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A Protobuf schema for capturing clinical phenotypes
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: base.proto
package org.phenopackets.schema.v1.core;
/**
*
* A Biosample refers to a unit of biological material from which the substrate
* molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g.
* sequencing, array hybridisation, mass-spectrometry) are extracted. Examples
* would be a tissue biopsy, a single cell from a culture for single cell genome
* sequencing or a protein fraction from a gradient centrifugation.
* Several instances (e.g. technical replicates) or types of experiments (e.g.
* genomic array as well as RNA-seq experiments) may refer to the same Biosample.
* FHIR mapping: Specimen (http://www.hl7.org/fhir/specimen.html).
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.Biosample}
*/
public final class Biosample extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.core.Biosample)
BiosampleOrBuilder {
private static final long serialVersionUID = 0L;
// Use Biosample.newBuilder() to construct.
private Biosample(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private Biosample() {
id_ = "";
individualId_ = "";
description_ = "";
phenotypicFeatures_ = java.util.Collections.emptyList();
diagnosticMarkers_ = java.util.Collections.emptyList();
htsFiles_ = java.util.Collections.emptyList();
variants_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new Biosample();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Biosample(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
}
int mutable_bitField0_ = 0;
com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
boolean done = false;
while (!done) {
int tag = input.readTag();
switch (tag) {
case 0:
done = true;
break;
case 10: {
java.lang.String s = input.readStringRequireUtf8();
id_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
individualId_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
description_ = s;
break;
}
case 34: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (sampledTissue_ != null) {
subBuilder = sampledTissue_.toBuilder();
}
sampledTissue_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(sampledTissue_);
sampledTissue_ = subBuilder.buildPartial();
}
break;
}
case 42: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
phenotypicFeatures_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
phenotypicFeatures_.add(
input.readMessage(org.phenopackets.schema.v1.core.PhenotypicFeature.parser(), extensionRegistry));
break;
}
case 50: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (taxonomy_ != null) {
subBuilder = taxonomy_.toBuilder();
}
taxonomy_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(taxonomy_);
taxonomy_ = subBuilder.buildPartial();
}
break;
}
case 58: {
org.phenopackets.schema.v1.core.Age.Builder subBuilder = null;
if (individualAgeAtCollectionCase_ == 7) {
subBuilder = ((org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_).toBuilder();
}
individualAgeAtCollection_ =
input.readMessage(org.phenopackets.schema.v1.core.Age.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom((org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_);
individualAgeAtCollection_ = subBuilder.buildPartial();
}
individualAgeAtCollectionCase_ = 7;
break;
}
case 66: {
org.phenopackets.schema.v1.core.AgeRange.Builder subBuilder = null;
if (individualAgeAtCollectionCase_ == 8) {
subBuilder = ((org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_).toBuilder();
}
individualAgeAtCollection_ =
input.readMessage(org.phenopackets.schema.v1.core.AgeRange.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom((org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_);
individualAgeAtCollection_ = subBuilder.buildPartial();
}
individualAgeAtCollectionCase_ = 8;
break;
}
case 74: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (histologicalDiagnosis_ != null) {
subBuilder = histologicalDiagnosis_.toBuilder();
}
histologicalDiagnosis_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(histologicalDiagnosis_);
histologicalDiagnosis_ = subBuilder.buildPartial();
}
break;
}
case 82: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (tumorProgression_ != null) {
subBuilder = tumorProgression_.toBuilder();
}
tumorProgression_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(tumorProgression_);
tumorProgression_ = subBuilder.buildPartial();
}
break;
}
case 90: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (tumorGrade_ != null) {
subBuilder = tumorGrade_.toBuilder();
}
tumorGrade_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(tumorGrade_);
tumorGrade_ = subBuilder.buildPartial();
}
break;
}
case 98: {
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
diagnosticMarkers_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
}
diagnosticMarkers_.add(
input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry));
break;
}
case 106: {
org.phenopackets.schema.v1.core.Procedure.Builder subBuilder = null;
if (procedure_ != null) {
subBuilder = procedure_.toBuilder();
}
procedure_ = input.readMessage(org.phenopackets.schema.v1.core.Procedure.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(procedure_);
procedure_ = subBuilder.buildPartial();
}
break;
}
case 114: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
htsFiles_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
htsFiles_.add(
input.readMessage(org.phenopackets.schema.v1.core.HtsFile.parser(), extensionRegistry));
break;
}
case 122: {
if (!((mutable_bitField0_ & 0x00000008) != 0)) {
variants_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000008;
}
variants_.add(
input.readMessage(org.phenopackets.schema.v1.core.Variant.parser(), extensionRegistry));
break;
}
case 128: {
isControlSample_ = input.readBool();
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
}
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000001) != 0)) {
phenotypicFeatures_ = java.util.Collections.unmodifiableList(phenotypicFeatures_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
diagnosticMarkers_ = java.util.Collections.unmodifiableList(diagnosticMarkers_);
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
htsFiles_ = java.util.Collections.unmodifiableList(htsFiles_);
}
if (((mutable_bitField0_ & 0x00000008) != 0)) {
variants_ = java.util.Collections.unmodifiableList(variants_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_Biosample_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_Biosample_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.phenopackets.schema.v1.core.Biosample.class, org.phenopackets.schema.v1.core.Biosample.Builder.class);
}
private int individualAgeAtCollectionCase_ = 0;
private java.lang.Object individualAgeAtCollection_;
public enum IndividualAgeAtCollectionCase
implements com.google.protobuf.Internal.EnumLite {
AGE_OF_INDIVIDUAL_AT_COLLECTION(7),
AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION(8),
INDIVIDUALAGEATCOLLECTION_NOT_SET(0);
private final int value;
private IndividualAgeAtCollectionCase(int value) {
this.value = value;
}
/**
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static IndividualAgeAtCollectionCase valueOf(int value) {
return forNumber(value);
}
public static IndividualAgeAtCollectionCase forNumber(int value) {
switch (value) {
case 7: return AGE_OF_INDIVIDUAL_AT_COLLECTION;
case 8: return AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION;
case 0: return INDIVIDUALAGEATCOLLECTION_NOT_SET;
default: return null;
}
}
public int getNumber() {
return this.value;
}
};
public IndividualAgeAtCollectionCase
getIndividualAgeAtCollectionCase() {
return IndividualAgeAtCollectionCase.forNumber(
individualAgeAtCollectionCase_);
}
public static final int ID_FIELD_NUMBER = 1;
private volatile java.lang.Object id_;
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
}
}
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int INDIVIDUAL_ID_FIELD_NUMBER = 2;
private volatile java.lang.Object individualId_;
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public java.lang.String getIndividualId() {
java.lang.Object ref = individualId_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
individualId_ = s;
return s;
}
}
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public com.google.protobuf.ByteString
getIndividualIdBytes() {
java.lang.Object ref = individualId_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
individualId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int DESCRIPTION_FIELD_NUMBER = 3;
private volatile java.lang.Object description_;
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public java.lang.String getDescription() {
java.lang.Object ref = description_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
description_ = s;
return s;
}
}
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public com.google.protobuf.ByteString
getDescriptionBytes() {
java.lang.Object ref = description_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
description_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int SAMPLED_TISSUE_FIELD_NUMBER = 4;
private org.phenopackets.schema.v1.core.OntologyClass sampledTissue_;
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public boolean hasSampledTissue() {
return sampledTissue_ != null;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass getSampledTissue() {
return sampledTissue_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : sampledTissue_;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getSampledTissueOrBuilder() {
return getSampledTissue();
}
public static final int PHENOTYPIC_FEATURES_FIELD_NUMBER = 5;
private java.util.List phenotypicFeatures_;
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public java.util.List getPhenotypicFeaturesList() {
return phenotypicFeatures_;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public java.util.List
getPhenotypicFeaturesOrBuilderList() {
return phenotypicFeatures_;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public int getPhenotypicFeaturesCount() {
return phenotypicFeatures_.size();
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature getPhenotypicFeatures(int index) {
return phenotypicFeatures_.get(index);
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder getPhenotypicFeaturesOrBuilder(
int index) {
return phenotypicFeatures_.get(index);
}
public static final int TAXONOMY_FIELD_NUMBER = 6;
private org.phenopackets.schema.v1.core.OntologyClass taxonomy_;
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public boolean hasTaxonomy() {
return taxonomy_ != null;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTaxonomy() {
return taxonomy_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : taxonomy_;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTaxonomyOrBuilder() {
return getTaxonomy();
}
public static final int AGE_OF_INDIVIDUAL_AT_COLLECTION_FIELD_NUMBER = 7;
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public boolean hasAgeOfIndividualAtCollection() {
return individualAgeAtCollectionCase_ == 7;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public org.phenopackets.schema.v1.core.Age getAgeOfIndividualAtCollection() {
if (individualAgeAtCollectionCase_ == 7) {
return (org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public org.phenopackets.schema.v1.core.AgeOrBuilder getAgeOfIndividualAtCollectionOrBuilder() {
if (individualAgeAtCollectionCase_ == 7) {
return (org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
public static final int AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION_FIELD_NUMBER = 8;
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public boolean hasAgeRangeOfIndividualAtCollection() {
return individualAgeAtCollectionCase_ == 8;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public org.phenopackets.schema.v1.core.AgeRange getAgeRangeOfIndividualAtCollection() {
if (individualAgeAtCollectionCase_ == 8) {
return (org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public org.phenopackets.schema.v1.core.AgeRangeOrBuilder getAgeRangeOfIndividualAtCollectionOrBuilder() {
if (individualAgeAtCollectionCase_ == 8) {
return (org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
public static final int HISTOLOGICAL_DIAGNOSIS_FIELD_NUMBER = 9;
private org.phenopackets.schema.v1.core.OntologyClass histologicalDiagnosis_;
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public boolean hasHistologicalDiagnosis() {
return histologicalDiagnosis_ != null;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass getHistologicalDiagnosis() {
return histologicalDiagnosis_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : histologicalDiagnosis_;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getHistologicalDiagnosisOrBuilder() {
return getHistologicalDiagnosis();
}
public static final int TUMOR_PROGRESSION_FIELD_NUMBER = 10;
private org.phenopackets.schema.v1.core.OntologyClass tumorProgression_;
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public boolean hasTumorProgression() {
return tumorProgression_ != null;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTumorProgression() {
return tumorProgression_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorProgression_;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTumorProgressionOrBuilder() {
return getTumorProgression();
}
public static final int TUMOR_GRADE_FIELD_NUMBER = 11;
private org.phenopackets.schema.v1.core.OntologyClass tumorGrade_;
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public boolean hasTumorGrade() {
return tumorGrade_ != null;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTumorGrade() {
return tumorGrade_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorGrade_;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTumorGradeOrBuilder() {
return getTumorGrade();
}
public static final int DIAGNOSTIC_MARKERS_FIELD_NUMBER = 12;
private java.util.List diagnosticMarkers_;
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public java.util.List getDiagnosticMarkersList() {
return diagnosticMarkers_;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public java.util.List
getDiagnosticMarkersOrBuilderList() {
return diagnosticMarkers_;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public int getDiagnosticMarkersCount() {
return diagnosticMarkers_.size();
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClass getDiagnosticMarkers(int index) {
return diagnosticMarkers_.get(index);
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getDiagnosticMarkersOrBuilder(
int index) {
return diagnosticMarkers_.get(index);
}
public static final int PROCEDURE_FIELD_NUMBER = 13;
private org.phenopackets.schema.v1.core.Procedure procedure_;
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public boolean hasProcedure() {
return procedure_ != null;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public org.phenopackets.schema.v1.core.Procedure getProcedure() {
return procedure_ == null ? org.phenopackets.schema.v1.core.Procedure.getDefaultInstance() : procedure_;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public org.phenopackets.schema.v1.core.ProcedureOrBuilder getProcedureOrBuilder() {
return getProcedure();
}
public static final int HTS_FILES_FIELD_NUMBER = 14;
private java.util.List htsFiles_;
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public java.util.List getHtsFilesList() {
return htsFiles_;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public java.util.List
getHtsFilesOrBuilderList() {
return htsFiles_;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public int getHtsFilesCount() {
return htsFiles_.size();
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index) {
return htsFiles_.get(index);
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFileOrBuilder getHtsFilesOrBuilder(
int index) {
return htsFiles_.get(index);
}
public static final int VARIANTS_FIELD_NUMBER = 15;
private java.util.List variants_;
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public java.util.List getVariantsList() {
return variants_;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public java.util.List
getVariantsOrBuilderList() {
return variants_;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public int getVariantsCount() {
return variants_.size();
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.Variant getVariants(int index) {
return variants_.get(index);
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.VariantOrBuilder getVariantsOrBuilder(
int index) {
return variants_.get(index);
}
public static final int IS_CONTROL_SAMPLE_FIELD_NUMBER = 16;
private boolean isControlSample_;
/**
*
* if true, this sample is being use as a normal control, often in combination with
* another sample that is thought to contain a pathological finding
* the default value is false
*
*
* bool is_control_sample = 16;
*/
public boolean getIsControlSample() {
return isControlSample_;
}
private byte memoizedIsInitialized = -1;
@java.lang.Override
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized == 1) return true;
if (isInitialized == 0) return false;
memoizedIsInitialized = 1;
return true;
}
@java.lang.Override
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
if (!getIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, id_);
}
if (!getIndividualIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, individualId_);
}
if (!getDescriptionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, description_);
}
if (sampledTissue_ != null) {
output.writeMessage(4, getSampledTissue());
}
for (int i = 0; i < phenotypicFeatures_.size(); i++) {
output.writeMessage(5, phenotypicFeatures_.get(i));
}
if (taxonomy_ != null) {
output.writeMessage(6, getTaxonomy());
}
if (individualAgeAtCollectionCase_ == 7) {
output.writeMessage(7, (org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_);
}
if (individualAgeAtCollectionCase_ == 8) {
output.writeMessage(8, (org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_);
}
if (histologicalDiagnosis_ != null) {
output.writeMessage(9, getHistologicalDiagnosis());
}
if (tumorProgression_ != null) {
output.writeMessage(10, getTumorProgression());
}
if (tumorGrade_ != null) {
output.writeMessage(11, getTumorGrade());
}
for (int i = 0; i < diagnosticMarkers_.size(); i++) {
output.writeMessage(12, diagnosticMarkers_.get(i));
}
if (procedure_ != null) {
output.writeMessage(13, getProcedure());
}
for (int i = 0; i < htsFiles_.size(); i++) {
output.writeMessage(14, htsFiles_.get(i));
}
for (int i = 0; i < variants_.size(); i++) {
output.writeMessage(15, variants_.get(i));
}
if (isControlSample_ != false) {
output.writeBool(16, isControlSample_);
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, id_);
}
if (!getIndividualIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, individualId_);
}
if (!getDescriptionBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(3, description_);
}
if (sampledTissue_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(4, getSampledTissue());
}
for (int i = 0; i < phenotypicFeatures_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(5, phenotypicFeatures_.get(i));
}
if (taxonomy_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(6, getTaxonomy());
}
if (individualAgeAtCollectionCase_ == 7) {
size += com.google.protobuf.CodedOutputStream
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}
if (individualAgeAtCollectionCase_ == 8) {
size += com.google.protobuf.CodedOutputStream
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}
if (histologicalDiagnosis_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, getHistologicalDiagnosis());
}
if (tumorProgression_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(10, getTumorProgression());
}
if (tumorGrade_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(11, getTumorGrade());
}
for (int i = 0; i < diagnosticMarkers_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(12, diagnosticMarkers_.get(i));
}
if (procedure_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(13, getProcedure());
}
for (int i = 0; i < htsFiles_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(14, htsFiles_.get(i));
}
for (int i = 0; i < variants_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(15, variants_.get(i));
}
if (isControlSample_ != false) {
size += com.google.protobuf.CodedOutputStream
.computeBoolSize(16, isControlSample_);
}
size += unknownFields.getSerializedSize();
memoizedSize = size;
return size;
}
@java.lang.Override
public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.phenopackets.schema.v1.core.Biosample)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.core.Biosample other = (org.phenopackets.schema.v1.core.Biosample) obj;
if (!getId()
.equals(other.getId())) return false;
if (!getIndividualId()
.equals(other.getIndividualId())) return false;
if (!getDescription()
.equals(other.getDescription())) return false;
if (hasSampledTissue() != other.hasSampledTissue()) return false;
if (hasSampledTissue()) {
if (!getSampledTissue()
.equals(other.getSampledTissue())) return false;
}
if (!getPhenotypicFeaturesList()
.equals(other.getPhenotypicFeaturesList())) return false;
if (hasTaxonomy() != other.hasTaxonomy()) return false;
if (hasTaxonomy()) {
if (!getTaxonomy()
.equals(other.getTaxonomy())) return false;
}
if (hasHistologicalDiagnosis() != other.hasHistologicalDiagnosis()) return false;
if (hasHistologicalDiagnosis()) {
if (!getHistologicalDiagnosis()
.equals(other.getHistologicalDiagnosis())) return false;
}
if (hasTumorProgression() != other.hasTumorProgression()) return false;
if (hasTumorProgression()) {
if (!getTumorProgression()
.equals(other.getTumorProgression())) return false;
}
if (hasTumorGrade() != other.hasTumorGrade()) return false;
if (hasTumorGrade()) {
if (!getTumorGrade()
.equals(other.getTumorGrade())) return false;
}
if (!getDiagnosticMarkersList()
.equals(other.getDiagnosticMarkersList())) return false;
if (hasProcedure() != other.hasProcedure()) return false;
if (hasProcedure()) {
if (!getProcedure()
.equals(other.getProcedure())) return false;
}
if (!getHtsFilesList()
.equals(other.getHtsFilesList())) return false;
if (!getVariantsList()
.equals(other.getVariantsList())) return false;
if (getIsControlSample()
!= other.getIsControlSample()) return false;
if (!getIndividualAgeAtCollectionCase().equals(other.getIndividualAgeAtCollectionCase())) return false;
switch (individualAgeAtCollectionCase_) {
case 7:
if (!getAgeOfIndividualAtCollection()
.equals(other.getAgeOfIndividualAtCollection())) return false;
break;
case 8:
if (!getAgeRangeOfIndividualAtCollection()
.equals(other.getAgeRangeOfIndividualAtCollection())) return false;
break;
case 0:
default:
}
if (!unknownFields.equals(other.unknownFields)) return false;
return true;
}
@java.lang.Override
public int hashCode() {
if (memoizedHashCode != 0) {
return memoizedHashCode;
}
int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + ID_FIELD_NUMBER;
hash = (53 * hash) + getId().hashCode();
hash = (37 * hash) + INDIVIDUAL_ID_FIELD_NUMBER;
hash = (53 * hash) + getIndividualId().hashCode();
hash = (37 * hash) + DESCRIPTION_FIELD_NUMBER;
hash = (53 * hash) + getDescription().hashCode();
if (hasSampledTissue()) {
hash = (37 * hash) + SAMPLED_TISSUE_FIELD_NUMBER;
hash = (53 * hash) + getSampledTissue().hashCode();
}
if (getPhenotypicFeaturesCount() > 0) {
hash = (37 * hash) + PHENOTYPIC_FEATURES_FIELD_NUMBER;
hash = (53 * hash) + getPhenotypicFeaturesList().hashCode();
}
if (hasTaxonomy()) {
hash = (37 * hash) + TAXONOMY_FIELD_NUMBER;
hash = (53 * hash) + getTaxonomy().hashCode();
}
if (hasHistologicalDiagnosis()) {
hash = (37 * hash) + HISTOLOGICAL_DIAGNOSIS_FIELD_NUMBER;
hash = (53 * hash) + getHistologicalDiagnosis().hashCode();
}
if (hasTumorProgression()) {
hash = (37 * hash) + TUMOR_PROGRESSION_FIELD_NUMBER;
hash = (53 * hash) + getTumorProgression().hashCode();
}
if (hasTumorGrade()) {
hash = (37 * hash) + TUMOR_GRADE_FIELD_NUMBER;
hash = (53 * hash) + getTumorGrade().hashCode();
}
if (getDiagnosticMarkersCount() > 0) {
hash = (37 * hash) + DIAGNOSTIC_MARKERS_FIELD_NUMBER;
hash = (53 * hash) + getDiagnosticMarkersList().hashCode();
}
if (hasProcedure()) {
hash = (37 * hash) + PROCEDURE_FIELD_NUMBER;
hash = (53 * hash) + getProcedure().hashCode();
}
if (getHtsFilesCount() > 0) {
hash = (37 * hash) + HTS_FILES_FIELD_NUMBER;
hash = (53 * hash) + getHtsFilesList().hashCode();
}
if (getVariantsCount() > 0) {
hash = (37 * hash) + VARIANTS_FIELD_NUMBER;
hash = (53 * hash) + getVariantsList().hashCode();
}
hash = (37 * hash) + IS_CONTROL_SAMPLE_FIELD_NUMBER;
hash = (53 * hash) + com.google.protobuf.Internal.hashBoolean(
getIsControlSample());
switch (individualAgeAtCollectionCase_) {
case 7:
hash = (37 * hash) + AGE_OF_INDIVIDUAL_AT_COLLECTION_FIELD_NUMBER;
hash = (53 * hash) + getAgeOfIndividualAtCollection().hashCode();
break;
case 8:
hash = (37 * hash) + AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION_FIELD_NUMBER;
hash = (53 * hash) + getAgeRangeOfIndividualAtCollection().hashCode();
break;
case 0:
default:
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.Biosample parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.Biosample parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.Biosample parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
@java.lang.Override
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.phenopackets.schema.v1.core.Biosample prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
? new Builder() : new Builder().mergeFrom(this);
}
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
*
* A Biosample refers to a unit of biological material from which the substrate
* molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g.
* sequencing, array hybridisation, mass-spectrometry) are extracted. Examples
* would be a tissue biopsy, a single cell from a culture for single cell genome
* sequencing or a protein fraction from a gradient centrifugation.
* Several instances (e.g. technical replicates) or types of experiments (e.g.
* genomic array as well as RNA-seq experiments) may refer to the same Biosample.
* FHIR mapping: Specimen (http://www.hl7.org/fhir/specimen.html).
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.Biosample}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.core.Biosample)
org.phenopackets.schema.v1.core.BiosampleOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_Biosample_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_Biosample_fieldAccessorTable
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org.phenopackets.schema.v1.core.Biosample.class, org.phenopackets.schema.v1.core.Biosample.Builder.class);
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// Construct using org.phenopackets.schema.v1.core.Biosample.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
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private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getPhenotypicFeaturesFieldBuilder();
getDiagnosticMarkersFieldBuilder();
getHtsFilesFieldBuilder();
getVariantsFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
id_ = "";
individualId_ = "";
description_ = "";
if (sampledTissueBuilder_ == null) {
sampledTissue_ = null;
} else {
sampledTissue_ = null;
sampledTissueBuilder_ = null;
}
if (phenotypicFeaturesBuilder_ == null) {
phenotypicFeatures_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
phenotypicFeaturesBuilder_.clear();
}
if (taxonomyBuilder_ == null) {
taxonomy_ = null;
} else {
taxonomy_ = null;
taxonomyBuilder_ = null;
}
if (histologicalDiagnosisBuilder_ == null) {
histologicalDiagnosis_ = null;
} else {
histologicalDiagnosis_ = null;
histologicalDiagnosisBuilder_ = null;
}
if (tumorProgressionBuilder_ == null) {
tumorProgression_ = null;
} else {
tumorProgression_ = null;
tumorProgressionBuilder_ = null;
}
if (tumorGradeBuilder_ == null) {
tumorGrade_ = null;
} else {
tumorGrade_ = null;
tumorGradeBuilder_ = null;
}
if (diagnosticMarkersBuilder_ == null) {
diagnosticMarkers_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
} else {
diagnosticMarkersBuilder_.clear();
}
if (procedureBuilder_ == null) {
procedure_ = null;
} else {
procedure_ = null;
procedureBuilder_ = null;
}
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
htsFilesBuilder_.clear();
}
if (variantsBuilder_ == null) {
variants_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
} else {
variantsBuilder_.clear();
}
isControlSample_ = false;
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_Biosample_descriptor;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.Biosample getDefaultInstanceForType() {
return org.phenopackets.schema.v1.core.Biosample.getDefaultInstance();
}
@java.lang.Override
public org.phenopackets.schema.v1.core.Biosample build() {
org.phenopackets.schema.v1.core.Biosample result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.Biosample buildPartial() {
org.phenopackets.schema.v1.core.Biosample result = new org.phenopackets.schema.v1.core.Biosample(this);
int from_bitField0_ = bitField0_;
result.id_ = id_;
result.individualId_ = individualId_;
result.description_ = description_;
if (sampledTissueBuilder_ == null) {
result.sampledTissue_ = sampledTissue_;
} else {
result.sampledTissue_ = sampledTissueBuilder_.build();
}
if (phenotypicFeaturesBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
phenotypicFeatures_ = java.util.Collections.unmodifiableList(phenotypicFeatures_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.phenotypicFeatures_ = phenotypicFeatures_;
} else {
result.phenotypicFeatures_ = phenotypicFeaturesBuilder_.build();
}
if (taxonomyBuilder_ == null) {
result.taxonomy_ = taxonomy_;
} else {
result.taxonomy_ = taxonomyBuilder_.build();
}
if (individualAgeAtCollectionCase_ == 7) {
if (ageOfIndividualAtCollectionBuilder_ == null) {
result.individualAgeAtCollection_ = individualAgeAtCollection_;
} else {
result.individualAgeAtCollection_ = ageOfIndividualAtCollectionBuilder_.build();
}
}
if (individualAgeAtCollectionCase_ == 8) {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
result.individualAgeAtCollection_ = individualAgeAtCollection_;
} else {
result.individualAgeAtCollection_ = ageRangeOfIndividualAtCollectionBuilder_.build();
}
}
if (histologicalDiagnosisBuilder_ == null) {
result.histologicalDiagnosis_ = histologicalDiagnosis_;
} else {
result.histologicalDiagnosis_ = histologicalDiagnosisBuilder_.build();
}
if (tumorProgressionBuilder_ == null) {
result.tumorProgression_ = tumorProgression_;
} else {
result.tumorProgression_ = tumorProgressionBuilder_.build();
}
if (tumorGradeBuilder_ == null) {
result.tumorGrade_ = tumorGrade_;
} else {
result.tumorGrade_ = tumorGradeBuilder_.build();
}
if (diagnosticMarkersBuilder_ == null) {
if (((bitField0_ & 0x00000002) != 0)) {
diagnosticMarkers_ = java.util.Collections.unmodifiableList(diagnosticMarkers_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.diagnosticMarkers_ = diagnosticMarkers_;
} else {
result.diagnosticMarkers_ = diagnosticMarkersBuilder_.build();
}
if (procedureBuilder_ == null) {
result.procedure_ = procedure_;
} else {
result.procedure_ = procedureBuilder_.build();
}
if (htsFilesBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
htsFiles_ = java.util.Collections.unmodifiableList(htsFiles_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.htsFiles_ = htsFiles_;
} else {
result.htsFiles_ = htsFilesBuilder_.build();
}
if (variantsBuilder_ == null) {
if (((bitField0_ & 0x00000008) != 0)) {
variants_ = java.util.Collections.unmodifiableList(variants_);
bitField0_ = (bitField0_ & ~0x00000008);
}
result.variants_ = variants_;
} else {
result.variants_ = variantsBuilder_.build();
}
result.isControlSample_ = isControlSample_;
result.individualAgeAtCollectionCase_ = individualAgeAtCollectionCase_;
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
}
@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
}
@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
}
@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
}
@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
}
@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.phenopackets.schema.v1.core.Biosample) {
return mergeFrom((org.phenopackets.schema.v1.core.Biosample)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.phenopackets.schema.v1.core.Biosample other) {
if (other == org.phenopackets.schema.v1.core.Biosample.getDefaultInstance()) return this;
if (!other.getId().isEmpty()) {
id_ = other.id_;
onChanged();
}
if (!other.getIndividualId().isEmpty()) {
individualId_ = other.individualId_;
onChanged();
}
if (!other.getDescription().isEmpty()) {
description_ = other.description_;
onChanged();
}
if (other.hasSampledTissue()) {
mergeSampledTissue(other.getSampledTissue());
}
if (phenotypicFeaturesBuilder_ == null) {
if (!other.phenotypicFeatures_.isEmpty()) {
if (phenotypicFeatures_.isEmpty()) {
phenotypicFeatures_ = other.phenotypicFeatures_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.addAll(other.phenotypicFeatures_);
}
onChanged();
}
} else {
if (!other.phenotypicFeatures_.isEmpty()) {
if (phenotypicFeaturesBuilder_.isEmpty()) {
phenotypicFeaturesBuilder_.dispose();
phenotypicFeaturesBuilder_ = null;
phenotypicFeatures_ = other.phenotypicFeatures_;
bitField0_ = (bitField0_ & ~0x00000001);
phenotypicFeaturesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getPhenotypicFeaturesFieldBuilder() : null;
} else {
phenotypicFeaturesBuilder_.addAllMessages(other.phenotypicFeatures_);
}
}
}
if (other.hasTaxonomy()) {
mergeTaxonomy(other.getTaxonomy());
}
if (other.hasHistologicalDiagnosis()) {
mergeHistologicalDiagnosis(other.getHistologicalDiagnosis());
}
if (other.hasTumorProgression()) {
mergeTumorProgression(other.getTumorProgression());
}
if (other.hasTumorGrade()) {
mergeTumorGrade(other.getTumorGrade());
}
if (diagnosticMarkersBuilder_ == null) {
if (!other.diagnosticMarkers_.isEmpty()) {
if (diagnosticMarkers_.isEmpty()) {
diagnosticMarkers_ = other.diagnosticMarkers_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.addAll(other.diagnosticMarkers_);
}
onChanged();
}
} else {
if (!other.diagnosticMarkers_.isEmpty()) {
if (diagnosticMarkersBuilder_.isEmpty()) {
diagnosticMarkersBuilder_.dispose();
diagnosticMarkersBuilder_ = null;
diagnosticMarkers_ = other.diagnosticMarkers_;
bitField0_ = (bitField0_ & ~0x00000002);
diagnosticMarkersBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getDiagnosticMarkersFieldBuilder() : null;
} else {
diagnosticMarkersBuilder_.addAllMessages(other.diagnosticMarkers_);
}
}
}
if (other.hasProcedure()) {
mergeProcedure(other.getProcedure());
}
if (htsFilesBuilder_ == null) {
if (!other.htsFiles_.isEmpty()) {
if (htsFiles_.isEmpty()) {
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureHtsFilesIsMutable();
htsFiles_.addAll(other.htsFiles_);
}
onChanged();
}
} else {
if (!other.htsFiles_.isEmpty()) {
if (htsFilesBuilder_.isEmpty()) {
htsFilesBuilder_.dispose();
htsFilesBuilder_ = null;
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000004);
htsFilesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getHtsFilesFieldBuilder() : null;
} else {
htsFilesBuilder_.addAllMessages(other.htsFiles_);
}
}
}
if (variantsBuilder_ == null) {
if (!other.variants_.isEmpty()) {
if (variants_.isEmpty()) {
variants_ = other.variants_;
bitField0_ = (bitField0_ & ~0x00000008);
} else {
ensureVariantsIsMutable();
variants_.addAll(other.variants_);
}
onChanged();
}
} else {
if (!other.variants_.isEmpty()) {
if (variantsBuilder_.isEmpty()) {
variantsBuilder_.dispose();
variantsBuilder_ = null;
variants_ = other.variants_;
bitField0_ = (bitField0_ & ~0x00000008);
variantsBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getVariantsFieldBuilder() : null;
} else {
variantsBuilder_.addAllMessages(other.variants_);
}
}
}
if (other.getIsControlSample() != false) {
setIsControlSample(other.getIsControlSample());
}
switch (other.getIndividualAgeAtCollectionCase()) {
case AGE_OF_INDIVIDUAL_AT_COLLECTION: {
mergeAgeOfIndividualAtCollection(other.getAgeOfIndividualAtCollection());
break;
}
case AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION: {
mergeAgeRangeOfIndividualAtCollection(other.getAgeRangeOfIndividualAtCollection());
break;
}
case INDIVIDUALAGEATCOLLECTION_NOT_SET: {
break;
}
}
this.mergeUnknownFields(other.unknownFields);
onChanged();
return this;
}
@java.lang.Override
public final boolean isInitialized() {
return true;
}
@java.lang.Override
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.phenopackets.schema.v1.core.Biosample parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.phenopackets.schema.v1.core.Biosample) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int individualAgeAtCollectionCase_ = 0;
private java.lang.Object individualAgeAtCollection_;
public IndividualAgeAtCollectionCase
getIndividualAgeAtCollectionCase() {
return IndividualAgeAtCollectionCase.forNumber(
individualAgeAtCollectionCase_);
}
public Builder clearIndividualAgeAtCollection() {
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
onChanged();
return this;
}
private int bitField0_;
private java.lang.Object id_ = "";
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
*
* The Biosample id This is unique in the
* context of the server instance.
*
*
* string id = 1;
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
private java.lang.Object individualId_ = "";
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public java.lang.String getIndividualId() {
java.lang.Object ref = individualId_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
individualId_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public com.google.protobuf.ByteString
getIndividualIdBytes() {
java.lang.Object ref = individualId_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
individualId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public Builder setIndividualId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
individualId_ = value;
onChanged();
return this;
}
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public Builder clearIndividualId() {
individualId_ = getDefaultInstance().getIndividualId();
onChanged();
return this;
}
/**
*
* The id of the individual this biosample was derived from.
*
*
* string individual_id = 2;
*/
public Builder setIndividualIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
individualId_ = value;
onChanged();
return this;
}
private java.lang.Object description_ = "";
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public java.lang.String getDescription() {
java.lang.Object ref = description_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
description_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public com.google.protobuf.ByteString
getDescriptionBytes() {
java.lang.Object ref = description_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
description_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public Builder setDescription(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
description_ = value;
onChanged();
return this;
}
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public Builder clearDescription() {
description_ = getDefaultInstance().getDescription();
onChanged();
return this;
}
/**
*
* The biosample's description. This attribute contains human readable text.
* The "description" attributes should not contain any structured data.
*
*
* string description = 3;
*/
public Builder setDescriptionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
description_ = value;
onChanged();
return this;
}
private org.phenopackets.schema.v1.core.OntologyClass sampledTissue_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> sampledTissueBuilder_;
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public boolean hasSampledTissue() {
return sampledTissueBuilder_ != null || sampledTissue_ != null;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass getSampledTissue() {
if (sampledTissueBuilder_ == null) {
return sampledTissue_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : sampledTissue_;
} else {
return sampledTissueBuilder_.getMessage();
}
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public Builder setSampledTissue(org.phenopackets.schema.v1.core.OntologyClass value) {
if (sampledTissueBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
sampledTissue_ = value;
onChanged();
} else {
sampledTissueBuilder_.setMessage(value);
}
return this;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public Builder setSampledTissue(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (sampledTissueBuilder_ == null) {
sampledTissue_ = builderForValue.build();
onChanged();
} else {
sampledTissueBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public Builder mergeSampledTissue(org.phenopackets.schema.v1.core.OntologyClass value) {
if (sampledTissueBuilder_ == null) {
if (sampledTissue_ != null) {
sampledTissue_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(sampledTissue_).mergeFrom(value).buildPartial();
} else {
sampledTissue_ = value;
}
onChanged();
} else {
sampledTissueBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public Builder clearSampledTissue() {
if (sampledTissueBuilder_ == null) {
sampledTissue_ = null;
onChanged();
} else {
sampledTissue_ = null;
sampledTissueBuilder_ = null;
}
return this;
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getSampledTissueBuilder() {
onChanged();
return getSampledTissueFieldBuilder().getBuilder();
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getSampledTissueOrBuilder() {
if (sampledTissueBuilder_ != null) {
return sampledTissueBuilder_.getMessageOrBuilder();
} else {
return sampledTissue_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : sampledTissue_;
}
}
/**
*
* UBERON class describing the tissue from which the specimen was collected.
* PDX-MI mapping: 'Specimen tumor tissue'
* FHIR mapping: Specimen.type
*
*
* .org.phenopackets.schema.v1.core.OntologyClass sampled_tissue = 4;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getSampledTissueFieldBuilder() {
if (sampledTissueBuilder_ == null) {
sampledTissueBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getSampledTissue(),
getParentForChildren(),
isClean());
sampledTissue_ = null;
}
return sampledTissueBuilder_;
}
private java.util.List phenotypicFeatures_ =
java.util.Collections.emptyList();
private void ensurePhenotypicFeaturesIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
phenotypicFeatures_ = new java.util.ArrayList(phenotypicFeatures_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.PhenotypicFeature, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder, org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder> phenotypicFeaturesBuilder_;
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public java.util.List getPhenotypicFeaturesList() {
if (phenotypicFeaturesBuilder_ == null) {
return java.util.Collections.unmodifiableList(phenotypicFeatures_);
} else {
return phenotypicFeaturesBuilder_.getMessageList();
}
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public int getPhenotypicFeaturesCount() {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.size();
} else {
return phenotypicFeaturesBuilder_.getCount();
}
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature getPhenotypicFeatures(int index) {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.get(index);
} else {
return phenotypicFeaturesBuilder_.getMessage(index);
}
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder setPhenotypicFeatures(
int index, org.phenopackets.schema.v1.core.PhenotypicFeature value) {
if (phenotypicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.set(index, value);
onChanged();
} else {
phenotypicFeaturesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder setPhenotypicFeatures(
int index, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder builderForValue) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.set(index, builderForValue.build());
onChanged();
} else {
phenotypicFeaturesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder addPhenotypicFeatures(org.phenopackets.schema.v1.core.PhenotypicFeature value) {
if (phenotypicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.add(value);
onChanged();
} else {
phenotypicFeaturesBuilder_.addMessage(value);
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder addPhenotypicFeatures(
int index, org.phenopackets.schema.v1.core.PhenotypicFeature value) {
if (phenotypicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.add(index, value);
onChanged();
} else {
phenotypicFeaturesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder addPhenotypicFeatures(
org.phenopackets.schema.v1.core.PhenotypicFeature.Builder builderForValue) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.add(builderForValue.build());
onChanged();
} else {
phenotypicFeaturesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder addPhenotypicFeatures(
int index, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder builderForValue) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.add(index, builderForValue.build());
onChanged();
} else {
phenotypicFeaturesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder addAllPhenotypicFeatures(
java.lang.Iterable values) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, phenotypicFeatures_);
onChanged();
} else {
phenotypicFeaturesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder clearPhenotypicFeatures() {
if (phenotypicFeaturesBuilder_ == null) {
phenotypicFeatures_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
phenotypicFeaturesBuilder_.clear();
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public Builder removePhenotypicFeatures(int index) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.remove(index);
onChanged();
} else {
phenotypicFeaturesBuilder_.remove(index);
}
return this;
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder getPhenotypicFeaturesBuilder(
int index) {
return getPhenotypicFeaturesFieldBuilder().getBuilder(index);
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder getPhenotypicFeaturesOrBuilder(
int index) {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.get(index); } else {
return phenotypicFeaturesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public java.util.List
getPhenotypicFeaturesOrBuilderList() {
if (phenotypicFeaturesBuilder_ != null) {
return phenotypicFeaturesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(phenotypicFeatures_);
}
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder addPhenotypicFeaturesBuilder() {
return getPhenotypicFeaturesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance());
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder addPhenotypicFeaturesBuilder(
int index) {
return getPhenotypicFeaturesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance());
}
/**
*
* Phenotypic characteristics of the BioSample, for example histological findings of a biopsy.
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 5;
*/
public java.util.List
getPhenotypicFeaturesBuilderList() {
return getPhenotypicFeaturesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.PhenotypicFeature, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder, org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder>
getPhenotypicFeaturesFieldBuilder() {
if (phenotypicFeaturesBuilder_ == null) {
phenotypicFeaturesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.PhenotypicFeature, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder, org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder>(
phenotypicFeatures_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
phenotypicFeatures_ = null;
}
return phenotypicFeaturesBuilder_;
}
private org.phenopackets.schema.v1.core.OntologyClass taxonomy_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> taxonomyBuilder_;
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public boolean hasTaxonomy() {
return taxonomyBuilder_ != null || taxonomy_ != null;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTaxonomy() {
if (taxonomyBuilder_ == null) {
return taxonomy_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : taxonomy_;
} else {
return taxonomyBuilder_.getMessage();
}
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public Builder setTaxonomy(org.phenopackets.schema.v1.core.OntologyClass value) {
if (taxonomyBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
taxonomy_ = value;
onChanged();
} else {
taxonomyBuilder_.setMessage(value);
}
return this;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public Builder setTaxonomy(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (taxonomyBuilder_ == null) {
taxonomy_ = builderForValue.build();
onChanged();
} else {
taxonomyBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public Builder mergeTaxonomy(org.phenopackets.schema.v1.core.OntologyClass value) {
if (taxonomyBuilder_ == null) {
if (taxonomy_ != null) {
taxonomy_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(taxonomy_).mergeFrom(value).buildPartial();
} else {
taxonomy_ = value;
}
onChanged();
} else {
taxonomyBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public Builder clearTaxonomy() {
if (taxonomyBuilder_ == null) {
taxonomy_ = null;
onChanged();
} else {
taxonomy_ = null;
taxonomyBuilder_ = null;
}
return this;
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getTaxonomyBuilder() {
onChanged();
return getTaxonomyFieldBuilder().getBuilder();
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTaxonomyOrBuilder() {
if (taxonomyBuilder_ != null) {
return taxonomyBuilder_.getMessageOrBuilder();
} else {
return taxonomy_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : taxonomy_;
}
}
/**
*
* NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606
*
*
* .org.phenopackets.schema.v1.core.OntologyClass taxonomy = 6;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getTaxonomyFieldBuilder() {
if (taxonomyBuilder_ == null) {
taxonomyBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getTaxonomy(),
getParentForChildren(),
isClean());
taxonomy_ = null;
}
return taxonomyBuilder_;
}
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder> ageOfIndividualAtCollectionBuilder_;
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public boolean hasAgeOfIndividualAtCollection() {
return individualAgeAtCollectionCase_ == 7;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public org.phenopackets.schema.v1.core.Age getAgeOfIndividualAtCollection() {
if (ageOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 7) {
return (org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
} else {
if (individualAgeAtCollectionCase_ == 7) {
return ageOfIndividualAtCollectionBuilder_.getMessage();
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public Builder setAgeOfIndividualAtCollection(org.phenopackets.schema.v1.core.Age value) {
if (ageOfIndividualAtCollectionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
individualAgeAtCollection_ = value;
onChanged();
} else {
ageOfIndividualAtCollectionBuilder_.setMessage(value);
}
individualAgeAtCollectionCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public Builder setAgeOfIndividualAtCollection(
org.phenopackets.schema.v1.core.Age.Builder builderForValue) {
if (ageOfIndividualAtCollectionBuilder_ == null) {
individualAgeAtCollection_ = builderForValue.build();
onChanged();
} else {
ageOfIndividualAtCollectionBuilder_.setMessage(builderForValue.build());
}
individualAgeAtCollectionCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public Builder mergeAgeOfIndividualAtCollection(org.phenopackets.schema.v1.core.Age value) {
if (ageOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 7 &&
individualAgeAtCollection_ != org.phenopackets.schema.v1.core.Age.getDefaultInstance()) {
individualAgeAtCollection_ = org.phenopackets.schema.v1.core.Age.newBuilder((org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_)
.mergeFrom(value).buildPartial();
} else {
individualAgeAtCollection_ = value;
}
onChanged();
} else {
if (individualAgeAtCollectionCase_ == 7) {
ageOfIndividualAtCollectionBuilder_.mergeFrom(value);
}
ageOfIndividualAtCollectionBuilder_.setMessage(value);
}
individualAgeAtCollectionCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public Builder clearAgeOfIndividualAtCollection() {
if (ageOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 7) {
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
onChanged();
}
} else {
if (individualAgeAtCollectionCase_ == 7) {
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
}
ageOfIndividualAtCollectionBuilder_.clear();
}
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public org.phenopackets.schema.v1.core.Age.Builder getAgeOfIndividualAtCollectionBuilder() {
return getAgeOfIndividualAtCollectionFieldBuilder().getBuilder();
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
public org.phenopackets.schema.v1.core.AgeOrBuilder getAgeOfIndividualAtCollectionOrBuilder() {
if ((individualAgeAtCollectionCase_ == 7) && (ageOfIndividualAtCollectionBuilder_ != null)) {
return ageOfIndividualAtCollectionBuilder_.getMessageOrBuilder();
} else {
if (individualAgeAtCollectionCase_ == 7) {
return (org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_individual_at_collection = 7;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder>
getAgeOfIndividualAtCollectionFieldBuilder() {
if (ageOfIndividualAtCollectionBuilder_ == null) {
if (!(individualAgeAtCollectionCase_ == 7)) {
individualAgeAtCollection_ = org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
ageOfIndividualAtCollectionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder>(
(org.phenopackets.schema.v1.core.Age) individualAgeAtCollection_,
getParentForChildren(),
isClean());
individualAgeAtCollection_ = null;
}
individualAgeAtCollectionCase_ = 7;
onChanged();;
return ageOfIndividualAtCollectionBuilder_;
}
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder> ageRangeOfIndividualAtCollectionBuilder_;
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public boolean hasAgeRangeOfIndividualAtCollection() {
return individualAgeAtCollectionCase_ == 8;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public org.phenopackets.schema.v1.core.AgeRange getAgeRangeOfIndividualAtCollection() {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 8) {
return (org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
} else {
if (individualAgeAtCollectionCase_ == 8) {
return ageRangeOfIndividualAtCollectionBuilder_.getMessage();
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public Builder setAgeRangeOfIndividualAtCollection(org.phenopackets.schema.v1.core.AgeRange value) {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
individualAgeAtCollection_ = value;
onChanged();
} else {
ageRangeOfIndividualAtCollectionBuilder_.setMessage(value);
}
individualAgeAtCollectionCase_ = 8;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public Builder setAgeRangeOfIndividualAtCollection(
org.phenopackets.schema.v1.core.AgeRange.Builder builderForValue) {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
individualAgeAtCollection_ = builderForValue.build();
onChanged();
} else {
ageRangeOfIndividualAtCollectionBuilder_.setMessage(builderForValue.build());
}
individualAgeAtCollectionCase_ = 8;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public Builder mergeAgeRangeOfIndividualAtCollection(org.phenopackets.schema.v1.core.AgeRange value) {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 8 &&
individualAgeAtCollection_ != org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance()) {
individualAgeAtCollection_ = org.phenopackets.schema.v1.core.AgeRange.newBuilder((org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_)
.mergeFrom(value).buildPartial();
} else {
individualAgeAtCollection_ = value;
}
onChanged();
} else {
if (individualAgeAtCollectionCase_ == 8) {
ageRangeOfIndividualAtCollectionBuilder_.mergeFrom(value);
}
ageRangeOfIndividualAtCollectionBuilder_.setMessage(value);
}
individualAgeAtCollectionCase_ = 8;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public Builder clearAgeRangeOfIndividualAtCollection() {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
if (individualAgeAtCollectionCase_ == 8) {
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
onChanged();
}
} else {
if (individualAgeAtCollectionCase_ == 8) {
individualAgeAtCollectionCase_ = 0;
individualAgeAtCollection_ = null;
}
ageRangeOfIndividualAtCollectionBuilder_.clear();
}
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public org.phenopackets.schema.v1.core.AgeRange.Builder getAgeRangeOfIndividualAtCollectionBuilder() {
return getAgeRangeOfIndividualAtCollectionFieldBuilder().getBuilder();
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
public org.phenopackets.schema.v1.core.AgeRangeOrBuilder getAgeRangeOfIndividualAtCollectionOrBuilder() {
if ((individualAgeAtCollectionCase_ == 8) && (ageRangeOfIndividualAtCollectionBuilder_ != null)) {
return ageRangeOfIndividualAtCollectionBuilder_.getMessageOrBuilder();
} else {
if (individualAgeAtCollectionCase_ == 8) {
return (org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_individual_at_collection = 8;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder>
getAgeRangeOfIndividualAtCollectionFieldBuilder() {
if (ageRangeOfIndividualAtCollectionBuilder_ == null) {
if (!(individualAgeAtCollectionCase_ == 8)) {
individualAgeAtCollection_ = org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
ageRangeOfIndividualAtCollectionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder>(
(org.phenopackets.schema.v1.core.AgeRange) individualAgeAtCollection_,
getParentForChildren(),
isClean());
individualAgeAtCollection_ = null;
}
individualAgeAtCollectionCase_ = 8;
onChanged();;
return ageRangeOfIndividualAtCollectionBuilder_;
}
private org.phenopackets.schema.v1.core.OntologyClass histologicalDiagnosis_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> histologicalDiagnosisBuilder_;
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public boolean hasHistologicalDiagnosis() {
return histologicalDiagnosisBuilder_ != null || histologicalDiagnosis_ != null;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass getHistologicalDiagnosis() {
if (histologicalDiagnosisBuilder_ == null) {
return histologicalDiagnosis_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : histologicalDiagnosis_;
} else {
return histologicalDiagnosisBuilder_.getMessage();
}
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public Builder setHistologicalDiagnosis(org.phenopackets.schema.v1.core.OntologyClass value) {
if (histologicalDiagnosisBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
histologicalDiagnosis_ = value;
onChanged();
} else {
histologicalDiagnosisBuilder_.setMessage(value);
}
return this;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public Builder setHistologicalDiagnosis(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (histologicalDiagnosisBuilder_ == null) {
histologicalDiagnosis_ = builderForValue.build();
onChanged();
} else {
histologicalDiagnosisBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public Builder mergeHistologicalDiagnosis(org.phenopackets.schema.v1.core.OntologyClass value) {
if (histologicalDiagnosisBuilder_ == null) {
if (histologicalDiagnosis_ != null) {
histologicalDiagnosis_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(histologicalDiagnosis_).mergeFrom(value).buildPartial();
} else {
histologicalDiagnosis_ = value;
}
onChanged();
} else {
histologicalDiagnosisBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public Builder clearHistologicalDiagnosis() {
if (histologicalDiagnosisBuilder_ == null) {
histologicalDiagnosis_ = null;
onChanged();
} else {
histologicalDiagnosis_ = null;
histologicalDiagnosisBuilder_ = null;
}
return this;
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getHistologicalDiagnosisBuilder() {
onChanged();
return getHistologicalDiagnosisFieldBuilder().getBuilder();
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getHistologicalDiagnosisOrBuilder() {
if (histologicalDiagnosisBuilder_ != null) {
return histologicalDiagnosisBuilder_.getMessageOrBuilder();
} else {
return histologicalDiagnosis_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : histologicalDiagnosis_;
}
}
/**
*
* This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the
* Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
* Normal samples would be tagged with the term "NCIT:C38757", "Negative Finding"
*
*
* .org.phenopackets.schema.v1.core.OntologyClass histological_diagnosis = 9;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getHistologicalDiagnosisFieldBuilder() {
if (histologicalDiagnosisBuilder_ == null) {
histologicalDiagnosisBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getHistologicalDiagnosis(),
getParentForChildren(),
isClean());
histologicalDiagnosis_ = null;
}
return histologicalDiagnosisBuilder_;
}
private org.phenopackets.schema.v1.core.OntologyClass tumorProgression_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> tumorProgressionBuilder_;
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public boolean hasTumorProgression() {
return tumorProgressionBuilder_ != null || tumorProgression_ != null;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTumorProgression() {
if (tumorProgressionBuilder_ == null) {
return tumorProgression_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorProgression_;
} else {
return tumorProgressionBuilder_.getMessage();
}
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public Builder setTumorProgression(org.phenopackets.schema.v1.core.OntologyClass value) {
if (tumorProgressionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
tumorProgression_ = value;
onChanged();
} else {
tumorProgressionBuilder_.setMessage(value);
}
return this;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public Builder setTumorProgression(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (tumorProgressionBuilder_ == null) {
tumorProgression_ = builderForValue.build();
onChanged();
} else {
tumorProgressionBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public Builder mergeTumorProgression(org.phenopackets.schema.v1.core.OntologyClass value) {
if (tumorProgressionBuilder_ == null) {
if (tumorProgression_ != null) {
tumorProgression_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(tumorProgression_).mergeFrom(value).buildPartial();
} else {
tumorProgression_ = value;
}
onChanged();
} else {
tumorProgressionBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public Builder clearTumorProgression() {
if (tumorProgressionBuilder_ == null) {
tumorProgression_ = null;
onChanged();
} else {
tumorProgression_ = null;
tumorProgressionBuilder_ = null;
}
return this;
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getTumorProgressionBuilder() {
onChanged();
return getTumorProgressionFieldBuilder().getBuilder();
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTumorProgressionOrBuilder() {
if (tumorProgressionBuilder_ != null) {
return tumorProgressionBuilder_.getMessageOrBuilder();
} else {
return tumorProgression_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorProgression_;
}
}
/**
*
* Is the specimen tissue from the primary tumor, a metastasis or a recurrence?
