Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

ABNORMAL_CELLULAR - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

abnormalSample() - Static method in class org.phenopackets.phenopackettools.builder.constants.MaterialSample

acmgNotProvided() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

acral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

actionabilityUnknown() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

actionable() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

actionable() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

addAdverseEvent(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

addAllAlternateIds(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addAllAlternateIds(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

addAllAlternateLabels(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

addAllAlternateSymbols(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addAllBiosamples(List<Biosample>) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addAllDiagnosticMarkers(List<OntologyClass>) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addAllDoseIntervals(List<DoseInterval>) - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

addAllEvidence(List<Evidence>) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

addAllFileAttributes(Map<String, String>) - Method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

addAllFiles(List<File>) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addAllJsonSchemaPaths(Iterable<Path>) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

Add JSON schemas in bulk.

addAllJsonSchemaUrls(List<URL>) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

Add JSON schemas in bulk.

addAllMeasurements(List<Measurement>) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addAllModifiers(List<OntologyClass>) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

addAllPathologicalTnmFindings(List<OntologyClass>) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addAllPersons(Collection<Pedigree.Person>) - Method in class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

addAllPersons(Pedigree.Person...) - Method in class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

addAllPhenotypicFeatures(List<PhenotypicFeature>) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addAllSemanticValidators(List<PhenopacketValidator<T>>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead

addAllSyntaxValidators(List<PhenopacketValidator<T>>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead

addAllXrefs(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addAllXrefs(List<String>) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

addAlternateId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addAlternateId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

addAlternateLabel(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

addAlternateSymbol(String) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addBiosample(Biosample) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addClinicalTnmFinding(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

addDiagnosticMarker(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addDisease(Disease) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addDiseases(List<Disease>) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addDiseaseStage(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

addDoseInterval(DoseInterval) - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

addEvidence(Evidence) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

addExpression(Expression) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

addExternalReference(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

addExternalReference(ExternalReference) - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

addFile(File) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addFile(File) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addFileAttribute(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

addGenomicInterpretation(GenomicInterpretation) - Method in class org.phenopackets.phenopackettools.builder.builders.DiagnosisBuilder

addInterpretation(Interpretation) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addJsonSchema(URL) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

Register a JSON schema present at a given url to be used as a validator.

addJsonSchema(Path) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

Register a JSON schema present at a given path to be used as a validator.

addMeasurement(Measurement) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addMeasurement(Measurement) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addMeasurements(List<Measurement>) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addMedicalAction(MedicalAction) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addMedicalActions(List<MedicalAction>) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addModifier(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

addPathologicalTnmFinding(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addPerson(Pedigree.Person) - Method in class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

addPhenotypicFeature(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addPhenotypicFeature(String, String) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addPhenotypicFeature(PhenotypicFeature) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

addPhenotypicFeature(PhenotypicFeature) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addPhenotypicFeatures(List<PhenotypicFeature>) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

addResource(Resource) - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

addResult(ValidatorInfo, ValidationResult) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationResults.Builder

addResults(ValidatorInfo, List<ValidationResult>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationResults.Builder

addSemanticValidator(PhenopacketValidator<T>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead

addSyntaxValidator(PhenopacketValidator<T>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead

addUpdate(Update) - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

addValidator(PhenopacketValidator<T>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

Add a validator to the end of the workflow.

addValidators(Collection<? extends PhenopacketValidator<T>>) - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

Add validators to the end of the workflow.

addXref(String) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

addXref(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

AdministrationRoute - Class in org.phenopackets.phenopackettools.builder.constants

AdministrationRoute() - Constructor for class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

adultOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

adultOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

adultOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

adverseEvent() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

adverseEvent() - Static method in class org.phenopackets.phenopackettools.builder.constants.TreatmentTermination

affected() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

age(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Ages

age(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

age(Age) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

ageAtLastEncounter(String) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

ageAtLastEncounter(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

ageRange(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Ages

ageRange(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

ageRange(AgeRange) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

Ages - Class in org.phenopackets.phenopackettools.builder.builders

alive() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

alive() - Static method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

allAdverseEvents(List<OntologyClass>) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

ALLELE_FREQUENCY - Static variable in class org.phenopackets.phenopackettools.builder.builders.Extensions

AlleleBuilder - Class in org.phenopackets.phenopackettools.builder.builders

Create a VRS Allele object such as {'_id': 'ga4gh:VA.GuPzvZoansqNHPoXkQLXKo31VkTpDKsM', 'type': 'Allele', 'location': {'type': 'SequenceLocation', 'sequence_id': 'ga4gh:SQ.FOWokFmA__GgqWLtqFoWWDLuNEvvGwIJ', 'interval': {'type': 'SequenceInterval', 'start': {'type': 'Number', 'value': 48941647}, 'end': {'type': 'Number', 'value': 48941648}}}, 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'T'}}

alleleFrequency(double) - Static method in class org.phenopackets.phenopackettools.builder.builders.Extensions

alleleFrequency(double) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

alleleLocation(String, int, int) - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

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.

AllelicState - Class in org.phenopackets.phenopackettools.builder.constants

AllelicState() - Constructor for class org.phenopackets.phenopackettools.builder.constants.AllelicState

altAllele(String) - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

antenatalOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

antenatalOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

apical() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

askedButUnknown() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

Assays - Class in org.phenopackets.phenopackettools.builder.constants

Assays() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Assays

authorStatementEvidence(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

authorStatementFromPublishedClinicalStudy() - Static method in class org.phenopackets.phenopackettools.builder.constants.Evidence

authorStatementFromPublishedClinicalStudyAutomaticAssertion() - Static method in class org.phenopackets.phenopackettools.builder.constants.Evidence

authorStatementFromPublishedClinicalStudyManualAssertion() - Static method in class org.phenopackets.phenopackettools.builder.constants.Evidence

authorStatementSupportedByTraceableReference() - Static method in class org.phenopackets.phenopackettools.builder.constants.Evidence

axial() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

B

baseSyntaxValidation() - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

benign() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

benign() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

bilateral() - Static method in class org.phenopackets.phenopackettools.builder.constants.Laterality

BiosampleBuilder - Class in org.phenopackets.phenopackettools.builder.builders

BiospecimenType - Class in org.phenopackets.phenopackettools.builder.constants

BiospecimenType() - Constructor for class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

BLOOD - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

bloodDNA() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

bodySite(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

boneMarrowAspirate() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

borderline() - Static method in class org.phenopackets.phenopackettools.builder.constants.Severity

brain() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

BREAST - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

bronchoalveolarLavageFluid() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

bronchocentric() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

build() - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.DiagnosisBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

build() - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

build() - Method in class org.phenopackets.phenopackettools.validator.core.ValidationResults.Builder

build() - Method in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

Finish building of the ValidationWorkflowRunner.

build() - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

Finish building the JsonSchemaValidationWorkflowRunner.

builder() - Static method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

builder() - Static method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

builder() - Static method in class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

builder() - Static method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

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

use VariationDescriptorBuilder.builder(String) instead. The id is a required field and it should not be possible to create a builder without an id.

