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A

AbstractDistanceMeasure - Class in org.corehunter.objectives.distance.measures
Caches pairwise distances upon computation.
AbstractDistanceMeasure() - Constructor for class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
 
AbstractDistanceMeasure(MissingValuesPolicy) - Constructor for class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
 
add(int, NearestEntry) - Method in class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Register the closest entry of a given item.
AllelicDiversityEvaluation - Class in org.corehunter.objectives.eval
 
AllelicDiversityEvaluation(Collection<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.AllelicDiversityEvaluation
Initialize evaluation based on IDs of selected items.
AllelicDiversityEvaluation(AllelicDiversityEvaluation, Set<Integer>, Set<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.AllelicDiversityEvaluation
Infer a modified evaluation by removing and/or adding some items from/to the selection.
API - Class in org.corehunter
Simple API used by the R interface and as a utility class.
API() - Constructor for class org.corehunter.API
 
AverageAccessionToNearestEntry - Class in org.corehunter.objectives
Evaluates a core set by computing the average distance between each item (selected or unselected) and the closest selected item.
AverageAccessionToNearestEntry(DistanceMeasure) - Constructor for class org.corehunter.objectives.AverageAccessionToNearestEntry
 
AverageEntryToEntry - Class in org.corehunter.objectives
Evaluates a core set by computing the average distance between all pairs of selected items.
AverageEntryToEntry(DistanceMeasure) - Constructor for class org.corehunter.objectives.AverageEntryToEntry
 
AverageEntryToNearestEntry - Class in org.corehunter.objectives
Evaluates a core set by computing the average distance between each selected item and the closest other selected item.
AverageEntryToNearestEntry(DistanceMeasure) - Constructor for class org.corehunter.objectives.AverageEntryToNearestEntry
 

B

BiAllelicGenotypeData - Interface in org.corehunter.data
Biallelic data contains the allele score (0/1/2) for markers that have two and only two alleles.

C

CavalliSforzaEdwardsDistance - Class in org.corehunter.objectives.distance.measures
 
CavalliSforzaEdwardsDistance() - Constructor for class org.corehunter.objectives.distance.measures.CavalliSforzaEdwardsDistance
 
CavalliSforzaEdwardsDistanceBiAllelic - Class in org.corehunter.objectives.distance.measures.biallelic
 
CavalliSforzaEdwardsDistanceBiAllelic() - Constructor for class org.corehunter.objectives.distance.measures.biallelic.CavalliSforzaEdwardsDistanceBiAllelic
 
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
Compute distance.
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.biallelic.CavalliSforzaEdwardsDistanceBiAllelic
 
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.biallelic.ModifiedRogersDistanceBiAllelic
 
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.CavalliSforzaEdwardsDistance
 
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.GowerDistance
 
computeDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.ModifiedRogersDistance
 
CoreHunter - Class in org.corehunter
A facade for executing Core Hunter searches.
CoreHunter() - Constructor for class org.corehunter.CoreHunter
 
CoreHunter(CoreHunterExecutionMode) - Constructor for class org.corehunter.CoreHunter
Create Core Hunter facade with the specified mode.
CoreHunterArguments - Class in org.corehunter
 
CoreHunterArguments(CoreHunterData, int, CoreHunterObjectiveType) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single objective configuration with no defined measure.
CoreHunterArguments(CoreHunterData, int, CoreHunterObjectiveType, CoreHunterMeasure) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single objective configuration.
CoreHunterArguments(CoreHunterData, int, List<CoreHunterObjective>) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single- or multi-objective configuration.
CoreHunterArguments(CoreHunterData, int, List<CoreHunterObjective>, Set<Integer>) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single- or multi-objective configuration with a set of always selected IDs.
CoreHunterArguments(CoreHunterData, int, List<CoreHunterObjective>, Set<Integer>, Set<Integer>) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single- or multi-objective configuration with a set of always and/or never selected IDs.
CoreHunterArguments(CoreHunterData, int, List<CoreHunterObjective>, Set<Integer>, Set<Integer>, boolean) - Constructor for class org.corehunter.CoreHunterArguments
Creates a single- or multi-objective configuration with set of always and/or never selected IDs.
CoreHunterConstants - Class in org.corehunter.util
Constants used by Core Hunter.
CoreHunterConstants() - Constructor for class org.corehunter.util.CoreHunterConstants
 
