Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class IndividualBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

public class IndividualBuilder
extends Object

An Individual in the version 2 phenopacket can have these attributes. Only the id is required.

1. id (string)
2. alternate_ids (a list)
3. date_of_birth (timestamp)
4. time_at_last_encounter (TimeElement)
5. vital_status (VitalStatus)
6. sex (Sex)
7. karyotypic_sex (KaryotypicSex)
8. taxonomy (Ontology term)

Author:

Peter N Robinson

Method Summary

Modifier and Type	Method	Description
IndividualBuilder	addAllAlternateIds(List<String> altIdList)
IndividualBuilder	addAlternateId(String altId)
IndividualBuilder	ageAtLastEncounter(String iso8601)
IndividualBuilder	ageAtLastEncounter(org.phenopackets.schema.v2.core.TimeElement timeElement)
IndividualBuilder	alive()
org.phenopackets.schema.v2.core.Individual	build()
static IndividualBuilder	builder(String id)
IndividualBuilder	dateOfBirth(String dobirth)
IndividualBuilder	dateOfBirth(LocalDate localDate)
IndividualBuilder	deceased()
IndividualBuilder	female()
IndividualBuilder	homoSapiens()
IndividualBuilder	male()
static org.phenopackets.schema.v2.core.Individual	of(String id)
IndividualBuilder	otherSex()
IndividualBuilder	taxonomy(org.phenopackets.schema.v2.core.OntologyClass taxon)
IndividualBuilder	timestampAtLastEncounter(String timestamp)
IndividualBuilder	unknownSex()
IndividualBuilder	vitalStatus(org.phenopackets.schema.v2.core.VitalStatus status)
IndividualBuilder	XO()
IndividualBuilder	XX()
IndividualBuilder	XXX()
IndividualBuilder	XXXX()
IndividualBuilder	XXXY()
IndividualBuilder	XXY()
IndividualBuilder	XXYY()
IndividualBuilder	XY()

Methods inherited from class java.lang.Object

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

Method Details

of

public static org.phenopackets.schema.v2.core.Individual of(String id)

builder

public static IndividualBuilder builder(String id)

addAlternateId

public IndividualBuilder addAlternateId(String altId)

addAllAlternateIds

public IndividualBuilder addAllAlternateIds(List<String> altIdList)

dateOfBirth

public IndividualBuilder dateOfBirth(LocalDate localDate)

dateOfBirth

public IndividualBuilder dateOfBirth(String dobirth)

timestampAtLastEncounter

public IndividualBuilder timestampAtLastEncounter(String timestamp)

ageAtLastEncounter

public IndividualBuilder ageAtLastEncounter(org.phenopackets.schema.v2.core.TimeElement timeElement)

ageAtLastEncounter

public IndividualBuilder ageAtLastEncounter(String iso8601)

alive

public IndividualBuilder alive()

deceased

public IndividualBuilder deceased()

vitalStatus

public IndividualBuilder vitalStatus(org.phenopackets.schema.v2.core.VitalStatus status)

male

public IndividualBuilder male()

female

public IndividualBuilder female()

unknownSex

public IndividualBuilder unknownSex()

otherSex

public IndividualBuilder otherSex()

XX

public IndividualBuilder XX()

XY

public IndividualBuilder XY()

XO

public IndividualBuilder XO()

XXY

public IndividualBuilder XXY()

XXX

public IndividualBuilder XXX()

XXYY

public IndividualBuilder XXYY()

XXXY

public IndividualBuilder XXXY()

XXXX

public IndividualBuilder XXXX()

taxonomy

public IndividualBuilder taxonomy(org.phenopackets.schema.v2.core.OntologyClass taxon)

homoSapiens

public IndividualBuilder homoSapiens()

build

public org.phenopackets.schema.v2.core.Individual build()