Package org.monarchinitiative.lirical.configuration

Class LiricalBuilder

java.lang.Object

org.monarchinitiative.lirical.configuration.LiricalBuilder

public class LiricalBuilder
extends Object

Build Lirical from provided resources.

The builder needs path to LIRICAL data directory (see LiricalDataResolver for more info) and that is enough for building Lirical with default settings.

Alternatively, a high-level LIRICAL's components can be provided via builder methods.

If shouldLoadOrpha2Gene(boolean) is set, the builder will throw an exception if the Orpha 2 gene mapping file is missing in the data directory.

Method Summary

Modifier and Type	Method	Description
LiricalBuilder	backgroundVariantFrequencyServiceFactory(BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory)
Lirical	build()
static LiricalBuilder	builder(Path liricalDataDirectory)
LiricalBuilder	clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild genomeBuild)
LiricalBuilder	exomiserResources(GenomeBuild genomeBuild, ExomiserResources resources)	Add paths for Exomiser resources required to support the genomeBuild.
LiricalBuilder	exomiserVariantDbPath(GenomeBuild genomeBuild, Path exomiserVariantDatabase)	Deprecated, for removal: This API element is subject to removal in a future version. use exomiserResources(GenomeBuild, ExomiserResources) instead
LiricalBuilder	parallelism(int parallelism)	Set the number threads/workers in the LIRICAL worker pool.
LiricalBuilder	phenotypeService(PhenotypeService phenotypeService)
LiricalBuilder	shouldLoadOrpha2Gene(boolean value)
LiricalBuilder	variantMetadataServiceFactory(VariantMetadataServiceFactory variantMetadataServiceFactory)

Methods inherited from class java.lang.Object

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

Method Details

builder

public static LiricalBuilder builder(Path liricalDataDirectory)
                              throws LiricalDataException

Throws:

LiricalDataException

exomiserVariantDbPath

@Deprecated(forRemoval=true,
            since="2.0.3")
public LiricalBuilder exomiserVariantDbPath(GenomeBuild genomeBuild,
 Path exomiserVariantDatabase)

Deprecated, for removal: This API element is subject to removal in a future version.

use exomiserResources(GenomeBuild, ExomiserResources) instead

Set path to exomiser variant database for given GenomeBuild.

Returns:

the builder

clearExomiserVariantDatabaseForGenomeBuild

public LiricalBuilder clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild genomeBuild)

exomiserResources

public LiricalBuilder exomiserResources(GenomeBuild genomeBuild,
 ExomiserResources resources)

Add paths for Exomiser resources required to support the genomeBuild.

backgroundVariantFrequencyServiceFactory

public LiricalBuilder backgroundVariantFrequencyServiceFactory(BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory)

phenotypeService

public LiricalBuilder phenotypeService(PhenotypeService phenotypeService)

variantMetadataServiceFactory

public LiricalBuilder variantMetadataServiceFactory(VariantMetadataServiceFactory variantMetadataServiceFactory)

shouldLoadOrpha2Gene

public LiricalBuilder shouldLoadOrpha2Gene(boolean value)

parallelism

public LiricalBuilder parallelism(int parallelism)

Set the number threads/workers in the LIRICAL worker pool.

build

public Lirical build()
              throws LiricalDataException

Throws:

LiricalDataException