Modifier and Type | Method and Description |
---|---|
CoreHunterData |
CoreHunterArguments.getData() |
Modifier and Type | Method and Description |
---|---|
static CoreHunterArguments |
API.createArguments(CoreHunterData data,
int size,
CoreHunterObjective[] objectives,
int[] alwaysSelected,
int[] neverSelected,
boolean normalizeMultiObjective) |
static CoreHunterObjective |
API.createDefaultObjective(CoreHunterData coreHunterData)
Creates a default allowed objective for the data.
|
static CoreHunterObjective |
API.createDefaultObjective(CoreHunterData coreHunterData,
List<CoreHunterObjective> currentObjectives)
Creates a default allowed objective for the data given a list existing
objectives.
|
static List<CoreHunterObjective> |
API.createDefaultObjectives(CoreHunterData coreHunterData)
Creates a list of default objectives, one for each type of data available, with equal weights.
|
double |
CoreHunter.evaluate(org.jamesframework.core.subset.SubsetSolution sol,
CoreHunterData data,
CoreHunterObjective objective)
Evaluate the given solution with the specified objective.
|
static double |
API.evaluateCore(int[] selected,
CoreHunterData data,
CoreHunterObjective obj)
Evaluate a core collection.
|
static List<CoreHunterObjective> |
API.getAllAllowedObjectives(CoreHunterData coreHunterData)
Creates a list of all possible Core Hunter objectives for a given data object, with equal weights.
|
static List<CoreHunterMeasure> |
API.getAllowedMeasures(CoreHunterData coreHunterData,
CoreHunterObjectiveType objectiveType)
Create a list of all possible Core Hunter measures for a given data object and objective type.
|
static List<CoreHunterObjectiveType> |
API.getAllowedObjectiveTypes(CoreHunterData coreHunterData)
Creates a list of all possible Core Hunter objective types for a given data object.
|
Constructor and Description |
---|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
CoreHunterObjectiveType objective)
Creates a single objective configuration with no defined measure.
|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
CoreHunterObjectiveType objective,
CoreHunterMeasure measure)
Creates a single objective configuration.
|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
List<CoreHunterObjective> objectives)
Creates a single- or multi-objective configuration.
|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
List<CoreHunterObjective> objectives,
Set<Integer> alwaysSelected)
Creates a single- or multi-objective configuration with a set of always selected IDs.
|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
List<CoreHunterObjective> objectives,
Set<Integer> alwaysSelected,
Set<Integer> neverSelected)
Creates a single- or multi-objective configuration with a set of always and/or never selected IDs.
|
CoreHunterArguments(CoreHunterData data,
int subsetSize,
List<CoreHunterObjective> objectives,
Set<Integer> alwaysSelected,
Set<Integer> neverSelected,
boolean normalize)
Creates a single- or multi-objective configuration with set of always and/or never selected IDs.
|
Modifier and Type | Method and Description |
---|---|
ShannonEvaluation |
Shannon.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
HeterozygousLociEvaluation |
HeterozygousLoci.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
CoverageEvaluation |
Coverage.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
NearestEntryEvaluation |
AverageEntryToNearestEntry.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
org.jamesframework.core.problems.objectives.evaluations.Evaluation |
AverageEntryToEntry.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
NearestEntryEvaluation |
AverageAccessionToNearestEntry.evaluate(org.jamesframework.core.search.neigh.Move move,
org.jamesframework.core.subset.SubsetSolution curSolution,
org.jamesframework.core.problems.objectives.evaluations.Evaluation curEvaluation,
CoreHunterData data) |
ShannonEvaluation |
Shannon.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
HeterozygousLociEvaluation |
HeterozygousLoci.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
CoverageEvaluation |
Coverage.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
NearestEntryEvaluation |
AverageEntryToNearestEntry.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
org.jamesframework.core.problems.objectives.evaluations.Evaluation |
AverageEntryToEntry.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
NearestEntryEvaluation |
AverageAccessionToNearestEntry.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
Modifier and Type | Method and Description |
---|---|
org.jamesframework.core.problems.objectives.evaluations.Evaluation |
ShannonBiAllelic.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
org.jamesframework.core.problems.objectives.evaluations.Evaluation |
HeterozygousLociBiAllelic.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
org.jamesframework.core.problems.objectives.evaluations.Evaluation |
CoverageBiAllelic.evaluate(org.jamesframework.core.subset.SubsetSolution solution,
CoreHunterData data) |
Modifier and Type | Method and Description |
---|---|
double |
DistanceMeasure.getDistance(int idX,
int idY,
CoreHunterData data)
Calculates the distance between two items with given ID.
|
Modifier and Type | Method and Description |
---|---|
double |
ModifiedRogersDistance.computeDistance(int idX,
int idY,
CoreHunterData data) |
double |
GowerDistance.computeDistance(int idX,
int idY,
CoreHunterData data) |
double |
CavalliSforzaEdwardsDistance.computeDistance(int idX,
int idY,
CoreHunterData data) |
protected abstract double |
AbstractDistanceMeasure.computeDistance(int idX,
int idY,
CoreHunterData data)
Compute distance.
|
double |
PrecomputedDistance.getDistance(int idX,
int idY,
CoreHunterData data) |
double |
AbstractDistanceMeasure.getDistance(int idX,
int idY,
CoreHunterData data)
Retrieve a distance from the cache.
|
Modifier and Type | Method and Description |
---|---|
double |
ModifiedRogersDistanceBiAllelic.computeDistance(int idX,
int idY,
CoreHunterData data) |
double |
CavalliSforzaEdwardsDistanceBiAllelic.computeDistance(int idX,
int idY,
CoreHunterData data) |
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