builder() - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

builder(Timestamp, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

Create a new MetaDataBuilder with time set to now.

builder(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiagnosisBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

builder(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

builder(String, String, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

builder(String, String, int, String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

builder(String, String, String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

builder(VariationDescriptor) - Static method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

builder(VariationDescriptorBuilder) - Static method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

builder(ExternalReference) - Static method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiagnosisBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

builder(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

builder(OntologyClass, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

builder(OntologyClass, ComplexValue) - Static method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

builder(OntologyClass, Value) - Static method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

builder(Procedure) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

builder(RadiationTherapy) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

builder(TherapeuticRegimen) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

builder(Treatment) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

builderWithParentsAsFounders(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

Founders are persons in a PED file whose parents are not included.

buildVariation() - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

Wrap the Allele message in a Variation message

buildVariation() - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

Wrap the Allele message in a Variation message

C

candidate() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

candidate() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

CARDIOVASCULAR - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

category() - Method in exception org.phenopackets.phenopackettools.validator.core.ConversionException

category() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

causative() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

causative() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

causeOfDeath(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

causeOfDeath(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

central() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

centrilobular() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

cerebellum() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

cerebrospinalFluidSample() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

chebiVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

childhoodOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

childhoodOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

childhoodOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

chromosomeLocation(String) - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

clVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

COHORT - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

cohortBuilder() - Static method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

cohortConverter() - Static method in class org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverters

cohortHpoAncestryValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry

Get PhenopacketValidator to validate ancestry Cohort using provided Ontology.

cohortHpoOrganSystemValidator(Ontology, Collection<TermId>) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.OrganSystem

Get PhenopacketValidator to validate annotation of organ systems in a Cohort using provided Ontology and a collection of organ system TermIds.

cohortHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators

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

use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(Ontology) instead

cohortHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary

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

cohortValidator() - Static method in class org.phenopackets.phenopackettools.validator.core.metadata.MetaDataValidators

Get PhenopacketValidator for checking that MetaData of CohortOrBuilder contains Resources for prefixes of all OntologyClass present in given CohortOrBuilder.

completed() - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

completed() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

completed(Diagnosis) - Method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

completeRemission() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

ComplexValueBuilder - Class in org.phenopackets.phenopackettools.builder.builders

comprehensiveCohort() - Static method in class org.phenopackets.phenopackettools.test.TestData.V1

comprehensiveCohort() - Static method in class org.phenopackets.phenopackettools.test.TestData.V2

comprehensiveFamily() - Static method in class org.phenopackets.phenopackettools.test.TestData.V1

comprehensiveFamily() - Static method in class org.phenopackets.phenopackettools.test.TestData.V2

comprehensivePhenopacket() - Static method in class org.phenopackets.phenopackettools.test.TestData.V1

comprehensivePhenopacket() - Static method in class org.phenopackets.phenopackettools.test.TestData.V2

congenitalOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

congenitalOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

congenitalOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

CONNECTIVE_TISSUE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

CONSTITUTIONAL - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

contributory() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

contributory() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

ConversionException - Exception in org.phenopackets.phenopackettools.validator.core

A PhenopacketToolsException that is thrown by PhenopacketConverter in case the provided data has incorrect format.

ConversionException() - Constructor for exception org.phenopackets.phenopackettools.validator.core.ConversionException

ConversionException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.validator.core.ConversionException

convertCohort(Cohort) - Method in interface org.phenopackets.phenopackettools.converter.converters.V1ToV2Converter

Convert v1 Cohort to v2 Cohort.

convertFamily(Family) - Method in interface org.phenopackets.phenopackettools.converter.converters.V1ToV2Converter

Convert v1 Family to v2 Family.

convertPhenopacket(Phenopacket) - Method in interface org.phenopackets.phenopackettools.converter.converters.V1ToV2Converter

Convert v1 Phenopacket to v2 Phenopacket.

CopyNumberBuilder - Class in org.phenopackets.phenopackettools.builder.builders

copyNumberId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

create(String) - Static method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

create(String, MetaData) - Static method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

creatineKinaseActivity() - Static method in class org.phenopackets.phenopackettools.builder.constants.Assays

cumulativeDose(Quantity) - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

D

dateOfBirth(String) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

dateOfBirth(LocalDate) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

deceased() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

deceased() - Static method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

degreeOfAngle() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

derivedFromId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

dermatomal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

description() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

description(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

DiagnosisBuilder - Class in org.phenopackets.phenopackettools.builder.builders

diffuse() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

DIGESTIVE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

diopter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

discontinued() - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

DiseaseBuilder - Class in org.phenopackets.phenopackettools.builder.builders

DiseaseGrade - Class in org.phenopackets.phenopackettools.builder.constants

DiseaseGrade() - Constructor for class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

DiseaseStage - Class in org.phenopackets.phenopackettools.builder.constants

DiseaseStage() - Constructor for class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

distal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

distributedAlongBlaschkoLines() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

DoseIntervalBuilder - Class in org.phenopackets.phenopackettools.builder.builders

drugCentralVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

E

ear() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

EAR - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

earlyYoungAdultOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

ecoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

efoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

ehrMedicationList() - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

ElementSniffer - Class in org.phenopackets.phenopackettools.util.format

Make an educated guess regarding which top-level element of Phenopacket schema is represented in the provided byte[] or InputStream.

ElementSniffException - Exception in org.phenopackets.phenopackettools.util.format

ElementSniffException() - Constructor for exception org.phenopackets.phenopackettools.util.format.ElementSniffException

ElementSniffException(String) - Constructor for exception org.phenopackets.phenopackettools.util.format.ElementSniffException

ElementSniffException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.ElementSniffException

ElementSniffException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.util.format.ElementSniffException

ElementSniffException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.ElementSniffException

embryonalOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

embryonalOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

embryonalOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

empty() - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

ENDOCRINE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

endTime(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

enzymeUnitPerLiter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

equals(Object) - Method in record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Indicates whether some other object is "equal to" this one.

error(ValidatorInfo, String, String) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

Create a ValidationLevel.ERROR result from given data.

