Module org.phenopackets.phenopackettools.validator.core

Package org.phenopackets.phenopackettools.validator.core.phenotype

Class HpoPhenotypeValidators.Primary

java.lang.Object

org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary

Enclosing class:

HpoPhenotypeValidators

public static class HpoPhenotypeValidators.Primary
extends Object

A static factory class for providing PhenopacketValidators that check if HPO terms of the Phenopacket schema elements are present in a given Ontology and if the terms are non-obsolete.

Constructor Summary

Constructors

Constructor	Description
Primary()

Method Summary

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	cohortHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator for performing primary validation Cohort using provided Ontology, as described in AbstractHpoPhenotypeValidator.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	familyHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator for validate Family using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	phenopacketHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate Phenopacket using provided Ontology.

Methods inherited from class java.lang.Object

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

Constructor Details

Primary

public Primary()

Method Details

phenopacketHpoPhenotypeValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder> phenopacketHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator to validate Phenopacket using provided Ontology.

Parameters:

hpo - HPO ontology

familyHpoPhenotypeValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder> familyHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator for validate Family using provided Ontology.

Parameters:

hpo - HPO ontology

cohortHpoPhenotypeValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder> cohortHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator for performing primary validation Cohort using provided Ontology, as described in AbstractHpoPhenotypeValidator.

Parameters:

hpo - HPO ontology