Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class VariationDescriptorBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

public class VariationDescriptorBuilder
extends Object

Method Summary

Modifier and Type	Method	Description
VariationDescriptorBuilder	addAllAlternateLabels(List<String> altLabels)
VariationDescriptorBuilder	addAllXrefs(List<String> xrefs)
VariationDescriptorBuilder	addAlternateLabel(String altLabel)
VariationDescriptorBuilder	addExpression(org.ga4gh.vrsatile.v1.Expression expression)
VariationDescriptorBuilder	addXref(String xref)
VariationDescriptorBuilder	alleleFrequency(double frequency)
org.ga4gh.vrsatile.v1.VariationDescriptor	build()
static VariationDescriptorBuilder	builder()	Deprecated, for removal: This API element is subject to removal in a future version. use builder(String) instead.
static VariationDescriptorBuilder	builder(String variantId)
VariationDescriptorBuilder	description(String desc)
VariationDescriptorBuilder	geneContext(org.ga4gh.vrsatile.v1.GeneDescriptor gene)
VariationDescriptorBuilder	genomic()
VariationDescriptorBuilder	hemizygous()
VariationDescriptorBuilder	heterozygous()
VariationDescriptorBuilder	hgvs(String value)
VariationDescriptorBuilder	homozygous()
VariationDescriptorBuilder	iscn(String value)
VariationDescriptorBuilder	label(String lbl)
VariationDescriptorBuilder	mosaicism(double percentage)
VariationDescriptorBuilder	protein()
VariationDescriptorBuilder	spdi(String value)
VariationDescriptorBuilder	structuralType(org.phenopackets.schema.v2.core.OntologyClass structuralType)
VariationDescriptorBuilder	transcript()
VariationDescriptorBuilder	unspecifiedZygosity()
VariationDescriptorBuilder	variation(org.ga4gh.vrs.v1.Variation variation)
VariationDescriptorBuilder	vcfHg37(String chromosome, int position, String ref, String alt)
VariationDescriptorBuilder	vcfHg38(String chromosome, int position, String ref, String alt)
VariationDescriptorBuilder	vcfRecord(org.ga4gh.vrsatile.v1.VcfRecord vcf)
VariationDescriptorBuilder	zygosity(org.phenopackets.schema.v2.core.OntologyClass zygo)

Methods inherited from class java.lang.Object

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

Method Details

builder

@Deprecated(forRemoval=true,
            since="0.4.8")
public static VariationDescriptorBuilder builder()

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

use builder(String) instead. The id is a required field and it should not be possible to create a builder without an id.

builder

public static VariationDescriptorBuilder builder(String variantId)

label

public VariationDescriptorBuilder label(String lbl)

variation

public VariationDescriptorBuilder variation(org.ga4gh.vrs.v1.Variation variation)

description

public VariationDescriptorBuilder description(String desc)

geneContext

public VariationDescriptorBuilder geneContext(org.ga4gh.vrsatile.v1.GeneDescriptor gene)

vcfRecord

public VariationDescriptorBuilder vcfRecord(org.ga4gh.vrsatile.v1.VcfRecord vcf)

addXref

public VariationDescriptorBuilder addXref(String xref)

addAllXrefs

public VariationDescriptorBuilder addAllXrefs(List<String> xrefs)

addAlternateLabel

public VariationDescriptorBuilder addAlternateLabel(String altLabel)

addAllAlternateLabels

public VariationDescriptorBuilder addAllAlternateLabels(List<String> altLabels)

genomic

public VariationDescriptorBuilder genomic()

protein

public VariationDescriptorBuilder protein()

transcript

public VariationDescriptorBuilder transcript()

structuralType

public VariationDescriptorBuilder structuralType(org.phenopackets.schema.v2.core.OntologyClass structuralType)

heterozygous

public VariationDescriptorBuilder heterozygous()

homozygous

public VariationDescriptorBuilder homozygous()

hemizygous

public VariationDescriptorBuilder hemizygous()

unspecifiedZygosity

public VariationDescriptorBuilder unspecifiedZygosity()

zygosity

public VariationDescriptorBuilder zygosity(org.phenopackets.schema.v2.core.OntologyClass zygo)

hgvs

public VariationDescriptorBuilder hgvs(String value)

spdi

public VariationDescriptorBuilder spdi(String value)

iscn

public VariationDescriptorBuilder iscn(String value)

addExpression

public VariationDescriptorBuilder addExpression(org.ga4gh.vrsatile.v1.Expression expression)

vcfHg38

public VariationDescriptorBuilder vcfHg38(String chromosome,
 int position,
 String ref,
 String alt)

vcfHg37

public VariationDescriptorBuilder vcfHg37(String chromosome,
 int position,
 String ref,
 String alt)

mosaicism

public VariationDescriptorBuilder mosaicism(double percentage)

Parameters:

percentage - estimated percentage of cells affected by mosaic variant, e.g., 40%

alleleFrequency

public VariationDescriptorBuilder alleleFrequency(double frequency)

Parameters:

frequency - estimated frequency (IN PERCENT) of an allele (generally a somatic mutation)

build

public org.ga4gh.vrsatile.v1.VariationDescriptor build()