CoreHunterData - Class in org.corehunter.data
Combines all data used in Core Hunter.
CoreHunterData(FrequencyGenotypeData, FeatureData, DistanceMatrixData) - Constructor for class org.corehunter.data.CoreHunterData
Initialize Core Hunter data consisting of genotypic data, phenotypic traits and/or a precomputed distance matrix.
CoreHunterData(FrequencyGenotypeData) - Constructor for class org.corehunter.data.CoreHunterData
Initialize Core Hunter data consisting only of genotypic data.
CoreHunterData(FeatureData) - Constructor for class org.corehunter.data.CoreHunterData
Initialize Core Hunter data consisting only of phenotypicData data.
CoreHunterData(DistanceMatrixData) - Constructor for class org.corehunter.data.CoreHunterData
Initialize Core Hunter data consisting only of distances data.
CoreHunterDataType - Enum in org.corehunter.data
 
CoreHunterException - Exception in org.corehunter.exceptions
 
CoreHunterException() - Constructor for exception org.corehunter.exceptions.CoreHunterException
 
CoreHunterException(String) - Constructor for exception org.corehunter.exceptions.CoreHunterException
 
CoreHunterException(String, Throwable) - Constructor for exception org.corehunter.exceptions.CoreHunterException
 
CoreHunterException(Throwable) - Constructor for exception org.corehunter.exceptions.CoreHunterException
 
CoreHunterExecutionMode - Enum in org.corehunter
Available execution modes.
CoreHunterListener - Interface in org.corehunter
Extends SearchListener with CoreHunter specific steps.
CoreHunterMeasure - Enum in org.corehunter
Available objective measures
CoreHunterObjective - Class in org.corehunter
Defines the objective by providing the objective type, optional measure and optional weight.
CoreHunterObjective(CoreHunterObjectiveType) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type with no defined measure.
CoreHunterObjective(CoreHunterObjectiveType, CoreHunterMeasure) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type and measure.
CoreHunterObjective(CoreHunterObjectiveType, double) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type and weight with no defined measure.
CoreHunterObjective(CoreHunterObjectiveType, CoreHunterMeasure, double) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type, measure and weight.
CoreHunterObjective(CoreHunterObjectiveType, double, Range<Double>) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type, weight and normalization range.
CoreHunterObjective(CoreHunterObjectiveType, CoreHunterMeasure, double, Range<Double>) - Constructor for class org.corehunter.CoreHunterObjective
Creates a Core Hunter objective with for specific object type, measure, weight and normalization range.
CoreHunterObjective(CoreHunterObjective) - Constructor for class org.corehunter.CoreHunterObjective
Creates a CoreHunter Objective from another objective.
CoreHunterObjectiveType - Enum in org.corehunter
Available objective types
Coverage - Class in org.corehunter.objectives
 
Coverage() - Constructor for class org.corehunter.objectives.Coverage
 
CoverageBiAllelic - Class in org.corehunter.objectives.biallelic
 
CoverageBiAllelic() - Constructor for class org.corehunter.objectives.biallelic.CoverageBiAllelic
 
CoverageEvaluation - Class in org.corehunter.objectives.eval
 
CoverageEvaluation(Collection<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.CoverageEvaluation
 
CoverageEvaluation(AllelicDiversityEvaluation, Set<Integer>, Set<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.CoverageEvaluation
 
createArguments(CoreHunterData, int, CoreHunterObjective[], int[], int[], boolean) - Static method in class org.corehunter.API
 
createBiparentalGenotypeData(byte[][], String[], String[], String[]) - Static method in class org.corehunter.API
 
createDefaultGenotypeData(String[][], String[], String[], String[]) - Static method in class org.corehunter.API
 
createDefaultObjective(CoreHunterData) - Static method in class org.corehunter.API
Creates a default allowed objective for the data.
createDefaultObjective(CoreHunterData, List<CoreHunterObjective>) - Static method in class org.corehunter.API
Creates a default allowed objective for the data given a list existing objectives.
createDefaultObjectives(CoreHunterData) - Static method in class org.corehunter.API
Creates a list of default objectives, one for each type of data available, with equal weights.
createDistanceMatrixData(double[][], String[], String[]) - Static method in class org.corehunter.API
 
createFrequencyGenotypeData(double[][], String[], String[], String[], String[]) - Static method in class org.corehunter.API
 
createFromAbbreviation(String) - Static method in enum org.corehunter.CoreHunterMeasure
Get Core Hunter measure from its abbreviation.
createFromAbbreviation(String) - Static method in enum org.corehunter.CoreHunterObjectiveType
Get Core Hunter objective type from its abbreviation.
createObjective(String, String, double) - Static method in class org.corehunter.API
 
createObjective(String, String, double, double, double) - Static method in class org.corehunter.API
 

D

DefaultGenotypeData - Interface in org.corehunter.data
Default genotype data with a fixed number of allele observations per individual, for each marker.
DistanceMatrixData - Interface in org.corehunter.data
A distance matrix that indicates how different each pair of entries is.
DistanceMeasure - Interface in org.corehunter.objectives.distance
 

E

equals(Object) - Method in class org.corehunter.CoreHunterObjective
 
evaluate(SubsetSolution, CoreHunterData, CoreHunterObjective) - Method in class org.corehunter.CoreHunter
Evaluate the given solution with the specified objective.
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.AverageAccessionToNearestEntry
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.AverageAccessionToNearestEntry
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.AverageEntryToEntry
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.AverageEntryToEntry
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.AverageEntryToNearestEntry
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.AverageEntryToNearestEntry
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.biallelic.CoverageBiAllelic
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.biallelic.HeterozygousLociBiAllelic
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.biallelic.ShannonBiAllelic
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.Coverage
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.Coverage
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.HeterozygousLoci
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.HeterozygousLoci
 
evaluate(SubsetSolution, CoreHunterData) - Method in class org.corehunter.objectives.Shannon
 
evaluate(Move, SubsetSolution, Evaluation, CoreHunterData) - Method in class org.corehunter.objectives.Shannon
 
evaluateCore(int[], CoreHunterData, CoreHunterObjective) - Static method in class org.corehunter.API
Evaluate a core collection.
execute(CoreHunterArguments) - Method in class org.corehunter.CoreHunter
 

F

FrequencyGenotypeData - Interface in org.corehunter.data
Frequency genotype data is the most general type of genotype data, containing relative frequencies of markers that have any number of alleles.

G

GenotypeDataFormat - Enum in org.corehunter.data
 
getAbbreviation() - Method in enum org.corehunter.CoreHunterMeasure
Gets the two letter abbreviation of the measure
getAbbreviation() - Method in enum org.corehunter.CoreHunterObjectiveType
Gets the two letter abbreviation of the type
getAllAllowedObjectives(CoreHunterData) - Static method in class org.corehunter.API
Creates a list of all possible Core Hunter objectives for a given data object, with equal weights.
getAlleleFrequencies(FrequencyGenotypeData) - Static method in class org.corehunter.API
 
getAlleleFrequency(int, int, int) - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the relative frequency of an allele for the given entry (sample/accession).
getAlleleFrequency(int, int, int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getAlleleFrequency(int, int, int) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getAlleleName(int, int) - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the name of an allele, if assigned.
getAlleleName(int, int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getAlleleName(int, int) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getAlleles(FrequencyGenotypeData) - Static method in class org.corehunter.API
 
getAlleleScore(int, int) - Method in interface org.corehunter.data.BiAllelicGenotypeData
Get the allele score of the marker for the given entry.
getAlleleScore(int, int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getAllowedMeasures(CoreHunterData, CoreHunterObjectiveType) - Static method in class org.corehunter.API
Create a list of all possible Core Hunter measures for a given data object and objective type.
getAllowedMeasures(boolean, boolean, boolean, CoreHunterObjectiveType) - Static method in class org.corehunter.API
Create a list of all possible Core Hunter measures for a given objective type taking into account whether genotypes, phenotypes and/or precomputed distances are available.
getAllowedObjectiveTypes(CoreHunterData) - Static method in class org.corehunter.API
Creates a list of all possible Core Hunter objective types for a given data object.
getAlwaysSelected() - Method in class org.corehunter.CoreHunterArguments
 
getAverageGenotype() - Method in class org.corehunter.objectives.eval.AllelicDiversityEvaluation
Get average genotype.
getClosest(int) - Method in class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Get the id of and distance to the closest selected item for an item with given id.
getData() - Method in class org.corehunter.CoreHunterArguments
 
