Index (Phenopacket-tools 1.0.0-RC4-SNAPSHOT API)

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(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry: Get PhenopacketValidator to validate ancestry Cohort using provided MinimalOntology.
cohortHpoOrganSystemValidator(MinimalOntology, 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 MinimalOntology and a collection of organ system TermIds.
cohortHpoPhenotypeValidator(MinimalOntology) - 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(MinimalOntology) instead
cohortHpoPhenotypeValidator(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary: Get PhenopacketValidator for performing primary validation Cohort using provided MinimalOntology, 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.
cohortValidator(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Unique: Get PhenopacketValidator to validate Cohort using provided ontology.
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(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry: Get PhenopacketValidator to validate ancestry Family using provided MinimalOntology.
familyHpoOrganSystemValidator(MinimalOntology, 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 MinimalOntology and a collection of organ system TermIds.
familyHpoPhenotypeValidator(MinimalOntology) - 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(MinimalOntology) instead
familyHpoPhenotypeValidator(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary: Get PhenopacketValidator for validate Family using provided MinimalOntology.
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.
familyValidator(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Unique: Get PhenopacketValidator to validate Family using provided ontology.
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: Add a VCF filter field.
findInstancesOfType(MessageOrBuilder, Class<T>) - Static method in class org.phenopackets.phenopackettools.util.message.MessageUtils: Find all instances of MessageUtils in a given message.
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.
HpoPhenotypeValidators.Unique - 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 unique - specified only once.
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
MessageUtils - Class in org.phenopackets.phenopackettools.util.message: A class with utility functions for working with protobuf messages.
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
moleculeContext(MoleculeContext) - Method in class org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder
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.message - package org.phenopackets.phenopackettools.util.message: Utility methods for working with protobuf messages.
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, the FILTER column is set to "PASS" and any other previously added filters are cleared.
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(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry: Get PhenopacketValidator to validate ancestry Phenopacket using provided MinimalOntology.
phenopacketHpoOrganSystemValidator(MinimalOntology, 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 MinimalOntology and a collection of organ system TermIds.
phenopacketHpoPhenotypeValidator(MinimalOntology) - 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(MinimalOntology) instead
phenopacketHpoPhenotypeValidator(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Primary: Get PhenopacketValidator to validate Phenopacket using provided MinimalOntology.
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(MinimalOntology) - Static method in class org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Unique: Get PhenopacketValidator to validate Phenopacket using provided ontology.
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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