* Most likely a child term of NCIT:C7062 (Neoplasm by Special Category)
* NCIT:C3677 (Benign Neoplasm)
* NCIT:C84509 (Primary Malignant Neoplasm)
* NCIT:C95606 (Second Primary Malignant Neoplasm)
* NCIT:C3261 (Metastatic Neoplasm)
* NCIT:C4813 (Recurrent Malignant Neoplasm)
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_progression = 10;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getTumorProgressionFieldBuilder() {
if (tumorProgressionBuilder_ == null) {
tumorProgressionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getTumorProgression(),
getParentForChildren(),
isClean());
tumorProgression_ = null;
}
return tumorProgressionBuilder_;
}
private org.phenopackets.schema.v1.core.OntologyClass tumorGrade_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> tumorGradeBuilder_;
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public boolean hasTumorGrade() {
return tumorGradeBuilder_ != null || tumorGrade_ != null;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public org.phenopackets.schema.v1.core.OntologyClass getTumorGrade() {
if (tumorGradeBuilder_ == null) {
return tumorGrade_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorGrade_;
} else {
return tumorGradeBuilder_.getMessage();
}
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public Builder setTumorGrade(org.phenopackets.schema.v1.core.OntologyClass value) {
if (tumorGradeBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
tumorGrade_ = value;
onChanged();
} else {
tumorGradeBuilder_.setMessage(value);
}
return this;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public Builder setTumorGrade(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (tumorGradeBuilder_ == null) {
tumorGrade_ = builderForValue.build();
onChanged();
} else {
tumorGradeBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public Builder mergeTumorGrade(org.phenopackets.schema.v1.core.OntologyClass value) {
if (tumorGradeBuilder_ == null) {
if (tumorGrade_ != null) {
tumorGrade_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(tumorGrade_).mergeFrom(value).buildPartial();
} else {
tumorGrade_ = value;
}
onChanged();
} else {
tumorGradeBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public Builder clearTumorGrade() {
if (tumorGradeBuilder_ == null) {
tumorGrade_ = null;
onChanged();
} else {
tumorGrade_ = null;
tumorGradeBuilder_ = null;
}
return this;
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getTumorGradeBuilder() {
onChanged();
return getTumorGradeFieldBuilder().getBuilder();
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTumorGradeOrBuilder() {
if (tumorGradeBuilder_ != null) {
return tumorGradeBuilder_.getMessageOrBuilder();
} else {
return tumorGrade_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : tumorGrade_;
}
}
/**
*
* Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent
* See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
*
*
* .org.phenopackets.schema.v1.core.OntologyClass tumor_grade = 11;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getTumorGradeFieldBuilder() {
if (tumorGradeBuilder_ == null) {
tumorGradeBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getTumorGrade(),
getParentForChildren(),
isClean());
tumorGrade_ = null;
}
return tumorGradeBuilder_;
}
private java.util.List diagnosticMarkers_ =
java.util.Collections.emptyList();
private void ensureDiagnosticMarkersIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
diagnosticMarkers_ = new java.util.ArrayList(diagnosticMarkers_);
bitField0_ |= 0x00000002;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> diagnosticMarkersBuilder_;
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public java.util.List getDiagnosticMarkersList() {
if (diagnosticMarkersBuilder_ == null) {
return java.util.Collections.unmodifiableList(diagnosticMarkers_);
} else {
return diagnosticMarkersBuilder_.getMessageList();
}
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public int getDiagnosticMarkersCount() {
if (diagnosticMarkersBuilder_ == null) {
return diagnosticMarkers_.size();
} else {
return diagnosticMarkersBuilder_.getCount();
}
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClass getDiagnosticMarkers(int index) {
if (diagnosticMarkersBuilder_ == null) {
return diagnosticMarkers_.get(index);
} else {
return diagnosticMarkersBuilder_.getMessage(index);
}
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder setDiagnosticMarkers(
int index, org.phenopackets.schema.v1.core.OntologyClass value) {
if (diagnosticMarkersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.set(index, value);
onChanged();
} else {
diagnosticMarkersBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder setDiagnosticMarkers(
int index, org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (diagnosticMarkersBuilder_ == null) {
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.set(index, builderForValue.build());
onChanged();
} else {
diagnosticMarkersBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder addDiagnosticMarkers(org.phenopackets.schema.v1.core.OntologyClass value) {
if (diagnosticMarkersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.add(value);
onChanged();
} else {
diagnosticMarkersBuilder_.addMessage(value);
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder addDiagnosticMarkers(
int index, org.phenopackets.schema.v1.core.OntologyClass value) {
if (diagnosticMarkersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.add(index, value);
onChanged();
} else {
diagnosticMarkersBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder addDiagnosticMarkers(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (diagnosticMarkersBuilder_ == null) {
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.add(builderForValue.build());
onChanged();
} else {
diagnosticMarkersBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder addDiagnosticMarkers(
int index, org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (diagnosticMarkersBuilder_ == null) {
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.add(index, builderForValue.build());
onChanged();
} else {
diagnosticMarkersBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder addAllDiagnosticMarkers(
java.lang.Iterable values) {
if (diagnosticMarkersBuilder_ == null) {
ensureDiagnosticMarkersIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, diagnosticMarkers_);
onChanged();
} else {
diagnosticMarkersBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder clearDiagnosticMarkers() {
if (diagnosticMarkersBuilder_ == null) {
diagnosticMarkers_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
} else {
diagnosticMarkersBuilder_.clear();
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public Builder removeDiagnosticMarkers(int index) {
if (diagnosticMarkersBuilder_ == null) {
ensureDiagnosticMarkersIsMutable();
diagnosticMarkers_.remove(index);
onChanged();
} else {
diagnosticMarkersBuilder_.remove(index);
}
return this;
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getDiagnosticMarkersBuilder(
int index) {
return getDiagnosticMarkersFieldBuilder().getBuilder(index);
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getDiagnosticMarkersOrBuilder(
int index) {
if (diagnosticMarkersBuilder_ == null) {
return diagnosticMarkers_.get(index); } else {
return diagnosticMarkersBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public java.util.List
getDiagnosticMarkersOrBuilderList() {
if (diagnosticMarkersBuilder_ != null) {
return diagnosticMarkersBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(diagnosticMarkers_);
}
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder addDiagnosticMarkersBuilder() {
return getDiagnosticMarkersFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance());
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder addDiagnosticMarkersBuilder(
int index) {
return getDiagnosticMarkersFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance());
}
/**
*
* Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy
* NCIT:C25294 (Laboratory Procedure).
* e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass diagnostic_markers = 12;
*/
public java.util.List
getDiagnosticMarkersBuilderList() {
return getDiagnosticMarkersFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getDiagnosticMarkersFieldBuilder() {
if (diagnosticMarkersBuilder_ == null) {
diagnosticMarkersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
diagnosticMarkers_,
((bitField0_ & 0x00000002) != 0),
getParentForChildren(),
isClean());
diagnosticMarkers_ = null;
}
return diagnosticMarkersBuilder_;
}
private org.phenopackets.schema.v1.core.Procedure procedure_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Procedure, org.phenopackets.schema.v1.core.Procedure.Builder, org.phenopackets.schema.v1.core.ProcedureOrBuilder> procedureBuilder_;
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public boolean hasProcedure() {
return procedureBuilder_ != null || procedure_ != null;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public org.phenopackets.schema.v1.core.Procedure getProcedure() {
if (procedureBuilder_ == null) {
return procedure_ == null ? org.phenopackets.schema.v1.core.Procedure.getDefaultInstance() : procedure_;
} else {
return procedureBuilder_.getMessage();
}
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public Builder setProcedure(org.phenopackets.schema.v1.core.Procedure value) {
if (procedureBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
procedure_ = value;
onChanged();
} else {
procedureBuilder_.setMessage(value);
}
return this;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public Builder setProcedure(
org.phenopackets.schema.v1.core.Procedure.Builder builderForValue) {
if (procedureBuilder_ == null) {
procedure_ = builderForValue.build();
onChanged();
} else {
procedureBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public Builder mergeProcedure(org.phenopackets.schema.v1.core.Procedure value) {
if (procedureBuilder_ == null) {
if (procedure_ != null) {
procedure_ =
org.phenopackets.schema.v1.core.Procedure.newBuilder(procedure_).mergeFrom(value).buildPartial();
} else {
procedure_ = value;
}
onChanged();
} else {
procedureBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public Builder clearProcedure() {
if (procedureBuilder_ == null) {
procedure_ = null;
onChanged();
} else {
procedure_ = null;
procedureBuilder_ = null;
}
return this;
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public org.phenopackets.schema.v1.core.Procedure.Builder getProcedureBuilder() {
onChanged();
return getProcedureFieldBuilder().getBuilder();
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
public org.phenopackets.schema.v1.core.ProcedureOrBuilder getProcedureOrBuilder() {
if (procedureBuilder_ != null) {
return procedureBuilder_.getMessageOrBuilder();
} else {
return procedure_ == null ?
org.phenopackets.schema.v1.core.Procedure.getDefaultInstance() : procedure_;
}
}
/**
*
* Clinical procedure performed on the subject in order to extract the biosample.