getDistance(int, int) - Method in interface org.corehunter.data.DistanceMatrixData
Get the distance between two entries.
getDistance(int, int) - Method in class org.corehunter.data.simple.SimpleDistanceMatrixData
 
getDistance(int, int, CoreHunterData) - Method in interface org.corehunter.objectives.distance.DistanceMeasure
Calculates the distance between two items with given ID.
getDistance() - Method in class org.corehunter.objectives.distance.eval.NearestEntry
 
getDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
Retrieve a distance from the cache.
getDistance(int, int, CoreHunterData) - Method in class org.corehunter.objectives.distance.measures.PrecomputedDistance
 
getDistancesData() - Method in class org.corehunter.data.CoreHunterData
 
getGenotypicData() - Method in class org.corehunter.data.CoreHunterData
 
getId() - Method in class org.corehunter.objectives.distance.eval.NearestEntry
 
getIds(Data) - Static method in class org.corehunter.API
 
getIdsFromIndices(Data, int[]) - Static method in class org.corehunter.API
Get unique identifier strings from item indices.
getIndicesFromIds(DataPojo, String[]) - Static method in class org.corehunter.API
Get item indices from their string identifiers.
getListener() - Method in class org.corehunter.CoreHunter
 
getLower() - Method in class org.corehunter.Range
 
getMarkerName(int) - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the name of a marker by index, if assigned.
getMarkerName(int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getMarkerName(int) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getMarkerNames(FrequencyGenotypeData) - Static method in class org.corehunter.API
 
getMaxSteps() - Method in class org.corehunter.CoreHunter
Get the maximum number of search steps.
getMaxStepsWithoutImprovement() - Method in class org.corehunter.CoreHunter
Get the maximum allowed number of search steps without finding an improvement.
getMaxTimeWithoutImprovement() - Method in class org.corehunter.CoreHunter
Get the maximum allowed time without finding an improvement (milliseconds).
getMeasure() - Method in class org.corehunter.CoreHunterObjective
Gets the measure for this objective if defined
getName() - Method in enum org.corehunter.CoreHunterMeasure
Gets the name of the measure
getName() - Method in enum org.corehunter.CoreHunterObjectiveType
Gets the name of the type
getName() - Method in enum org.corehunter.data.CoreHunterDataType
 
getNames(Data) - Static method in class org.corehunter.API
 
getNeverSelected() - Method in class org.corehunter.CoreHunterArguments
 
getNormalizationRange() - Method in class org.corehunter.CoreHunterObjective
Gets the normalization range of this objective when used in a multi-objective configuration.
getNormalizationRanges(CoreHunterArguments, String, int, int, long, long, long) - Static method in class org.corehunter.API
Get normalization ranges of all objectives in a multi-objective configuration.
getNumberOfAlleles(int) - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the number of alleles for a given marker.
getNumberOfAlleles(int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getNumberOfAlleles(int) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getNumberOfMarkers() - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the total number of markers used in this dataset.
getNumberOfMarkers() - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getNumberOfMarkers() - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getNumberOfObservedAllelesPerIndividual(int) - Method in interface org.corehunter.data.DefaultGenotypeData
Get the number of observed alleles per individual for a given marker.
getNumberOfObservedAllelesPerIndividual(int) - Method in class org.corehunter.data.simple.SimpleDefaultGenotypeData
 
getNumSelected() - Method in class org.corehunter.objectives.eval.AllelicDiversityEvaluation
 
getObjectives() - Method in class org.corehunter.CoreHunterArguments
 
getObjectiveType() - Method in class org.corehunter.CoreHunterObjective
Gets the objective type for this objective
getObservedAllele(int, int, int) - Method in interface org.corehunter.data.DefaultGenotypeData
Get the reference of the i-th observed allele for the given marker, in the given entry.
getObservedAllele(int, int, int) - Method in class org.corehunter.data.simple.SimpleDefaultGenotypeData
 
getPhenotypicData() - Method in class org.corehunter.data.CoreHunterData
 
getPrefix() - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
getRanges(SimplePhenotypeData) - Static method in class org.corehunter.API
 
