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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
 

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