A B C D E F G H I J K L M N O P Q R S T U V X Y

A

A - Static variable in class org.jaga.exampleApplications.proteinLocation.Locator

ANDNode - class org.jaga.reproduction.booleanFormulas.nodes.ANDNode.

TODO: Complete these comments.

ANDNode() - Constructor for class org.jaga.reproduction.booleanFormulas.nodes.ANDNode

AbsoluteFitness - class org.jaga.selection.AbsoluteFitness.

TODO: Complete these comments.

AbsoluteFitness() - Constructor for class org.jaga.selection.AbsoluteFitness

AbsoluteFitness(double) - Constructor for class org.jaga.selection.AbsoluteFitness

AbsoluteFitnessIndividualComparator - class org.jaga.selection.AbsoluteFitnessIndividualComparator.

TODO: Complete these comments.

AbsoluteFitnessIndividualComparator() - Constructor for class org.jaga.selection.AbsoluteFitnessIndividualComparator

Aliphatic - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty

Aliphatic - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory

AminoAcid - class org.jaga.individualRepresentation.proteinLocation.AminoAcid.

TODO: Complete these comments.

AminoAcid() - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcid

AminoAcid(String, String, int) - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcid

AminoAcidFactory - class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory.

TODO: Complete these comments.

AminoAcidFactory() - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

AminoAcidGroup - class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup.

TODO: Complete these comments.

AminoAcidGroup() - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

AminoAcidProperty - class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty.

TODO: Complete these comments.

AminoAcidProperty() - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty

AminoAcidProperty(int) - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty

AminoAcidPropertyFactory - class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory.

TODO: Complete these comments.

AminoAcidPropertyFactory() - Constructor for class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory

AnalysisFrameUpdateThread - class org.jaga.hooks.AnalysisFrameUpdateThread.

TODO: Complete these comments.

AnalysisFrameUpdateThread(long, GAAnalysisFrame, AnalysisHook) - Constructor for class org.jaga.hooks.AnalysisFrameUpdateThread

AnalysisGraphPanel - class org.jaga.hooks.AnalysisGraphPanel.

TODO: Complete these comments.

AnalysisGraphPanel() - Constructor for class org.jaga.hooks.AnalysisGraphPanel

AnalysisGraphPanel(AnalysisHook) - Constructor for class org.jaga.hooks.AnalysisGraphPanel

AnalysisHook - class org.jaga.hooks.AnalysisHook.

TODO: Complete these comments.

AnalysisHook() - Constructor for class org.jaga.hooks.AnalysisHook

AnalysisHook(PrintStream) - Constructor for class org.jaga.hooks.AnalysisHook

AnalysisHook(boolean) - Constructor for class org.jaga.hooks.AnalysisHook

AnalysisHook(PrintStream, boolean) - Constructor for class org.jaga.hooks.AnalysisHook

AnalysisHook.Entry - class org.jaga.hooks.AnalysisHook.Entry.

Statistical data entry.

AnalysisHook.Entry() - Constructor for class org.jaga.hooks.AnalysisHook.Entry

AnalysisHook.Entry(int, double) - Constructor for class org.jaga.hooks.AnalysisHook.Entry

Aromatic - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty

Aromatic - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory

acids - Variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

actualScores - Variable in class org.jaga.individualRepresentation.proteinLocation.Blosum62

add(Individual) - Method in interface org.jaga.definitions.Population

Adds a specified individual to the population.

add(Protein) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

add(ProteinGroup) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

add(Individual) - Method in class org.jaga.util.SimpleCollectionOfIndividuals

addAcidToStats(AminoAcid) - Method in class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

addAll(Individual[]) - Method in interface org.jaga.definitions.Population

Adds a list of individuals to the population.

addAll(Individual[]) - Method in class org.jaga.util.SimpleCollectionOfIndividuals

addHook(SimpleGAHook) - Method in class org.jaga.masterAlgorithm.SimpleGA

addResidue(AminoAcid) - Method in class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

addToNodeList(BooleanFormulaTreeNode, int) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTree

align(Protein, ProteinLocationClassifier) - Method in class org.jaga.exampleApplications.proteinLocation.Locator

align(PolypeptidePattern, int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

alignInProteins(PolypeptidePattern, int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

alignInSubgroups(PolypeptidePattern, int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

alignProtein(Protein, PolypeptidePattern, int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

aliphaticAminoAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

allAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix

allAminoAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

allNegatives - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

allNegativesIndex - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

allPositives - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

allPositivesIndex - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

allowConstants - Variable in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

allowedNodeTypes - Variable in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

aminoAcidChance - Variable in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

aminoAcid_cloneChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

aminoAcid_deleteChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

aminoAcid_generaliseToGroupChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

aminoAcid_generaliseToPropertyChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

aminoAcid_mutateChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

aminoAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

analyseBestFitness - Variable in class org.jaga.hooks.AnalysisHook

analyseGenAge - Variable in class org.jaga.hooks.AnalysisHook

analyseGenAverageFit - Variable in class org.jaga.hooks.AnalysisHook

analyseGenDump - Variable in class org.jaga.hooks.AnalysisHook

analyseGenFitStdDeviation - Variable in class org.jaga.hooks.AnalysisHook

analyseGenMaxFit - Variable in class org.jaga.hooks.AnalysisHook

analyseGenMinFit - Variable in class org.jaga.hooks.AnalysisHook

analyseResults(Protein, boolean[]) - Method in class org.jaga.exampleApplications.proteinLocation.Locator

analyseRunTime - Variable in class org.jaga.hooks.AnalysisHook

analyseTotalFitEvals - Variable in class org.jaga.hooks.AnalysisHook

applicableClass - Variable in class org.jaga.reproduction.CombinedReproductionAlgorithm

applicableClass - Static variable in class org.jaga.reproduction.booleanFormulas.FunctionTreeMutation

applicableClass - Static variable in class org.jaga.reproduction.booleanFormulas.FunctionTreeXOver

applicableClass - Static variable in class org.jaga.reproduction.greycodedNumbers.SimpleBinaryMutation

applicableClass - Static variable in class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOver

applicableFitnessClass - Static variable in class org.jaga.selection.RouletteWheelSelection

applicableFitnessClass - Static variable in class org.jaga.selection.TournamentSelection

applicableFitnessClass - Static variable in class org.jaga.selection.TwoTournamentProbabalisticSelection

aromaticAminoAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

averagePatternLen - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

averagePatternLenGen - Variable in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook