Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class CopyNumberBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

public class CopyNumberBuilder
extends Object

Method Summary

Modifier and Type	Method	Description
CopyNumberBuilder	alleleLocation(String contig, int interbaseStartPos, int interbaseEndPos)	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.
org.ga4gh.vrs.v1.CopyNumber	build()
static CopyNumberBuilder	builder()
org.ga4gh.vrs.v1.Variation	buildVariation()	Wrap the Allele message in a Variation message
CopyNumberBuilder	copyNumberId(String id)
CopyNumberBuilder	nCopies(int n)
CopyNumberBuilder	oneCopy()
CopyNumberBuilder	threeCopies()
CopyNumberBuilder	twoCopies()

Methods inherited from class java.lang.Object

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

Method Details

copyNumberId

public CopyNumberBuilder copyNumberId(String id)

alleleLocation

public CopyNumberBuilder alleleLocation(String contig,
 int interbaseStartPos,
 int interbaseEndPos)

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.

build

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

oneCopy

public CopyNumberBuilder oneCopy()

twoCopies

public CopyNumberBuilder twoCopies()

threeCopies

public CopyNumberBuilder threeCopies()

nCopies

public CopyNumberBuilder nCopies(int n)

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.

builder

public static CopyNumberBuilder builder()