getSubsetSize() - Method in class org.corehunter.CoreHunterArguments
 
getTimeLimit() - Method in class org.corehunter.CoreHunter
Get execution time limit (milliseconds).
getTotalNumberOfAlleles() - Method in interface org.corehunter.data.FrequencyGenotypeData
Get the total number of allele across all markers.
getTotalNumberOfAlleles() - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
getTotalNumberOfAlleles() - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
getUpper() - Method in class org.corehunter.Range
 
getValidMeasures(CoreHunterObjectiveType) - Method in class org.corehunter.data.CoreHunterData
 
getValidObjectiveTypes() - Method in class org.corehunter.data.CoreHunterData
 
getValue() - Method in class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Compute average distance from each registered item to closest selected item.
getValue() - Method in class org.corehunter.objectives.eval.CoverageEvaluation
 
getValue() - Method in class org.corehunter.objectives.eval.HeterozygousLociEvaluation
 
getValue() - Method in class org.corehunter.objectives.eval.ShannonEvaluation
 
getWeight() - Method in class org.corehunter.CoreHunterObjective
Gets the relative weight of this objective when used in conjunction with another objective.
GowerDistance - Class in org.corehunter.objectives.distance.measures
 
GowerDistance() - Constructor for class org.corehunter.objectives.distance.measures.GowerDistance
 

H

hasDistances() - Method in class org.corehunter.data.CoreHunterData
 
hasGenotypes() - Method in class org.corehunter.data.CoreHunterData
 
hashCode() - Method in class org.corehunter.CoreHunterObjective
 
hasMissingValues(int, int) - Method in interface org.corehunter.data.FrequencyGenotypeData
Indicates whether there are missing values (frequencies) for the given entry (sample/accession) at the given marker.
hasMissingValues(int, int) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
hasMissingValues(int, int) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
hasPhenotypes() - Method in class org.corehunter.data.CoreHunterData
 
HeterozygousLoci - Class in org.corehunter.objectives
Expected proportion of heterozygous loci in offspring.
HeterozygousLoci() - Constructor for class org.corehunter.objectives.HeterozygousLoci
 
HeterozygousLociBiAllelic - Class in org.corehunter.objectives.biallelic
 
HeterozygousLociBiAllelic() - Constructor for class org.corehunter.objectives.biallelic.HeterozygousLociBiAllelic
 
HeterozygousLociEvaluation - Class in org.corehunter.objectives.eval
 
HeterozygousLociEvaluation(Collection<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.HeterozygousLociEvaluation
 
HeterozygousLociEvaluation(AllelicDiversityEvaluation, Set<Integer>, Set<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.HeterozygousLociEvaluation
 

I

inferMarkerNames(String[]) - Static method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
Infer marker names and number of columns per marker from column names.
isBlank(String) - Static method in class org.corehunter.util.StringUtils
Checks whether the given string is blank.
isMinimizing() - Method in class org.corehunter.objectives.AverageAccessionToNearestEntry
 
isMinimizing() - Method in class org.corehunter.objectives.AverageEntryToEntry
 
isMinimizing() - Method in class org.corehunter.objectives.AverageEntryToNearestEntry
 
isMinimizing() - Method in class org.corehunter.objectives.biallelic.CoverageBiAllelic
 
isMinimizing() - Method in class org.corehunter.objectives.biallelic.HeterozygousLociBiAllelic
 
isMinimizing() - Method in class org.corehunter.objectives.biallelic.ShannonBiAllelic
 
isMinimizing() - Method in class org.corehunter.objectives.Coverage
 
isMinimizing() - Method in class org.corehunter.objectives.HeterozygousLoci
 
isMinimizing() - Method in class org.corehunter.objectives.Shannon
 
isNormalized() - Method in class org.corehunter.CoreHunterArguments
 
isSameObjective(CoreHunterObjective) - Method in class org.corehunter.CoreHunterObjective
Determines if this objective is the same except for the weights and normalizationRange, which can any be value

M

MISSING_ALLELE_SCORE - Static variable in class org.corehunter.util.CoreHunterConstants
Byte value used to indicate missing allele scores.
missingValueContribution(double) - Method in class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
 
MissingValuesPolicy - Enum in org.corehunter.objectives.distance.measures
 
ModifiedRogersDistance - Class in org.corehunter.objectives.distance.measures
 
ModifiedRogersDistance() - Constructor for class org.corehunter.objectives.distance.measures.ModifiedRogersDistance
 
