Optimization API optimization-33 (20130530172738)
A B C E F G I N O S T

A

AbstractSubSetFitnessFunction - Class in edu.cornell.med.icb.optimization
 
AbstractSubSetFitnessFunction() - Constructor for class edu.cornell.med.icb.optimization.AbstractSubSetFitnessFunction
 

B

BulkFitnessNoOffset - Class in edu.cornell.med.icb.optimization
This class implements BulkFitnessFunction, but does not remove a population offset from the fitness value.
BulkFitnessNoOffset(FitnessFunction) - Constructor for class edu.cornell.med.icb.optimization.BulkFitnessNoOffset
 

C

configure() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 

E

edu.cornell.med.icb.optimization - package edu.cornell.med.icb.optimization
 
evaluate(IntSet, double...) - Method in class edu.cornell.med.icb.optimization.AbstractSubSetFitnessFunction
 
evaluate(IntSet) - Method in class edu.cornell.med.icb.optimization.AbstractSubSetFitnessFunction
 
evaluate(Population) - Method in class edu.cornell.med.icb.optimization.BulkFitnessNoOffset
 
evaluate(IChromosome) - Method in class edu.cornell.med.icb.optimization.FitnessFunctionAdapter
 
evaluate(IntSet, double...) - Method in interface edu.cornell.med.icb.optimization.SubSetFitnessFunction
Evaluate the fitness function given a subset.
evaluate(IntSet) - Method in interface edu.cornell.med.icb.optimization.SubSetFitnessFunction
Evaluate the fitness function given a subset.

F

FitnessFunctionAdapter - Class in edu.cornell.med.icb.optimization
 
FitnessFunctionAdapter(IntSet, int, SubSetFitnessFunction, double[][]) - Constructor for class edu.cornell.med.icb.optimization.FitnessFunctionAdapter
 

G

getFitestFunctionValue() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
getFitestParameterValues() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
getFitestSubset() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
Get the fittest subset of elements.
getNumberOfIterationsPerformed() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
getNumberOfParameters() - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
getParameterValues(IChromosome, double[][]) - Static method in class edu.cornell.med.icb.optimization.FitnessFunctionAdapter
 
getSubSet() - Method in class edu.cornell.med.icb.optimization.SubsetSuperGene
 

I

isValid(Gene[], Supergene) - Method in class edu.cornell.med.icb.optimization.SubsetSuperGene
 

N

newGene() - Method in class edu.cornell.med.icb.optimization.SubsetSuperGene
 
nextBoolean() - Method in class edu.cornell.med.icb.optimization.TwisterGenerator
 
nextInt(int) - Method in class edu.cornell.med.icb.optimization.TwisterGenerator
 

O

optimize(int, double) - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
Find an optimal subset, given the convergenceCriterion.
OptimizeSubSet - Class in edu.cornell.med.icb.optimization
Optimize a subset of elements according to some convergenceCriterion.
OptimizeSubSet(IntSet, int, SubSetFitnessFunction) - Constructor for class edu.cornell.med.icb.optimization.OptimizeSubSet
 
OptimizeSubSet(IntSet, int, SubSetFitnessFunction, String...) - Constructor for class edu.cornell.med.icb.optimization.OptimizeSubSet
 
OptimizeSubSet(IntSet, int, SubSetFitnessFunction, int, String...) - Constructor for class edu.cornell.med.icb.optimization.OptimizeSubSet
 

S

setLog(Logger) - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
setModuloProgressReport(int) - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
setPopulationSize(int) - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
Set the number of individuals in the population used by the genetic algorithm.
setRandomSeed(int) - Method in class edu.cornell.med.icb.optimization.OptimizeSubSet
 
setToRandomValue(RandomGenerator) - Method in class edu.cornell.med.icb.optimization.SubsetSuperGene
 
SubSetFitnessFunction - Interface in edu.cornell.med.icb.optimization
 
SubsetSuperGene - Class in edu.cornell.med.icb.optimization
 
SubsetSuperGene() - Constructor for class edu.cornell.med.icb.optimization.SubsetSuperGene
 
SubsetSuperGene(Configuration) - Constructor for class edu.cornell.med.icb.optimization.SubsetSuperGene
 
SubsetSuperGene(Configuration, Gene[]) - Constructor for class edu.cornell.med.icb.optimization.SubsetSuperGene
 
SubsetSuperGene(Configuration, Gene[], int[]) - Constructor for class edu.cornell.med.icb.optimization.SubsetSuperGene
 

T

toString() - Method in class edu.cornell.med.icb.optimization.SubsetSuperGene
 
TwisterGenerator - Class in edu.cornell.med.icb.optimization
An adapter to use the Colt MersenneTwister random engine with JGAP.
TwisterGenerator(Date) - Constructor for class edu.cornell.med.icb.optimization.TwisterGenerator
 
TwisterGenerator() - Constructor for class edu.cornell.med.icb.optimization.TwisterGenerator
 
TwisterGenerator(int) - Constructor for class edu.cornell.med.icb.optimization.TwisterGenerator
 

A B C E F G I N O S T
Optimization API optimization-33 (20130530172738)

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