Package org.monarchinitiative.lirical.core.analysis

Class AnalysisOptions.Builder

java.lang.Object

org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder

Enclosing interface:

AnalysisOptions

public static class AnalysisOptions.Builder
extends Object

A builder for AnalysisOptions.

Method Summary

Modifier and Type	Method	Description
AnalysisOptions.Builder	addDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)
AnalysisOptions.Builder	addDiseaseDatabases(org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase... diseaseDatabases)
AnalysisOptions	build()
AnalysisOptions.Builder	clearDiseaseDatabases()
AnalysisOptions.Builder	defaultVariantBackgroundFrequency(double defaultVariantBackgroundFrequency)
AnalysisOptions.Builder	genomeBuild(GenomeBuild genomeBuild)
AnalysisOptions.Builder	includeDiseasesWithNoDeleteriousVariants(boolean includeDiseasesWithNoDeleteriousVariants)
AnalysisOptions.Builder	pretestProbability(PretestDiseaseProbability pretestDiseaseProbability)
AnalysisOptions.Builder	setDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)
AnalysisOptions.Builder	transcriptDatabase(TranscriptDatabase transcriptDatabase)
AnalysisOptions.Builder	useGlobal(boolean useGlobal)
AnalysisOptions.Builder	useStrictPenalties(boolean useStrictPenalties)
AnalysisOptions.Builder	variantDeleteriousnessThreshold(float variantDeleteriousnessThreshold)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

genomeBuild

public AnalysisOptions.Builder genomeBuild(GenomeBuild genomeBuild)

transcriptDatabase

public AnalysisOptions.Builder transcriptDatabase(TranscriptDatabase transcriptDatabase)

clearDiseaseDatabases

public AnalysisOptions.Builder clearDiseaseDatabases()

addDiseaseDatabases

public AnalysisOptions.Builder addDiseaseDatabases(org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase... diseaseDatabases)

addDiseaseDatabases

public AnalysisOptions.Builder addDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)

setDiseaseDatabases

public AnalysisOptions.Builder setDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)

variantDeleteriousnessThreshold

public AnalysisOptions.Builder variantDeleteriousnessThreshold(float variantDeleteriousnessThreshold)

defaultVariantBackgroundFrequency

public AnalysisOptions.Builder defaultVariantBackgroundFrequency(double defaultVariantBackgroundFrequency)

useStrictPenalties

public AnalysisOptions.Builder useStrictPenalties(boolean useStrictPenalties)

useGlobal

public AnalysisOptions.Builder useGlobal(boolean useGlobal)

pretestProbability

public AnalysisOptions.Builder pretestProbability(PretestDiseaseProbability pretestDiseaseProbability)

includeDiseasesWithNoDeleteriousVariants

public AnalysisOptions.Builder includeDiseasesWithNoDeleteriousVariants(boolean includeDiseasesWithNoDeleteriousVariants)

build

public AnalysisOptions build()