*
*
* .org.phenopackets.schema.v1.core.Procedure procedure = 13;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Procedure, org.phenopackets.schema.v1.core.Procedure.Builder, org.phenopackets.schema.v1.core.ProcedureOrBuilder>
getProcedureFieldBuilder() {
if (procedureBuilder_ == null) {
procedureBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Procedure, org.phenopackets.schema.v1.core.Procedure.Builder, org.phenopackets.schema.v1.core.ProcedureOrBuilder>(
getProcedure(),
getParentForChildren(),
isClean());
procedure_ = null;
}
return procedureBuilder_;
}
private java.util.List htsFiles_ =
java.util.Collections.emptyList();
private void ensureHtsFilesIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
htsFiles_ = new java.util.ArrayList(htsFiles_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.HtsFile, org.phenopackets.schema.v1.core.HtsFile.Builder, org.phenopackets.schema.v1.core.HtsFileOrBuilder> htsFilesBuilder_;
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public java.util.List getHtsFilesList() {
if (htsFilesBuilder_ == null) {
return java.util.Collections.unmodifiableList(htsFiles_);
} else {
return htsFilesBuilder_.getMessageList();
}
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public int getHtsFilesCount() {
if (htsFilesBuilder_ == null) {
return htsFiles_.size();
} else {
return htsFilesBuilder_.getCount();
}
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index) {
if (htsFilesBuilder_ == null) {
return htsFiles_.get(index);
} else {
return htsFilesBuilder_.getMessage(index);
}
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder setHtsFiles(
int index, org.phenopackets.schema.v1.core.HtsFile value) {
if (htsFilesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHtsFilesIsMutable();
htsFiles_.set(index, value);
onChanged();
} else {
htsFilesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder setHtsFiles(
int index, org.phenopackets.schema.v1.core.HtsFile.Builder builderForValue) {
if (htsFilesBuilder_ == null) {
ensureHtsFilesIsMutable();
htsFiles_.set(index, builderForValue.build());
onChanged();
} else {
htsFilesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder addHtsFiles(org.phenopackets.schema.v1.core.HtsFile value) {
if (htsFilesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHtsFilesIsMutable();
htsFiles_.add(value);
onChanged();
} else {
htsFilesBuilder_.addMessage(value);
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder addHtsFiles(
int index, org.phenopackets.schema.v1.core.HtsFile value) {
if (htsFilesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHtsFilesIsMutable();
htsFiles_.add(index, value);
onChanged();
} else {
htsFilesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder addHtsFiles(
org.phenopackets.schema.v1.core.HtsFile.Builder builderForValue) {
if (htsFilesBuilder_ == null) {
ensureHtsFilesIsMutable();
htsFiles_.add(builderForValue.build());
onChanged();
} else {
htsFilesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder addHtsFiles(
int index, org.phenopackets.schema.v1.core.HtsFile.Builder builderForValue) {
if (htsFilesBuilder_ == null) {
ensureHtsFilesIsMutable();
htsFiles_.add(index, builderForValue.build());
onChanged();
} else {
htsFilesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder addAllHtsFiles(
java.lang.Iterable values) {
if (htsFilesBuilder_ == null) {
ensureHtsFilesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, htsFiles_);
onChanged();
} else {
htsFilesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder clearHtsFiles() {
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
htsFilesBuilder_.clear();
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public Builder removeHtsFiles(int index) {
if (htsFilesBuilder_ == null) {
ensureHtsFilesIsMutable();
htsFiles_.remove(index);
onChanged();
} else {
htsFilesBuilder_.remove(index);
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFile.Builder getHtsFilesBuilder(
int index) {
return getHtsFilesFieldBuilder().getBuilder(index);
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFileOrBuilder getHtsFilesOrBuilder(
int index) {
if (htsFilesBuilder_ == null) {
return htsFiles_.get(index); } else {
return htsFilesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public java.util.List
getHtsFilesOrBuilderList() {
if (htsFilesBuilder_ != null) {
return htsFilesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(htsFiles_);
}
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFile.Builder addHtsFilesBuilder() {
return getHtsFilesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.HtsFile.getDefaultInstance());
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public org.phenopackets.schema.v1.core.HtsFile.Builder addHtsFilesBuilder(
int index) {
return getHtsFilesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.HtsFile.getDefaultInstance());
}
/**
*
* Pointer to the relevant HTS file(s) for the biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 14;
*/
public java.util.List
getHtsFilesBuilderList() {
return getHtsFilesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.HtsFile, org.phenopackets.schema.v1.core.HtsFile.Builder, org.phenopackets.schema.v1.core.HtsFileOrBuilder>
getHtsFilesFieldBuilder() {
if (htsFilesBuilder_ == null) {
htsFilesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.HtsFile, org.phenopackets.schema.v1.core.HtsFile.Builder, org.phenopackets.schema.v1.core.HtsFileOrBuilder>(
htsFiles_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
htsFiles_ = null;
}
return htsFilesBuilder_;
}
private java.util.List variants_ =
java.util.Collections.emptyList();
private void ensureVariantsIsMutable() {
if (!((bitField0_ & 0x00000008) != 0)) {
variants_ = new java.util.ArrayList(variants_);
bitField0_ |= 0x00000008;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Variant, org.phenopackets.schema.v1.core.Variant.Builder, org.phenopackets.schema.v1.core.VariantOrBuilder> variantsBuilder_;
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public java.util.List getVariantsList() {
if (variantsBuilder_ == null) {
return java.util.Collections.unmodifiableList(variants_);
} else {
return variantsBuilder_.getMessageList();
}
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public int getVariantsCount() {
if (variantsBuilder_ == null) {
return variants_.size();
} else {
return variantsBuilder_.getCount();
}
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.Variant getVariants(int index) {
if (variantsBuilder_ == null) {
return variants_.get(index);
} else {
return variantsBuilder_.getMessage(index);
}
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder setVariants(
int index, org.phenopackets.schema.v1.core.Variant value) {
if (variantsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureVariantsIsMutable();
variants_.set(index, value);
onChanged();
} else {
variantsBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder setVariants(
int index, org.phenopackets.schema.v1.core.Variant.Builder builderForValue) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
variants_.set(index, builderForValue.build());
onChanged();
} else {
variantsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder addVariants(org.phenopackets.schema.v1.core.Variant value) {
if (variantsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureVariantsIsMutable();
variants_.add(value);
onChanged();
} else {
variantsBuilder_.addMessage(value);
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder addVariants(
int index, org.phenopackets.schema.v1.core.Variant value) {
if (variantsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureVariantsIsMutable();
variants_.add(index, value);
onChanged();
} else {
variantsBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder addVariants(
org.phenopackets.schema.v1.core.Variant.Builder builderForValue) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
variants_.add(builderForValue.build());
onChanged();
} else {
variantsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder addVariants(
int index, org.phenopackets.schema.v1.core.Variant.Builder builderForValue) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
variants_.add(index, builderForValue.build());
onChanged();
} else {
variantsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder addAllVariants(
java.lang.Iterable values) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, variants_);
onChanged();
} else {
variantsBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder clearVariants() {
if (variantsBuilder_ == null) {
variants_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
onChanged();
} else {
variantsBuilder_.clear();
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public Builder removeVariants(int index) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
variants_.remove(index);
onChanged();
} else {
variantsBuilder_.remove(index);
}
return this;
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.Variant.Builder getVariantsBuilder(
int index) {
return getVariantsFieldBuilder().getBuilder(index);
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.VariantOrBuilder getVariantsOrBuilder(
int index) {
if (variantsBuilder_ == null) {
return variants_.get(index); } else {
return variantsBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public java.util.List
getVariantsOrBuilderList() {
if (variantsBuilder_ != null) {
return variantsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(variants_);
}
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.Variant.Builder addVariantsBuilder() {
return getVariantsFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Variant.getDefaultInstance());
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public org.phenopackets.schema.v1.core.Variant.Builder addVariantsBuilder(
int index) {
return getVariantsFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Variant.getDefaultInstance());
}
/**
*
* Field for variants relevant to this biosample.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 15;
*/
public java.util.List
getVariantsBuilderList() {
return getVariantsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Variant, org.phenopackets.schema.v1.core.Variant.Builder, org.phenopackets.schema.v1.core.VariantOrBuilder>
getVariantsFieldBuilder() {
if (variantsBuilder_ == null) {
variantsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Variant, org.phenopackets.schema.v1.core.Variant.Builder, org.phenopackets.schema.v1.core.VariantOrBuilder>(
variants_,
((bitField0_ & 0x00000008) != 0),
getParentForChildren(),
isClean());
variants_ = null;
}
return variantsBuilder_;
}
private boolean isControlSample_ ;
/**
*
* if true, this sample is being use as a normal control, often in combination with
* another sample that is thought to contain a pathological finding
* the default value is false
*
*
* bool is_control_sample = 16;
*/
public boolean getIsControlSample() {
return isControlSample_;
}
/**
*
* if true, this sample is being use as a normal control, often in combination with
* another sample that is thought to contain a pathological finding
* the default value is false
*
*
* bool is_control_sample = 16;
*/
public Builder setIsControlSample(boolean value) {
isControlSample_ = value;
onChanged();
return this;
}
/**
*
* if true, this sample is being use as a normal control, often in combination with
* another sample that is thought to contain a pathological finding
* the default value is false
*
*
* bool is_control_sample = 16;
*/
public Builder clearIsControlSample() {
isControlSample_ = false;
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:org.phenopackets.schema.v1.core.Biosample)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.Biosample)
private static final org.phenopackets.schema.v1.core.Biosample DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.core.Biosample();
}
public static org.phenopackets.schema.v1.core.Biosample getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Biosample parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Biosample(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.Biosample getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}