ModifiedRogersDistanceBiAllelic - Class in org.corehunter.objectives.distance.measures.biallelic
 
ModifiedRogersDistanceBiAllelic() - Constructor for class org.corehunter.objectives.distance.measures.biallelic.ModifiedRogersDistanceBiAllelic
 

N

NearestEntry - Class in org.corehunter.objectives.distance.eval
 
NearestEntry(int, double) - Constructor for class org.corehunter.objectives.distance.eval.NearestEntry
 
NearestEntryEvaluation - Class in org.corehunter.objectives.distance.eval
Stores metadata for efficient delta evaluation in AverageEntryToNearestEntry and AverageAccessionToNearestEntry.
NearestEntryEvaluation(double) - Constructor for class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
 
NearestEntryEvaluation(NearestEntryEvaluation) - Constructor for class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Deep copy constructor
newBestSolution(Search<? extends SubsetSolution>, SubsetSolution, Evaluation, Validation) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
normalize(CoreHunterArguments) - Method in class org.corehunter.CoreHunter
Determine normalization ranges of all objectives in a multi-objective configuration, based on the Pareto minima/maxima.

O

org.corehunter - package org.corehunter
 
org.corehunter.data - package org.corehunter.data
 
org.corehunter.data.simple - package org.corehunter.data.simple
 
org.corehunter.exceptions - package org.corehunter.exceptions
 
org.corehunter.listener - package org.corehunter.listener
 
org.corehunter.objectives - package org.corehunter.objectives
 
org.corehunter.objectives.biallelic - package org.corehunter.objectives.biallelic
 
org.corehunter.objectives.distance - package org.corehunter.objectives.distance
 
org.corehunter.objectives.distance.eval - package org.corehunter.objectives.distance.eval
 
org.corehunter.objectives.distance.measures - package org.corehunter.objectives.distance.measures
 
org.corehunter.objectives.distance.measures.biallelic - package org.corehunter.objectives.distance.measures.biallelic
 
org.corehunter.objectives.eval - package org.corehunter.objectives.eval
 
org.corehunter.util - package org.corehunter.util
 

P

PhenotypeData - Interface in org.corehunter.data
Phenotype data contains features
PrecomputedDistance - Class in org.corehunter.objectives.distance.measures
 
PrecomputedDistance() - Constructor for class org.corehunter.objectives.distance.measures.PrecomputedDistance
 
preprocessingStarted(String) - Method in interface org.corehunter.CoreHunterListener
Fired when the pre-processing has started.
preprocessingStarted(String) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
preprocessingStopped(String) - Method in interface org.corehunter.CoreHunterListener
Fired when the pre-processing has stopped.
preprocessingStopped(String) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 

R

Range<T extends Number> - Class in org.corehunter
A closed range with a given lower and upper bound.
Range(T, T) - Constructor for class org.corehunter.Range
 
readData(Path, FileType) - Method in enum org.corehunter.data.GenotypeDataFormat
 
readData(Path, FileType) - Static method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
Read biallelic genotype data from file.
readData(Path, FileType) - Static method in class org.corehunter.data.simple.SimpleDefaultGenotypeData
Read default genotype data from file.
readData(Path, FileType) - Static method in class org.corehunter.data.simple.SimpleDistanceMatrixData
Read distance matrix data from file.
readData(Path, FileType) - Static method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
Read genotype data from file.
readDistanceMatrixData(String) - Static method in class org.corehunter.API
 
readGenotypeData(String, String) - Static method in class org.corehunter.API
 
readPhenotypeData(String) - Static method in class org.corehunter.API
 
readPhenotypeData(Path, FileType, DataOption...) - Static method in class org.corehunter.data.simple.SimplePhenotypeData
 
remove(int) - Method in class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Remove item and the registered closest entry (if any).

