Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class AlleleBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

public class AlleleBuilder
extends Object

Create a VRS Allele object such as {'_id': 'ga4gh:VA.GuPzvZoansqNHPoXkQLXKo31VkTpDKsM', 'type': 'Allele', 'location': {'type': 'SequenceLocation', 'sequence_id': 'ga4gh:SQ.FOWokFmA__GgqWLtqFoWWDLuNEvvGwIJ', 'interval': {'type': 'SequenceInterval', 'start': {'type': 'Number', 'value': 48941647}, 'end': {'type': 'Number', 'value': 48941648}}}, 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'T'}}

Method Summary

Modifier and Type	Method	Description
AlleleBuilder	altAllele(String alt)
org.ga4gh.vrs.v1.Allele	build()
static AlleleBuilder	builder()
org.ga4gh.vrs.v1.Variation	buildVariation()	Wrap the Allele message in a Variation message
AlleleBuilder	chromosomeLocation(String chrom)
AlleleBuilder	interbaseStartEnd(int start, int end)	Sequence ranges use an interbase coordinate system, which involves Two integers that define the start and end positions of a range of residues, possibly with length zero, and specified using “0-start, half-open” coordinates.
AlleleBuilder	sequenceId(String sequenceId)
AlleleBuilder	variantId(String id)

Methods inherited from class java.lang.Object

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

Method Details

variantId

public AlleleBuilder variantId(String id)

chromosomeLocation

public AlleleBuilder chromosomeLocation(String chrom)

interbaseStartEnd

public AlleleBuilder interbaseStartEnd(int start,
 int end)

Sequence ranges use an interbase coordinate system, which involves Two integers that define the start and end positions of a range of residues, possibly with length zero, and specified using “0-start, half-open” coordinates.

altAllele

public AlleleBuilder altAllele(String alt)

sequenceId

public AlleleBuilder sequenceId(String sequenceId)

builder

public static AlleleBuilder builder()

build

public org.ga4gh.vrs.v1.Allele build()

buildVariation

public org.ga4gh.vrs.v1.Variation buildVariation()

Wrap the Allele message in a Variation message

Returns:

The constructed Variant message that contains the Allele and if provided SequenceLocation information.