ERROR - Enum constant in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

The level for pointing out an issue pertaining to a required field as described in the Phenopacket Schema requirements

Evidence - Class in org.phenopackets.phenopackettools.builder.constants

Evidence() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Evidence

EvidenceBuilder - Class in org.phenopackets.phenopackettools.builder.builders

excluded() - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

excluded() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

Expressions - Class in org.phenopackets.phenopackettools.builder.builders

Expressions() - Constructor for class org.phenopackets.phenopackettools.builder.builders.Expressions

Extensions - Class in org.phenopackets.phenopackettools.builder.builders

Extensions() - Constructor for class org.phenopackets.phenopackettools.builder.builders.Extensions

ExternalReferenceBuilder - Class in org.phenopackets.phenopackettools.builder.builders

eye() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

EYE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

F

FAMILY - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

familyBuilder() - Static method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

FamilyBuilder - Class in org.phenopackets.phenopackettools.builder

familyConverter() - Static method in class org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverters

familyHpoAncestryValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry

Get PhenopacketValidator to validate ancestry Family using provided Ontology.

familyHpoOrganSystemValidator(Ontology, Collection<TermId>) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.OrganSystem

Get PhenopacketValidator to validate annotation of organ systems in a Family using provided Ontology and a collection of organ system TermIds.

familyHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators

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

use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(Ontology) instead

familyHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary

Get PhenopacketValidator for validate Family using provided Ontology.

familyValidator() - Static method in class org.phenopackets.phenopackettools.validator.core.metadata.MetaDataValidators

Get PhenopacketValidator for checking that MetaData of FamilyOrBuilder contains Resources for prefixes of all OntologyClass present in given FamilyOrBuilder.

favorableResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

female() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

female() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

femaleToMaleTranssexual() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

fetalOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

fetalOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

fetalOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

file(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

file(File) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

FileBuilder - Class in org.phenopackets.phenopackettools.builder.builders

files(List<File>) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

filter(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

focal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

forFormat(PhenopacketSchemaVersion) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParserFactory

Get a PhenopacketParser to parse phenopacket with given PhenopacketSchemaVersion.

forFormat(PhenopacketSchemaVersion, PhenopacketFormat) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketPrinterFactory

formalinFixedParaffinEmbeddedDNA() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

FormatSniffer - Class in org.phenopackets.phenopackettools.util.format

Make an educated guess of the format of a top-level element of Phenopacket schema.

FormatSniffException - Exception in org.phenopackets.phenopackettools.util.format

An exception thrown when sniffing of the top-level element of Phenopacket schema cannot be performed.

FormatSniffException() - Constructor for exception org.phenopackets.phenopackettools.util.format.FormatSniffException

FormatSniffException(String) - Constructor for exception org.phenopackets.phenopackettools.util.format.FormatSniffException

FormatSniffException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.FormatSniffException

FormatSniffException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.FormatSniffException

fourTimesDaily() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

fromInstant(Instant) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

fromISO8601(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

Accepts strings like 2021-10-01T18:58:43Z (also valid RFC3339) OR an ISO date time e.g.

fromISO8601LocalDate(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

Accepts strings with the ISO8601 date format e.g.

G

Gender - Class in org.phenopackets.phenopackettools.builder.constants

Gender() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Gender

geneContext(GeneDescriptor) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

geneDescriptor(GeneDescriptor) - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

GeneDescriptorBuilder - Class in org.phenopackets.phenopackettools.builder.builders

generalized() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

GENITOURINARY - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

genomic() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

GenomicInterpretationBuilder - Class in org.phenopackets.phenopackettools.builder.builders

genoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

gestationalAge(int) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

gestationalAge(int, int) - Static method in class org.phenopackets.phenopackettools.builder.builders.Ages

gestationalAge(int, int) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

getInstance() - Static method in interface org.phenopackets.phenopackettools.io.PhenopacketParserFactory

getInstance() - Static method in interface org.phenopackets.phenopackettools.io.PhenopacketPrinterFactory

getParser() - Static method in class org.phenopackets.phenopackettools.util.print.PhenopacketPrintUtil

Get a parser configured for parsing Phenopacket Schema elements from JSON format.

getPrinter() - Static method in class org.phenopackets.phenopackettools.util.print.PhenopacketPrintUtil

Get a printer configured for printing Phenopacket Schema elements into JSON while respecting the special requirements of the schema.

grade1() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

grade2() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

grade3() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

grade3a() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

grade3b() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

grade4() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseGrade

gram() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

gramPerKilogram() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

GROWTH - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

H

hashCode() - Method in record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Returns a hash code value for this object.

HEAD_AND_NECK - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

heart() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

hemizygous() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

hemizygous() - Static method in class org.phenopackets.phenopackettools.builder.constants.AllelicState

herpetiform() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

heterozygous() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

heterozygous() - Static method in class org.phenopackets.phenopackettools.builder.constants.AllelicState

hg37vcf(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

hg38vcf(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

hgncVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

hgvs(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

hgvsCdna(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Expressions

An Human Genome Variation Society (HGVS) expression that denotes a DNA variant https://varnomen.hgvs.org/

histologicalDiagnosis(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

homoSapiens() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

homozygous() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

homozygous() - Static method in class org.phenopackets.phenopackettools.builder.constants.AllelicState

HpoOrganSystems - Class in org.phenopackets.phenopackettools.validator.core.phenotype

A class with constants that correspond to the upper-level HPO organ-system phenotypic abnormalities.

HpoPhenotypeValidators - Class in org.phenopackets.phenopackettools.validator.core.phenotype

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

HpoPhenotypeValidators.Ancestry - Class in org.phenopackets.phenopackettools.validator.core.phenotype

A static factory class for providing validators for pointing out violations of the annotation propagation rule.

HpoPhenotypeValidators.OrganSystem - Class in org.phenopackets.phenopackettools.validator.core.phenotype

A static factory class for providing validators for checking annotation of organ systems.

HpoPhenotypeValidators.Primary - Class in org.phenopackets.phenopackettools.validator.core.phenotype

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.

hpoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

I

id(String) - Method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

id(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

Identifier: Semicolon-separated list of unique identifiers where available If this is a dbSNP/dbVAR variant these rsID/nsvID(s) should be used.

identifiesAsFemale() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

identifiesAsMale() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

identifiesAsNonConforming() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

IMMUNOLOGY - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

individual(Individual) - Method in class org.phenopackets.phenopackettools.builder.PhenopacketBuilder

IndividualBuilder - Class in org.phenopackets.phenopackettools.builder.builders

An Individual in the version 2 phenopacket can have these attributes.

individualId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

individualToFileIdentifier(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.FileBuilder

infantileOnset() - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

infantileOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

infantileOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

info(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

inProgress() - Method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

inProgress() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

inputValidator() - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

Get ValidatorInfo to represent anonymous validator to associate with errors related to data format errors.

INTEGUMENT - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

interbaseStartEnd(int, int) - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

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.

intermediateYoungAdultOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

InterpretationBuilder - Class in org.phenopackets.phenopackettools.builder.builders

interval(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

interval(Instant, Instant) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

intraarterial() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

intraArterialAdministration() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

intrathecal() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

intravenous() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

intravenousAdministration() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

intravenousAdministration(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

intravenousAdministration(OntologyClass, Quantity, OntologyClass, TimeInterval) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

iRECISTCompleteResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

iRECISTConfirmedProgressiveDisease() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

iRECISTPartialResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

iRECISTStableDisease() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

iRECISTUnconfirmedProgressiveDisease() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

iscn(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

isError() - Method in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

iso8601onset(String) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

isValid() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

isWarning() - Method in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

J

jointExtensorSurfaceLocalization() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

jointFlexorSurfaceLocalization() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

JSON - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

jsonSchemaUrls - Variable in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

JsonSchemaValidationWorkflowRunner<T extends com.google.protobuf.MessageOrBuilder> - Class in org.phenopackets.phenopackettools.validator.jsonschema

Validates if given top-level element satisfies the following criteria: data format requirements - for instance if the element is a valid JSON document if JSON input is provided basic Phenopacket schema syntax requirements - the requirements described by the reference documentation.

