Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class PhenotypicFeatureBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

public class PhenotypicFeatureBuilder
extends Object

This has convenience methods for building PhenotypicFeature messages with some commonly used options.

Author:

Peter N Robinson

Method Summary

Modifier and Type	Method	Description
PhenotypicFeatureBuilder	addAllEvidence(List<org.phenopackets.schema.v2.core.Evidence> evidenceList)
PhenotypicFeatureBuilder	addAllModifiers(List<org.phenopackets.schema.v2.core.OntologyClass> modifiers)
PhenotypicFeatureBuilder	addEvidence(org.phenopackets.schema.v2.core.Evidence evidence)
PhenotypicFeatureBuilder	addModifier(org.phenopackets.schema.v2.core.OntologyClass modifier)
PhenotypicFeatureBuilder	adultOnset()
org.phenopackets.schema.v2.core.PhenotypicFeature	build()
static PhenotypicFeatureBuilder	builder(String id, String label)
static PhenotypicFeatureBuilder	builder(org.phenopackets.schema.v2.core.OntologyClass feature)
PhenotypicFeatureBuilder	childhoodOnset()
PhenotypicFeatureBuilder	congenitalOnset()
PhenotypicFeatureBuilder	description(String text)
PhenotypicFeatureBuilder	embryonalOnset()
PhenotypicFeatureBuilder	excluded()
PhenotypicFeatureBuilder	fetalOnset()
PhenotypicFeatureBuilder	infantileOnset()
PhenotypicFeatureBuilder	iso8601onset(String iso8601)
static org.phenopackets.schema.v2.core.PhenotypicFeature	of(String id, String label)
static org.phenopackets.schema.v2.core.PhenotypicFeature	of(org.phenopackets.schema.v2.core.OntologyClass feature)
PhenotypicFeatureBuilder	onset(org.phenopackets.schema.v2.core.TimeElement time)
PhenotypicFeatureBuilder	resolution(org.phenopackets.schema.v2.core.TimeElement time)
PhenotypicFeatureBuilder	severity(String id, String label)
PhenotypicFeatureBuilder	severity(org.phenopackets.schema.v2.core.OntologyClass severity)

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.PhenotypicFeature of(org.phenopackets.schema.v2.core.OntologyClass feature)

of

public static org.phenopackets.schema.v2.core.PhenotypicFeature of(String id,
 String label)

builder

public static PhenotypicFeatureBuilder builder(org.phenopackets.schema.v2.core.OntologyClass feature)

builder

public static PhenotypicFeatureBuilder builder(String id,
 String label)

onset

public PhenotypicFeatureBuilder onset(org.phenopackets.schema.v2.core.TimeElement time)

iso8601onset

public PhenotypicFeatureBuilder iso8601onset(String iso8601)

Parameters:

iso8601 - A string such as P10Y4M2D representing the age of onset/observation

congenitalOnset

public PhenotypicFeatureBuilder congenitalOnset()

embryonalOnset

public PhenotypicFeatureBuilder embryonalOnset()

fetalOnset

public PhenotypicFeatureBuilder fetalOnset()

infantileOnset

public PhenotypicFeatureBuilder infantileOnset()

childhoodOnset

public PhenotypicFeatureBuilder childhoodOnset()

adultOnset

public PhenotypicFeatureBuilder adultOnset()

resolution

public PhenotypicFeatureBuilder resolution(org.phenopackets.schema.v2.core.TimeElement time)

severity

public PhenotypicFeatureBuilder severity(String id,
 String label)

severity

public PhenotypicFeatureBuilder severity(org.phenopackets.schema.v2.core.OntologyClass severity)

excluded

public PhenotypicFeatureBuilder excluded()

addEvidence

public PhenotypicFeatureBuilder addEvidence(org.phenopackets.schema.v2.core.Evidence evidence)

addAllEvidence

public PhenotypicFeatureBuilder addAllEvidence(List<org.phenopackets.schema.v2.core.Evidence> evidenceList)

addModifier

public PhenotypicFeatureBuilder addModifier(org.phenopackets.schema.v2.core.OntologyClass modifier)

addAllModifiers

public PhenotypicFeatureBuilder addAllModifiers(List<org.phenopackets.schema.v2.core.OntologyClass> modifiers)

description

public PhenotypicFeatureBuilder description(String text)

build

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