column in PWM at the specified position.
private static PWM	ReproductionMethods.deleteColumn(PWM parentPWM, java.util.Map priors) Deletes random column in PWM.
private static PWM	ReproductionMethods.addColumn(PWM parentPWM, int position, java.util.Map priors) Adds column into PWM at the specified position.
private static PWM	ReproductionMethods.addColumn(PWM parentPWM, java.util.Map priors) Adds column into PWM at random position.
private boolean	GeneticAlgorithm.isUniquePWM(PWM childPWM, java.util.List children)
static void	FitnessFunction.setFitnessValue(java.util.Map data, PWM pwm, int GOOD_ALL, java.lang.String FITNESS_FUNCTION) Counts fitness value of specified PWM in given data.
static java.util.List	FitnessFunction.calculateAllWeights(java.util.Map data, PWM pwm) Calculates all weights for specified Position-Weight-Matrix in given data.
private static void	FitnessFunction.getOptimalRocArea(java.util.List weights, PWM pwm, int GOOD_ALL)
private static void	FitnessFunction.getOptimalPValue(java.util.List weights, PWM pwm, int GOOD_ALL)
private static void	FitnessFunction.calculateOptimalPValue(java.util.List weights, PWM pwm) Calculates optimal pValue.
private static void	FitnessFunction.calculateOptimalPValue(java.util.List weights, PWM pwm, int goodAll) Calculates optimal pValue.
private static void	FitnessFunction.setBestValue(PWM pwm, int good, int goodAll, int bad, int badAll, double threshold)