JsonSchemaValidationWorkflowRunnerBuilder<T extends com.google.protobuf.MessageOrBuilder> - Class in org.phenopackets.phenopackettools.validator.jsonschema

A builder for JsonSchemaValidationWorkflowRunner.

JsonSchemaValidationWorkflowRunnerBuilder() - Constructor for class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunnerBuilder

juvenileOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

juvenileOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

K

kidney() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

kilogram() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

L

label(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

largeIntestine() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

lateFirstTrimesterOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

lateOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

lateOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

lateral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

laterality(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

Laterality - Class in org.phenopackets.phenopackettools.builder.constants

Laterality() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Laterality

lateYoungAdultOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

left() - Static method in class org.phenopackets.phenopackettools.builder.constants.Laterality

level() - Method in exception org.phenopackets.phenopackettools.validator.core.ConversionException

level() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

likelyBenign() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

likelyBenign() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

likelyPathogenic() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

likelyPathogenic() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

LIMBS - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

liter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

liver() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

localized() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

loincVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

lowerBodyPredominance() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

lung() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

M

male() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

male() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

maleToFemaleTranssexual() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

materialSample(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

MaterialSample - Class in org.phenopackets.phenopackettools.builder.constants

MaterialSample() - Constructor for class org.phenopackets.phenopackettools.builder.constants.MaterialSample

MeasurementBuilder - Class in org.phenopackets.phenopackettools.builder.builders

MedicalActionBuilder - Class in org.phenopackets.phenopackettools.builder.builders

MedicalActions - Class in org.phenopackets.phenopackettools.builder.constants

MedicalActions() - Constructor for class org.phenopackets.phenopackettools.builder.constants.MedicalActions

message() - Method in exception org.phenopackets.phenopackettools.validator.core.ConversionException

message() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

METABOLISM - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

metaData(MetaData) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

MetaDataBuilder - Class in org.phenopackets.phenopackettools.builder.builders

MetaDataValidators - Class in org.phenopackets.phenopackettools.validator.core.metadata

Static factory class for providing PhenopacketValidators for performing metadata validation.

metastaticNeoplasm() - Static method in class org.phenopackets.phenopackettools.builder.constants.TumorProgression

meter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

mgPerKg() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

microgram() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

microgramPerDeciliter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

microgramPerLiter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

microliter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

micrometer() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

middleAgeOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

middleAgeOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

midperipheral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

mild() - Static method in class org.phenopackets.phenopackettools.builder.constants.Severity

miliary() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

milligram() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

milligramPerDay() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

milligramPerDeciliter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

milliliter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

millimeter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

millimole() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

minimalResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

missing() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

mmHg() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

moderate() - Static method in class org.phenopackets.phenopackettools.builder.constants.Severity

mole() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

molePerLiter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

molePerMilliliter() - Static method in class org.phenopackets.phenopackettools.builder.constants.Unit

mondoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

morbilliform() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

mosaicism(double) - Static method in class org.phenopackets.phenopackettools.builder.builders.Extensions

mosaicism(double) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

MOSAICISM - Static variable in class org.phenopackets.phenopackettools.builder.builders.Extensions

multifocal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

MUSCLE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

N

ncbiTaxonVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

ncitVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

nCopies(int) - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

nebulizer() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

neonatalOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

neonatalOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

NEOPLASM - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

NERVOUS_SYSTEM - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

noResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

nose() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

notActionable() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

notActionable() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

now() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

nyhaClassI() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

nyhaClassII() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

nyhaClassIII() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

nyhaClassIII_or_IV() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

nyhaClassIV() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

O

of(boolean) - Static method in interface org.phenopackets.phenopackettools.converter.converters.V1ToV2Converter

of(Timestamp, Timestamp) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeIntervalBuilder

of(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.GeneDescriptorBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeIntervalBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

of(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(String, String, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

of(String, String, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(String, String, double, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.ReferenceRangeBuilder

of(String, String, double, ReferenceRange) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

of(String, String, int, String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

of(String, String, String) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

of(String, Interpretation.ProgressStatus, Diagnosis, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

of(List<ValidatorInfo>, List<ValidationResult>) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

of(List<TypedQuantity>) - Static method in class org.phenopackets.phenopackettools.builder.builders.ComplexValueBuilder

of(VariationDescriptor, AcmgPathogenicityClassification) - Static method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

of(VariationDescriptor, AcmgPathogenicityClassification, TherapeuticActionability) - Static method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

of(ValidationWorkflowRunner<Phenopacket>, ValidationWorkflowRunner<Family>, ValidationWorkflowRunner<Cohort>) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

of(ValidatorInfo, ValidationLevel, String, String) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

Create a ValidationResult from given data.

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

of(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(OntologyClass, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

of(OntologyClass, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(OntologyClass, double, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.ReferenceRangeBuilder

of(OntologyClass, double, double, double) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(OntologyClass, double, ReferenceRange) - Static method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

of(OntologyClass, double, ReferenceRange) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(OntologyClass, ComplexValue) - Static method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

of(OntologyClass, ExternalReference) - Static method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

of(OntologyClass, Quantity) - Static method in class org.phenopackets.phenopackettools.builder.builders.ComplexValueBuilder

of(OntologyClass, Quantity) - Static method in class org.phenopackets.phenopackettools.builder.builders.TypedQuantityBuilder

of(OntologyClass, Value) - Static method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

of(Quantity) - Static method in class org.phenopackets.phenopackettools.builder.builders.ValueBuilder

of(Quantity, OntologyClass, String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.DoseIntervalBuilder

of(Quantity, OntologyClass, TimeInterval) - Static method in class org.phenopackets.phenopackettools.builder.builders.DoseIntervalBuilder

of(TypedQuantity) - Static method in class org.phenopackets.phenopackettools.builder.builders.ComplexValueBuilder

of(TypedQuantity...) - Static method in class org.phenopackets.phenopackettools.builder.builders.ComplexValueBuilder

of(VitalStatus.Status) - Static method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

omimVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

once() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

onceDaily() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

oneCopy() - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

onset(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

onset(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

Onset - Class in org.phenopackets.phenopackettools.builder.constants

Onset() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Onset

ontologyClass(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.OntologyClassBuilder

ontologyClass(String, String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

ontologyClass(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

ontologyClass(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

OntologyClassBuilder - Class in org.phenopackets.phenopackettools.builder.builders

oral() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

oralAdministration() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

oralAdministration(OntologyClass) - Static method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

oralAdministration(OntologyClass, Quantity, OntologyClass, TimeInterval) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

org.phenopackets.phenopackettools.builder - module org.phenopackets.phenopackettools.builder

A module with pre-defined ontology constants, convenience methods, and concise builders to simplify phenopacket construction.

org.phenopackets.phenopackettools.builder - package org.phenopackets.phenopackettools.builder

A package with builders for top-level elements of Phenopacket Schema.

org.phenopackets.phenopackettools.builder.builders - package org.phenopackets.phenopackettools.builder.builders

A package with convenience methods and builders for creating Phenopacket Schema building blocks.

org.phenopackets.phenopackettools.builder.constants - package org.phenopackets.phenopackettools.builder.constants

The org.phenopackets.phenopackettools.builder.constants provides pre-defined constants from the recommended ontologies.

org.phenopackets.phenopackettools.converter - module org.phenopackets.phenopackettools.converter

A module for converting between the PhenopacketSchemaVersions.

org.phenopackets.phenopackettools.converter.converters - package org.phenopackets.phenopackettools.converter.converters

The package provides a V1ToV2Converter to convert from PhenopacketSchemaVersion.V1 to PhenopacketSchemaVersion.V2.

org.phenopackets.phenopackettools.core - module org.phenopackets.phenopackettools.core

The module defines core concepts shared by (almost) all modules of phenopacket-tools.

org.phenopackets.phenopackettools.core - package org.phenopackets.phenopackettools.core

A package with constants and types used across the entire application, including the base exception classes.

org.phenopackets.phenopackettools.io - module org.phenopackets.phenopackettools.io

A module for reading and writing top-level elements of Phenopacket Schema.

org.phenopackets.phenopackettools.io - package org.phenopackets.phenopackettools.io

The org.phenopackets.phenopackettools.io package offers functionality for reading and writing top-level elements of Phenopacket Schema.

org.phenopackets.phenopackettools.test - module org.phenopackets.phenopackettools.test

A module with example phenopackets suitable for unit tests.

org.phenopackets.phenopackettools.test - package org.phenopackets.phenopackettools.test

A package with TestData - a static utility class for serving hard-coded phenopacket examples.

org.phenopackets.phenopackettools.util - module org.phenopackets.phenopackettools.util

A module with utility functions.

org.phenopackets.phenopackettools.util.format - package org.phenopackets.phenopackettools.util.format

Defines utility methods for working with PhenopacketElements and PhenopacketFormats.

org.phenopackets.phenopackettools.util.print - package org.phenopackets.phenopackettools.util.print

The package includes utilities for parsing and printing Phenopacket Schema elements from/to JSON format.

org.phenopackets.phenopackettools.validator.core - module org.phenopackets.phenopackettools.validator.core

Defines the base APIs for phenopacket validation.

org.phenopackets.phenopackettools.validator.core - package org.phenopackets.phenopackettools.validator.core

The package provides APIs and default implementations of phenopacket validation.

org.phenopackets.phenopackettools.validator.core.except - package org.phenopackets.phenopackettools.validator.core.except

A package with exceptions that can be thrown by the validation code.

org.phenopackets.phenopackettools.validator.core.metadata - package org.phenopackets.phenopackettools.validator.core.metadata

The package provides PhenopacketValidators for metadata validation - checking that MetaData of the top-level elements of the Phenopacket schema contains a Resource for all OntologyClasses of the element.

org.phenopackets.phenopackettools.validator.core.phenotype - package org.phenopackets.phenopackettools.validator.core.phenotype

Package with off-the-shelf validators that work with Human Phenotype Ontology (HPO).

org.phenopackets.phenopackettools.validator.core.writer - package org.phenopackets.phenopackettools.validator.core.writer

A package with API for serialization of ValidationResults.

org.phenopackets.phenopackettools.validator.jsonschema - module org.phenopackets.phenopackettools.validator.jsonschema

Defines a ValidationWorkflowRunner with base validation backed by a JSON schema.

org.phenopackets.phenopackettools.validator.jsonschema - package org.phenopackets.phenopackettools.validator.jsonschema

The package provides JsonSchemaValidationWorkflowRunner and JsonSchemaValidationWorkflowRunnerBuilder for validating phenopackets.

Organ - Class in org.phenopackets.phenopackettools.builder.constants

Organ() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Organ

otherGender() - Static method in class org.phenopackets.phenopackettools.builder.constants.Gender

otherSex() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

P

paracentral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

paraseptal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

parse(InputStream) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(String) - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

parse(String) - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

parse(Path) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketElement, InputStream) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketElement, Path) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketFormat, InputStream) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketFormat, Path) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketFormat, PhenopacketElement, InputStream) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

parse(PhenopacketFormat, PhenopacketElement, Path) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketParser

partialRemission() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

pass() - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

If this method is called, "PASS" is added to the FILTER column

path() - Method in record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Returns the value of the path record component.

pathogenic() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

pathogenic() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

pathologicalStage(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

PathologicalTnm - Class in org.phenopackets.phenopackettools.builder.constants

PathologicalTnm() - Constructor for class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

patoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

pedigree(Pedigree) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

PedigreeBuilder - Class in org.phenopackets.phenopackettools.builder.builders

PedigreeBuilder() - Constructor for class org.phenopackets.phenopackettools.builder.builders.PedigreeBuilder

performed(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.ProcedureBuilder

pericardialFluidSpecimen() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

pericentral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

peridural() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

perilobular() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

perilymphatic() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

peripheral() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

peritonealFluidSample() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

PersonBuilder - Class in org.phenopackets.phenopackettools.builder.builders

phenopacket(Phenopacket) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

PHENOPACKET - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

phenopacketBuilder() - Static method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

PhenopacketBuilder - Class in org.phenopackets.phenopackettools.builder

phenopacketConverter() - Static method in class org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverters

PhenopacketElement - Enum Class in org.phenopackets.phenopackettools.core

The enum members represent the top-level elements of the Phenopacket schema.

PhenopacketFormat - Enum Class in org.phenopackets.phenopackettools.core

The enum members represent the supported representations of the top-level elements of the Phenopacket schema.

PhenopacketFormatConverter<T extends com.google.protobuf.MessageOrBuilder> - Interface in org.phenopackets.phenopackettools.validator.core

The implementors allow to convert between formats of the top-level elements of Phenopacket schema.

PhenopacketFormatConverters - Class in org.phenopackets.phenopackettools.validator.core

Static class to get PhenopacketFormatConverters for top-level elements of the Phenopacket schema.

phenopacketHpoAncestryValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry

Get PhenopacketValidator to validate ancestry Phenopacket using provided Ontology.

phenopacketHpoOrganSystemValidator(Ontology, Collection<TermId>) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.OrganSystem

Get PhenopacketValidator to validate annotation of organ systems in a Phenopacket using provided Ontology and a collection of organ system TermIds.

phenopacketHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators

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

use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(Ontology) instead

phenopacketHpoPhenotypeValidator(Ontology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary

Get PhenopacketValidator to validate Phenopacket using provided Ontology.

PhenopacketParser - Interface in org.phenopackets.phenopackettools.io

PhenopacketParserFactory - Interface in org.phenopackets.phenopackettools.io

PhenopacketParserFactoryException - Exception in org.phenopackets.phenopackettools.io

PhenopacketParserFactoryException() - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketParserFactoryException

PhenopacketParserFactoryException(String) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketParserFactoryException

PhenopacketParserFactoryException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketParserFactoryException

PhenopacketParserFactoryException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketParserFactoryException

PhenopacketParserFactoryException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketParserFactoryException

PhenopacketPrinter - Interface in org.phenopackets.phenopackettools.io

The implementors can serialize a top-level element of Phenopacket schema into provided OutputStream.

PhenopacketPrinterFactory - Interface in org.phenopackets.phenopackettools.io

The implementors provide PhenopacketPrinters for serializing top-level phenopacket elements into PhenopacketFormat using PhenopacketSchemaVersion.

PhenopacketPrinterFactoryException - Exception in org.phenopackets.phenopackettools.io

PhenopacketPrinterFactoryException() - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketPrinterFactoryException

PhenopacketPrinterFactoryException(String) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketPrinterFactoryException

PhenopacketPrinterFactoryException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketPrinterFactoryException

PhenopacketPrinterFactoryException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketPrinterFactoryException

PhenopacketPrinterFactoryException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.io.PhenopacketPrinterFactoryException

PhenopacketPrintUtil - Class in org.phenopackets.phenopackettools.util.print

A static utility class for obtaining JsonFormat.Parser and JsonFormat.Printer configured for printing Phenopacket Schema elements.

PhenopacketSchemaVersion - Enum Class in org.phenopackets.phenopackettools.core

An enum with currently supported Phenopacket schema versions.

PhenopacketToolsException - Exception in org.phenopackets.phenopackettools.core

Base checked exception thrown by phenopacket-tools.

PhenopacketToolsException() - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsException

PhenopacketToolsException(String) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsException

PhenopacketToolsException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsException

PhenopacketToolsException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsException

PhenopacketToolsException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsException

PhenopacketToolsRuntimeException - Exception in org.phenopackets.phenopackettools.core

Base unchecked exception thrown by phenopacket-tools.

PhenopacketToolsRuntimeException() - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsRuntimeException

PhenopacketToolsRuntimeException(String) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsRuntimeException

PhenopacketToolsRuntimeException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsRuntimeException

PhenopacketToolsRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsRuntimeException

PhenopacketToolsRuntimeException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.core.PhenopacketToolsRuntimeException

phenopacketValidator() - Static method in class org.phenopackets.phenopackettools.validator.core.metadata.MetaDataValidators

Get PhenopacketValidator for checking that MetaData of PhenopacketOrBuilder contains Resources for prefixes of all OntologyClass present in given PhenopacketOrBuilder.

PhenopacketValidator<T extends com.google.protobuf.MessageOrBuilder> - Interface in org.phenopackets.phenopackettools.validator.core

PhenopacketValidator represents a single step of the validation workflow.

PhenopacketValidatorException - Exception in org.phenopackets.phenopackettools.validator.core.except

PhenopacketValidatorException() - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorException

PhenopacketValidatorException(String) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorException

PhenopacketValidatorInputException - Exception in org.phenopackets.phenopackettools.validator.core.except

PhenopacketValidatorInputException() - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorInputException

PhenopacketValidatorInputException(String) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorInputException

PhenopacketValidatorRuntimeException - Exception in org.phenopackets.phenopackettools.validator.core.except

PhenopacketValidatorRuntimeException() - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorRuntimeException

PhenopacketValidatorRuntimeException(String) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorRuntimeException

PhenopacketValidatorRuntimeException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorRuntimeException

PhenopacketValidatorRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorRuntimeException

PhenopacketValidatorRuntimeException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.validator.core.except.PhenopacketValidatorRuntimeException

PhenotypicFeatureBuilder - Class in org.phenopackets.phenopackettools.builder.builders

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

pM0StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pM1aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pM1bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pM1cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pM1StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN0StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN1aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN1bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN1cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN1StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN2aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN2bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN2cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN2StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN3aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN3bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN3cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pN3StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

polycyclic() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

predominantSmallJointLocalization() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

PRENATAL - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

prescription() - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

Primary() - Constructor for class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary

primaryNeoplasm() - Static method in class org.phenopackets.phenopackettools.builder.constants.TumorProgression

primaryRefractory() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

primarySite(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

print(Message, OutputStream) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketPrinter

print(Message, Path) - Method in interface org.phenopackets.phenopackettools.io.PhenopacketPrinter

procedure(Procedure) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

procedure(Procedure) - Method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

procedure(Procedure) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

ProcedureBuilder - Class in org.phenopackets.phenopackettools.builder.builders

procedureRelated() - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

profound() - Static method in class org.phenopackets.phenopackettools.builder.constants.Severity

protein() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

PROTOBUF - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

proximal() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

pT0StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT1aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT1bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT1cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT1StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT2aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT2bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT2cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT2StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT3aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT3bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT3cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT3StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT4aStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT4bStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT4cStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT4dStageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

pT4StageFinding() - Static method in class org.phenopackets.phenopackettools.builder.constants.PathologicalTnm

Q

qual(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

QuantityBuilder - Class in org.phenopackets.phenopackettools.builder.builders

R

radiationTherapy(RadiationTherapy) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

recurrentNeoplasm() - Static method in class org.phenopackets.phenopackettools.builder.constants.TumorProgression

reference() - Static method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

reference(String) - Method in class org.phenopackets.phenopackettools.builder.builders.ExternalReferenceBuilder

reference(ExternalReference) - Method in class org.phenopackets.phenopackettools.builder.builders.EvidenceBuilder

referenceRange(String, String, double, double) - Method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

referenceRange(OntologyClass, double, double) - Method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

referenceRange(ReferenceRange) - Method in class org.phenopackets.phenopackettools.builder.builders.QuantityBuilder

ReferenceRangeBuilder - Class in org.phenopackets.phenopackettools.builder.builders

Simple wrapper for a ReferenceRange unit: id: "UO:0000316" label: "cells per microliter" low: 150000.0 high: 450000.0

referenceSample() - Static method in class org.phenopackets.phenopackettools.builder.constants.MaterialSample

rejected() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

rejected() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

relatives(List<Phenopacket>) - Method in class org.phenopackets.phenopackettools.builder.FamilyBuilder

resolution(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.DiseaseBuilder

resolution(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

Resources - Class in org.phenopackets.phenopackettools.builder.builders

RESPIRATORY - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

Response - Class in org.phenopackets.phenopackettools.builder.constants

Response() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Response

responseToTreatment(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

results() - Method in record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Returns the value of the results record component.

reticular() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

right() - Static method in class org.phenopackets.phenopackettools.builder.constants.Laterality

routeOfAdministration(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.TreatmentBuilder

S

sampledTissue(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

sampledType(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

sampleProcessing(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

sampleStorage(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

seconds(long) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

secondTrimesterOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

selfReportedPatientStatementEvidence() - Static method in class org.phenopackets.phenopackettools.builder.constants.Evidence

semanticValidators - Variable in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.validators instead

sequenceId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

severe() - Static method in class org.phenopackets.phenopackettools.builder.constants.Severity

severity(String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

severity(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.PhenotypicFeatureBuilder

