Uses of Enum Class
org.monarchinitiative.lirical.core.model.TranscriptDatabase

Packages that use TranscriptDatabase

Package	Description
org.monarchinitiative.lirical.background
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.
org.monarchinitiative.lirical.core.io	APIs for reading and annotation of genomic variants.
org.monarchinitiative.lirical.core.model	Package with data models.
org.monarchinitiative.lirical.core.service	Package with services used across LIRICAL.
org.monarchinitiative.lirical.io	Parsers for LIRICAL.
org.monarchinitiative.lirical.io.service
org.monarchinitiative.lirical.io.vcf

Uses of TranscriptDatabase in org.monarchinitiative.lirical.background

Fields in org.monarchinitiative.lirical.background declared as TranscriptDatabase

Modifier and Type	Field	Description
protected TranscriptDatabase	BackgroundFrequencyCommand.transcriptDb

Uses of TranscriptDatabase in org.monarchinitiative.lirical.core.analysis

Methods in org.monarchinitiative.lirical.core.analysis that return TranscriptDatabase

Modifier and Type	Method	Description
TranscriptDatabase	AnalysisOptions.transcriptDatabase()

Methods in org.monarchinitiative.lirical.core.analysis with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
AnalysisOptions.Builder	AnalysisOptions.Builder.transcriptDatabase(TranscriptDatabase transcriptDatabase)

Uses of TranscriptDatabase in org.monarchinitiative.lirical.core.io

Methods in org.monarchinitiative.lirical.core.io with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
Optional<VariantParser>	VariantParserFactory.forPath(Path variantResource, GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)

Uses of TranscriptDatabase in org.monarchinitiative.lirical.core.model

Methods in org.monarchinitiative.lirical.core.model that return TranscriptDatabase

Modifier and Type	Method	Description
static TranscriptDatabase	TranscriptDatabase.valueOf(String name)	Returns the enum constant of this class with the specified name.
static TranscriptDatabase[]	TranscriptDatabase.values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods in org.monarchinitiative.lirical.core.model that return types with arguments of type TranscriptDatabase

Modifier and Type	Method	Description
static Optional<TranscriptDatabase>	TranscriptDatabase.parse(String value)

Uses of TranscriptDatabase in org.monarchinitiative.lirical.core.service

Methods in org.monarchinitiative.lirical.core.service with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
Optional<FunctionalVariantAnnotator>	FunctionalVariantAnnotatorService.getFunctionalAnnotator(GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)	Get FunctionalVariantAnnotator for a combination of GenomeBuild and TranscriptDatabase.

Uses of TranscriptDatabase in org.monarchinitiative.lirical.io

Methods in org.monarchinitiative.lirical.io with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
Path	LiricalDataResolver.transcriptCacheFor(GenomeBuild genomeBuild, TranscriptDatabase txDb)

Uses of TranscriptDatabase in org.monarchinitiative.lirical.io.service

Methods in org.monarchinitiative.lirical.io.service with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
Optional<FunctionalVariantAnnotator>	JannovarFunctionalVariantAnnotatorService.getFunctionalAnnotator(GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)

Uses of TranscriptDatabase in org.monarchinitiative.lirical.io.vcf

Methods in org.monarchinitiative.lirical.io.vcf with parameters of type TranscriptDatabase

Modifier and Type	Method	Description
Optional<VariantParser>	VcfVariantParserFactory.forPath(Path path, GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)