Module org.phenopackets.phenopackettools.validator.core

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

Class HpoPhenotypeValidators

java.lang.Object

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

public class HpoPhenotypeValidators
extends Object

Static factory class for getting PhenopacketValidators for top-level Phenopacket schema components.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	HpoPhenotypeValidators.Ancestry	A static factory class for providing validators for pointing out violations of the annotation propagation rule.
static class	HpoPhenotypeValidators.OrganSystem	A static factory class for providing validators for checking annotation of organ systems.
static class	HpoPhenotypeValidators.Primary	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.

Method Summary

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	cohortHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(Ontology) instead
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	familyHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(Ontology) instead
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	phenopacketHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(Ontology) instead

Methods inherited from class java.lang.Object

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

Method Details

phenopacketHpoPhenotypeValidator

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

Deprecated, for removal: This API element is subject to removal in a future version.

use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(Ontology) instead

Get PhenopacketValidator to validate Phenopacket using provided Ontology.

Parameters:

hpo - HPO ontology

familyHpoPhenotypeValidator

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

Deprecated, for removal: This API element is subject to removal in a future version.

use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(Ontology) instead

Get PhenopacketValidator for validate Family using provided Ontology.

Parameters:

hpo - HPO ontology

cohortHpoPhenotypeValidator

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

Deprecated, for removal: This API element is subject to removal in a future version.

use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(Ontology) instead

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

Parameters:

hpo - HPO ontology