Severity - Class in org.phenopackets.phenopackettools.builder.constants

Severity() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Severity

SKELETAL - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

smallIntestine() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

sniff(byte[]) - Static method in class org.phenopackets.phenopackettools.util.format.FormatSniffer

Make an educated guess of PhenopacketFormat based on given payload.

sniff(byte[], PhenopacketFormat) - Static method in class org.phenopackets.phenopackettools.util.format.ElementSniffer

Make an educated guess of PhenopacketElement based on given payload.

sniff(byte[], PhenopacketSchemaVersion, PhenopacketFormat) - Static method in class org.phenopackets.phenopackettools.util.format.ElementSniffer

Deprecated.

in favor of ElementSniffer.sniff(byte[], PhenopacketFormat)

sniff(InputStream) - Static method in class org.phenopackets.phenopackettools.util.format.FormatSniffer

Make an educated guess of PhenopacketFormat present in given input.

sniff(InputStream, PhenopacketFormat) - Static method in class org.phenopackets.phenopackettools.util.format.ElementSniffer

Make an educated guess of PhenopacketElement present in given input.

sniff(InputStream, PhenopacketSchemaVersion, PhenopacketFormat) - Static method in class org.phenopackets.phenopackettools.util.format.ElementSniffer

Deprecated.

in favor of ElementSniffer.sniff(InputStream, PhenopacketFormat).

SniffException - Exception in org.phenopackets.phenopackettools.util.format

A checked exception thrown in case of encountering some content sniffing issues.

SniffException() - Constructor for exception org.phenopackets.phenopackettools.util.format.SniffException

SniffException(String) - Constructor for exception org.phenopackets.phenopackettools.util.format.SniffException

SniffException(String, Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.SniffException

SniffException(String, Throwable, boolean, boolean) - Constructor for exception org.phenopackets.phenopackettools.util.format.SniffException

SniffException(Throwable) - Constructor for exception org.phenopackets.phenopackettools.util.format.SniffException

solved() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

solved(Diagnosis) - Method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

soVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

SpatialPattern - Class in org.phenopackets.phenopackettools.builder.constants

SpatialPattern() - Constructor for class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

spdi(String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

spinalCord() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

spleen() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

stage0() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

stageI() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

stageII() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

stageIII() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

stageIV() - Static method in class org.phenopackets.phenopackettools.builder.constants.DiseaseStage

started() - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

startTime(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

Status - Class in org.phenopackets.phenopackettools.builder.constants

Catch-all class for succinct provision of status codes.

stringentCompleteResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

structuralType(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

submittedBy(String) - Method in class org.phenopackets.phenopackettools.builder.builders.MetaDataBuilder

suffix() - Method in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

Get file name suffix for the given PhenopacketFormat (e.g.

summary(String) - Method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

survivalTimeInDays(int) - Method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

syntaxValidators - Variable in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

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

use ValidationWorkflowRunnerBuilder.validators instead

T

taxonomy(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

taxonomy(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

TestData - Class in org.phenopackets.phenopackettools.test

A class to serve comprehensive but not necessarily medically correct top-level elements of the Phenopacket schema, mainly usable for testing.

TestData.V1 - Class in org.phenopackets.phenopackettools.test

TestData.V2 - Class in org.phenopackets.phenopackettools.test

therapeuticRegimen(TherapeuticRegimen) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

TherapeuticRegimenBuilder - Class in org.phenopackets.phenopackettools.builder.builders

thirdTrimesterOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

THORACIC_CAVITY - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

threeCopies() - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

threeTimesDaily() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

thymus() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

TimeElements - Class in org.phenopackets.phenopackettools.builder.builders

The TimeElement is used in many places in the Phenopacket.

TimeIntervalBuilder - Class in org.phenopackets.phenopackettools.builder.builders

timeObserved(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.MeasurementBuilder

timeOfCollection(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

timeOfDeath(TimeElement) - Method in class org.phenopackets.phenopackettools.builder.builders.VitalStatusBuilder

timestamp(int, int, int) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

timestamp(int, int, int, int, int) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

timestamp(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

timestamp(Instant) - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

timestampAtLastEncounter(String) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

TimestampBuilder - Class in org.phenopackets.phenopackettools.builder.builders

TimestampBuilder(long) - Constructor for class org.phenopackets.phenopackettools.builder.builders.TimestampBuilder

toItem(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverter

Convert the payload into Protobuf representation of a top-level element.

toItem(String) - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverter

Convert JSON payload into Protobuf representation of a top-level element.

toJson(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverter

Convert the payload into a JSON string.

toJson(T) - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketFormatConverter

Convert Protobuf representation of a top-level element into a JSON string.

tongue() - Static method in class org.phenopackets.phenopackettools.builder.constants.Organ

topical() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

toString() - Method in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

toString() - Method in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

toString() - Method in record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Returns a string representation of this record class.

totalRNA() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

transcript() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

transcriptReference(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Expressions

The identifier of the transcript that is used as a reference for a variant

transdermal() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

treatment(Treatment) - Static method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

TreatmentBuilder - Class in org.phenopackets.phenopackettools.builder.builders

treatmentCompletedAsPrescribed() - Static method in class org.phenopackets.phenopackettools.builder.constants.TreatmentTermination

treatmentIntent(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

treatmentOnHold() - Static method in class org.phenopackets.phenopackettools.builder.constants.TreatmentTermination

treatmentTarget(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

treatmentTerminatedDueToToxicity() - Static method in class org.phenopackets.phenopackettools.builder.constants.TreatmentTermination

TreatmentTermination - Class in org.phenopackets.phenopackettools.builder.constants

TreatmentTermination() - Constructor for class org.phenopackets.phenopackettools.builder.constants.TreatmentTermination

treatmentTerminationReason(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.MedicalActionBuilder

tumorGrade(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

tumorProgression(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder

TumorProgression - Class in org.phenopackets.phenopackettools.builder.constants

TumorProgression() - Constructor for class org.phenopackets.phenopackettools.builder.constants.TumorProgression

tumorTissue() - Static method in class org.phenopackets.phenopackettools.builder.constants.BiospecimenType

twiceDaily() - Static method in class org.phenopackets.phenopackettools.builder.constants.MedicalActions

twoCopies() - Method in class org.phenopackets.phenopackettools.builder.builders.CopyNumberBuilder

TypedQuantityBuilder - Class in org.phenopackets.phenopackettools.builder.builders

U

uberonVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

ucum() - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

ucumVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

unaffected() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

uncertainSignificance() - Method in class org.phenopackets.phenopackettools.builder.builders.VariantInterpretationBuilder

uncertainSignificance() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

unfavorableResponse() - Static method in class org.phenopackets.phenopackettools.builder.constants.Response

unilateral() - Static method in class org.phenopackets.phenopackettools.builder.constants.Laterality

Unit - Class in org.phenopackets.phenopackettools.builder.constants

Unit() - Constructor for class org.phenopackets.phenopackettools.builder.constants.Unit

unknown() - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

unknown() - Method in class org.phenopackets.phenopackettools.builder.builders.TherapeuticRegimenBuilder

unknownSex() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

unknownSex() - Method in class org.phenopackets.phenopackettools.builder.builders.PersonBuilder

unsolved() - Method in class org.phenopackets.phenopackettools.builder.builders.InterpretationBuilder

unsolved() - Static method in class org.phenopackets.phenopackettools.builder.constants.Status

unspecifiedZygosity() - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

unspecifiedZygosity() - Static method in class org.phenopackets.phenopackettools.builder.constants.AllelicState

uoVersion(String) - Static method in class org.phenopackets.phenopackettools.builder.builders.Resources

upperBodyPredominance() - Static method in class org.phenopackets.phenopackettools.builder.constants.SpatialPattern

V

V1 - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion

The version 1 of the GA4GH Phenopacket schema released in 2019 to elicit community response.