S

sampleCore(CoreHunterArguments, String, int, int, long, long, long, boolean) - Static method in class org.corehunter.API
Sample a core collection.
searchStarted(Search<? extends SubsetSolution>) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
searchStopped(Search<? extends SubsetSolution>) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
setListener(CoreHunterListener) - Method in class org.corehunter.CoreHunter
 
setMaxSteps(long) - Method in class org.corehunter.CoreHunter
Sets the maximum number of search steps.
setMaxStepsWithoutImprovement(long) - Method in class org.corehunter.CoreHunter
Sets the maximum allowed number of search steps without finding an improvement.
setMaxTimeWithoutImprovement(long) - Method in class org.corehunter.CoreHunter
Sets the maximum time without finding any improvements (in milliseconds).
setMeasure(CoreHunterMeasure) - Method in class org.corehunter.CoreHunterObjective
Gets the measure for this objective if defined
setMissingValuesPolicy(MissingValuesPolicy) - Method in interface org.corehunter.objectives.distance.DistanceMeasure
Determines the contribution of variables (markers/features) with missing values to the distance between two items.
setMissingValuesPolicy(MissingValuesPolicy) - Method in class org.corehunter.objectives.distance.measures.AbstractDistanceMeasure
 
setMissingValuesPolicy(MissingValuesPolicy) - Method in class org.corehunter.objectives.distance.measures.PrecomputedDistance
 
setNormalizationRange(Range<Double>) - Method in class org.corehunter.CoreHunterObjective
Sets the normalization range of this objective when used in a multi-objective configuration.
setObjectiveType(CoreHunterObjectiveType) - Method in class org.corehunter.CoreHunterObjective
Sets the objective type for this objective
setPrefix(String) - Method in class org.corehunter.listener.SimpleCoreHunterListener
 
setSeed(long) - Method in class org.corehunter.CoreHunter
 
setTimeLimit(long) - Method in class org.corehunter.CoreHunter
Sets the absolute time limit (in milliseconds).
setWeight(double) - Method in class org.corehunter.CoreHunterObjective
Sets the relative weight of this objective when used in conjunction with another objective.
Shannon - Class in org.corehunter.objectives
 
Shannon() - Constructor for class org.corehunter.objectives.Shannon
 
ShannonBiAllelic - Class in org.corehunter.objectives.biallelic
 
ShannonBiAllelic() - Constructor for class org.corehunter.objectives.biallelic.ShannonBiAllelic
 
ShannonEvaluation - Class in org.corehunter.objectives.eval
 
ShannonEvaluation(Collection<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.ShannonEvaluation
 
ShannonEvaluation(AllelicDiversityEvaluation, Set<Integer>, Set<Integer>, FrequencyGenotypeData) - Constructor for class org.corehunter.objectives.eval.ShannonEvaluation
 
SimpleBiAllelicGenotypeData - Class in org.corehunter.data.simple
 
SimpleBiAllelicGenotypeData(SimpleEntity[], String[], byte[][]) - Constructor for class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
Create data with name "Biallelic marker data".
SimpleBiAllelicGenotypeData(String, SimpleEntity[], String[], byte[][]) - Constructor for class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
Create data with given dataset name, item headers, marker names and allele scores.
SimpleCoreHunterListener - Class in org.corehunter.listener
 
SimpleCoreHunterListener() - Constructor for class org.corehunter.listener.SimpleCoreHunterListener
 
SimpleCoreHunterListener(PrintStream) - Constructor for class org.corehunter.listener.SimpleCoreHunterListener
 
SimpleDefaultGenotypeData - Class in org.corehunter.data.simple
 
SimpleDefaultGenotypeData(SimpleEntity[], String[], String[][][]) - Constructor for class org.corehunter.data.simple.SimpleDefaultGenotypeData
Create data with name "Default marker data".
SimpleDefaultGenotypeData(String, SimpleEntity[], String[], String[][][]) - Constructor for class org.corehunter.data.simple.SimpleDefaultGenotypeData
Create data with given dataset name, item headers, marker/allele names and allele frequencies.
SimpleDistanceMatrixData - Class in org.corehunter.data.simple
Simple implementation of a distance matrix that stores all values in a two-dimensional double array.
SimpleDistanceMatrixData(SimpleEntity[], double[][]) - Constructor for class org.corehunter.data.simple.SimpleDistanceMatrixData
Create distance matrix data given the item headers and distances.
SimpleDistanceMatrixData(String, SimpleEntity[], double[][]) - Constructor for class org.corehunter.data.simple.SimpleDistanceMatrixData
Create distance matrix data given the dataset name, item headers and distances.
SimpleFrequencyGenotypeData - Class in org.corehunter.data.simple
 