V1ToV2Converter - Interface in org.phenopackets.phenopackettools.converter.converters

Convert top-level elements of the phenopacket schema from v1 to v2 format.

V2 - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion

The version 2 of the GA4GH Phenopacket schema.

validate(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

Validate a top-level element starting from a pile of bytes.

validate(byte[]) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

validate(InputStream) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

validate(String) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

Validate a top-level element starting from a string.

validate(String) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

validate(Path) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

validate(T) - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketValidator

Validate the component and summarize the results into a List of ValidationResults.

validate(T) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

Validate a top-level element starting from a protobuf item.

validate(T) - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

validateCohort(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a cohort starting from a pile of bytes.

validateCohort(String) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a cohort starting from a string.

validateCohort(Cohort) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a cohort starting from a protobuf object.

validateFamily(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a family starting from a pile of bytes.

validateFamily(String) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a family starting from a string.

validateFamily(Family) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a family starting from a protobuf object.

validatePhenopacket(byte[]) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a phenopacket starting from a pile of bytes.

validatePhenopacket(String) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a phenopacket starting from a string.

validatePhenopacket(Phenopacket) - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowDispatcher

Validate a phenopacket starting from a protobuf object.

ValidationLevel - Enum Class in org.phenopackets.phenopackettools.validator.core

ValidationLevel represents a severity level for ValidationResult.

ValidationResult - Interface in org.phenopackets.phenopackettools.validator.core

ValidationResult contains results of a single validation step performed by a PhenopacketValidator.

validationResults() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

ValidationResults - Interface in org.phenopackets.phenopackettools.validator.core

ValidationResults contain validation results for one Phenopacket schema top-level element (Phenopacket, Family, or Cohort).

ValidationResults.Builder - Class in org.phenopackets.phenopackettools.validator.core

A builder for creating ValidationResults.

ValidationResultsAndPath - Record Class in org.phenopackets.phenopackettools.validator.core.writer

A record to use for writing ValidationResults by ValidationResultsWriter.

ValidationResultsAndPath(ValidationResults, Path) - Constructor for record class org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsAndPath

Creates an instance of a ValidationResultsAndPath record class.

ValidationResultsWriter - Interface in org.phenopackets.phenopackettools.validator.core.writer

Write out validation results obtained from validation of a top-level Phenopacket schema element.

ValidationWorkflowDispatcher - Interface in org.phenopackets.phenopackettools.validator.core

ValidationWorkflowDispatcher exposes endpoints for validating top-level elements of Phenopacket Schema and dispatches the data into the appropriate ValidationWorkflowRunner.

ValidationWorkflowRunner<T extends com.google.protobuf.MessageOrBuilder> - Interface in org.phenopackets.phenopackettools.validator.core

ValidationWorkflowRunner validates selected top-level element of the Phenopacket Schema.

ValidationWorkflowRunnerBuilder<T extends com.google.protobuf.MessageOrBuilder> - Class in org.phenopackets.phenopackettools.validator.core

The base builder for constructing ValidationWorkflowRunner.

ValidationWorkflowRunnerBuilder() - Constructor for class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

validatorId() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

validatorInfo() - Method in exception org.phenopackets.phenopackettools.validator.core.ConversionException

validatorInfo() - Method in interface org.phenopackets.phenopackettools.validator.core.PhenopacketValidator

validatorInfo() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

ValidatorInfo - Interface in org.phenopackets.phenopackettools.validator.core

A description of a PhenopacketValidator.

validatorName() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidatorInfo

validators - Variable in class org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder

validators() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationResults

validators() - Method in interface org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner

validators() - Method in class org.phenopackets.phenopackettools.validator.jsonschema.JsonSchemaValidationWorkflowRunner

ValueBuilder - Class in org.phenopackets.phenopackettools.builder.builders

valueOf(String) - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

Returns the enum constant of this class with the specified name.

values() - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketElement

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

Returns an array containing the constants of this enum class, in the order they are declared.

variantId(String) - Method in class org.phenopackets.phenopackettools.builder.builders.AlleleBuilder

variantInterpretation(VariantInterpretationBuilder) - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

variantInterpretation(VariantInterpretation) - Method in class org.phenopackets.phenopackettools.builder.builders.GenomicInterpretationBuilder

VariantInterpretationBuilder - Class in org.phenopackets.phenopackettools.builder.builders

variation(Variation) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

VariationDescriptorBuilder - Class in org.phenopackets.phenopackettools.builder.builders

vcfHg37(String, int, String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

vcfHg38(String, int, String, String) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

vcfRecord(VcfRecord) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

VcfRecordBuilder - Class in org.phenopackets.phenopackettools.builder.builders

vitalStatus(VitalStatus) - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

VitalStatusBuilder - Class in org.phenopackets.phenopackettools.builder.builders

VOICE - Static variable in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems

W

warning(ValidatorInfo, String, String) - Static method in interface org.phenopackets.phenopackettools.validator.core.ValidationResult

Create a ValidationLevel.WARNING result from given data.

WARNING - Enum constant in enum class org.phenopackets.phenopackettools.validator.core.ValidationLevel

The level for pointing out an issue pertaining to a recommended field as described in the Phenopacket Schema requirements

woundIrrigation() - Static method in class org.phenopackets.phenopackettools.builder.constants.AdministrationRoute

writeValidationResults(List<ValidatorInfo>, List<ValidationResultsAndPath>) - Method in interface org.phenopackets.phenopackettools.validator.core.writer.ValidationResultsWriter

Write out the provided validators and results.

X

XO() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XX() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XXX() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XXXX() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XXXY() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XXY() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XXYY() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

XY() - Method in class org.phenopackets.phenopackettools.builder.builders.IndividualBuilder

Y

YAML - Enum constant in enum class org.phenopackets.phenopackettools.core.PhenopacketFormat

youngAdultOnset() - Static method in class org.phenopackets.phenopackettools.builder.builders.TimeElements

youngAdultOnset() - Static method in class org.phenopackets.phenopackettools.builder.constants.Onset

Z

zygosity(OntologyClass) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder

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