SimpleFrequencyGenotypeData(SimpleEntity[], String[], String[][], double[][][]) - Constructor for class org.corehunter.data.simple.SimpleFrequencyGenotypeData
Create data with name "Allele frequency data".
SimpleFrequencyGenotypeData(String, SimpleEntity[], String[], String[][], double[][][]) - Constructor for class org.corehunter.data.simple.SimpleFrequencyGenotypeData
Create data with given dataset name, item headers, marker/allele names and allele frequencies.
SimplePhenotypeData - Class in org.corehunter.data.simple
 
SimplePhenotypeData(String, Feature[], Object[][]) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, List<? extends Feature>, List<List<Object>>) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, List<? extends Feature>, List<SimpleEntity>, List<List<Object>>) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, List<? extends Feature>, SimpleEntity[], Object[][]) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, String, Feature[], Object[][]) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, String, List<? extends Feature>, List<List<Object>>) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, String, List<? extends Feature>, List<SimpleEntity>, List<List<Object>>) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(String, String, List<? extends Feature>, SimpleEntity[], Object[][]) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
SimplePhenotypeData(ArrayFeatureData) - Constructor for class org.corehunter.data.simple.SimplePhenotypeData
 
StringUtils - Class in org.corehunter.util
 

T

toString() - Method in class org.corehunter.CoreHunterObjective
 
toString() - Method in enum org.corehunter.CoreHunterObjectiveType
 
toString() - Method in class org.corehunter.objectives.AverageAccessionToNearestEntry
 
toString() - Method in class org.corehunter.objectives.AverageEntryToEntry
 
toString() - Method in class org.corehunter.objectives.AverageEntryToNearestEntry
 
toString() - Method in class org.corehunter.objectives.Coverage
 
toString() - Method in class org.corehunter.objectives.distance.measures.CavalliSforzaEdwardsDistance
 
toString() - Method in class org.corehunter.objectives.distance.measures.GowerDistance
 
toString() - Method in class org.corehunter.objectives.distance.measures.ModifiedRogersDistance
 
toString() - Method in class org.corehunter.objectives.distance.measures.PrecomputedDistance
 
toString() - Method in class org.corehunter.objectives.HeterozygousLoci
 
toString() - Method in class org.corehunter.objectives.Shannon
 

U

unquote(String) - Static method in class org.corehunter.util.StringUtils
Removes single or double quote characters from a string.
unquote(String[]) - Static method in class org.corehunter.util.StringUtils
Unquote all strings in the given array.
update(int, NearestEntry) - Method in class org.corehunter.objectives.distance.eval.NearestEntryEvaluation
Update the closest entry of a previously registered item.

V

valueOf(String) - Static method in enum org.corehunter.CoreHunterExecutionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.corehunter.CoreHunterMeasure
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.corehunter.CoreHunterObjectiveType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.corehunter.data.CoreHunterDataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.corehunter.data.GenotypeDataFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.corehunter.objectives.distance.measures.MissingValuesPolicy
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.corehunter.CoreHunterExecutionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.corehunter.CoreHunterMeasure
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.corehunter.CoreHunterObjectiveType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.corehunter.data.CoreHunterDataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.corehunter.data.GenotypeDataFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.corehunter.objectives.distance.measures.MissingValuesPolicy
Returns an array containing the constants of this enum type, in the order they are declared.

W

writeData(Path, FileType) - Method in interface org.corehunter.data.FrequencyGenotypeData
Write data to file.
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in interface org.corehunter.data.FrequencyGenotypeData
Write selected data to file.
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in class org.corehunter.data.simple.SimpleBiAllelicGenotypeData
 
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in class org.corehunter.data.simple.SimpleDefaultGenotypeData
 
writeData(Path, FileType) - Method in class org.corehunter.data.simple.SimpleDistanceMatrixData
Write distance matrix to file.
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in class org.corehunter.data.simple.SimpleDistanceMatrixData
Write subset of the distance matrix to file and in the order of ids in the solution.
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in class org.corehunter.data.simple.SimpleFrequencyGenotypeData
 
writeData(Path, FileType, SubsetSolution, boolean, boolean, boolean) - Method in class org.corehunter.data.simple.SimplePhenotypeData
Write phenotype data to file.
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