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A Protobuf schema for capturing clinical phenotypes
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: phenopackets.proto
package org.phenopackets.schema.v1;
/**
*
* An anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses.
* This is a bundle of high-level concepts with no specifically defined relational concepts. It is expected that the
* resources sharing the phenopackets will define and enforce their own semantics and level of requirements for included
* fields.
*
*
* Protobuf type {@code org.phenopackets.schema.v1.Phenopacket}
*/
public final class Phenopacket extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.Phenopacket)
PhenopacketOrBuilder {
private static final long serialVersionUID = 0L;
// Use Phenopacket.newBuilder() to construct.
private Phenopacket(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private Phenopacket() {
id_ = "";
phenotypicFeatures_ = java.util.Collections.emptyList();
biosamples_ = java.util.Collections.emptyList();
genes_ = java.util.Collections.emptyList();
variants_ = java.util.Collections.emptyList();
diseases_ = java.util.Collections.emptyList();
htsFiles_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new Phenopacket();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Phenopacket(
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: {
org.phenopackets.schema.v1.core.Individual.Builder subBuilder = null;
if (subject_ != null) {
subBuilder = subject_.toBuilder();
}
subject_ = input.readMessage(org.phenopackets.schema.v1.core.Individual.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(subject_);
subject_ = subBuilder.buildPartial();
}
break;
}
case 26: {
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 34: {
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
biosamples_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
}
biosamples_.add(
input.readMessage(org.phenopackets.schema.v1.core.Biosample.parser(), extensionRegistry));
break;
}
case 42: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
genes_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
genes_.add(
input.readMessage(org.phenopackets.schema.v1.core.Gene.parser(), extensionRegistry));
break;
}
case 50: {
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 58: {
if (!((mutable_bitField0_ & 0x00000010) != 0)) {
diseases_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000010;
}
diseases_.add(
input.readMessage(org.phenopackets.schema.v1.core.Disease.parser(), extensionRegistry));
break;
}
case 66: {
if (!((mutable_bitField0_ & 0x00000020) != 0)) {
htsFiles_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000020;
}
htsFiles_.add(
input.readMessage(org.phenopackets.schema.v1.core.HtsFile.parser(), extensionRegistry));
break;
}
case 74: {
org.phenopackets.schema.v1.core.MetaData.Builder subBuilder = null;
if (metaData_ != null) {
subBuilder = metaData_.toBuilder();
}
metaData_ = input.readMessage(org.phenopackets.schema.v1.core.MetaData.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(metaData_);
metaData_ = subBuilder.buildPartial();
}
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)) {
biosamples_ = java.util.Collections.unmodifiableList(biosamples_);
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
genes_ = java.util.Collections.unmodifiableList(genes_);
}
if (((mutable_bitField0_ & 0x00000008) != 0)) {
variants_ = java.util.Collections.unmodifiableList(variants_);
}
if (((mutable_bitField0_ & 0x00000010) != 0)) {
diseases_ = java.util.Collections.unmodifiableList(diseases_);
}
if (((mutable_bitField0_ & 0x00000020) != 0)) {
htsFiles_ = java.util.Collections.unmodifiableList(htsFiles_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Phenopacket_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Phenopacket_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.phenopackets.schema.v1.Phenopacket.class, org.phenopackets.schema.v1.Phenopacket.Builder.class);
}
public static final int ID_FIELD_NUMBER = 1;
private volatile java.lang.Object id_;
/**
*
* An identifier specific for this phenopacket.
*
*
* 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;
}
}
/**
*
* An identifier specific for this phenopacket.
*
*
* 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 SUBJECT_FIELD_NUMBER = 2;
private org.phenopackets.schema.v1.core.Individual subject_;
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public boolean hasSubject() {
return subject_ != null;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public org.phenopackets.schema.v1.core.Individual getSubject() {
return subject_ == null ? org.phenopackets.schema.v1.core.Individual.getDefaultInstance() : subject_;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public org.phenopackets.schema.v1.core.IndividualOrBuilder getSubjectOrBuilder() {
return getSubject();
}
public static final int PHENOTYPIC_FEATURES_FIELD_NUMBER = 3;
private java.util.List phenotypicFeatures_;
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public java.util.List getPhenotypicFeaturesList() {
return phenotypicFeatures_;
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public java.util.List
getPhenotypicFeaturesOrBuilderList() {
return phenotypicFeatures_;
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public int getPhenotypicFeaturesCount() {
return phenotypicFeatures_.size();
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature getPhenotypicFeatures(int index) {
return phenotypicFeatures_.get(index);
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder getPhenotypicFeaturesOrBuilder(
int index) {
return phenotypicFeatures_.get(index);
}
public static final int BIOSAMPLES_FIELD_NUMBER = 4;
private java.util.List biosamples_;
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public java.util.List getBiosamplesList() {
return biosamples_;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public java.util.List
getBiosamplesOrBuilderList() {
return biosamples_;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public int getBiosamplesCount() {
return biosamples_.size();
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.Biosample getBiosamples(int index) {
return biosamples_.get(index);
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.BiosampleOrBuilder getBiosamplesOrBuilder(
int index) {
return biosamples_.get(index);
}
public static final int GENES_FIELD_NUMBER = 5;
private java.util.List genes_;
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public java.util.List getGenesList() {
return genes_;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public java.util.List
getGenesOrBuilderList() {
return genes_;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public int getGenesCount() {
return genes_.size();
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.Gene getGenes(int index) {
return genes_.get(index);
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.GeneOrBuilder getGenesOrBuilder(
int index) {
return genes_.get(index);
}
public static final int VARIANTS_FIELD_NUMBER = 6;
private java.util.List variants_;
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public java.util.List getVariantsList() {
return variants_;
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public java.util.List
getVariantsOrBuilderList() {
return variants_;
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public int getVariantsCount() {
return variants_.size();
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.Variant getVariants(int index) {
return variants_.get(index);
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.VariantOrBuilder getVariantsOrBuilder(
int index) {
return variants_.get(index);
}
public static final int DISEASES_FIELD_NUMBER = 7;
private java.util.List diseases_;
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public java.util.List getDiseasesList() {
return diseases_;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public java.util.List
getDiseasesOrBuilderList() {
return diseases_;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public int getDiseasesCount() {
return diseases_.size();
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.Disease getDiseases(int index) {
return diseases_.get(index);
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.DiseaseOrBuilder getDiseasesOrBuilder(
int index) {
return diseases_.get(index);
}
public static final int HTS_FILES_FIELD_NUMBER = 8;
private java.util.List htsFiles_;
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public java.util.List getHtsFilesList() {
return htsFiles_;
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public java.util.List
getHtsFilesOrBuilderList() {
return htsFiles_;
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public int getHtsFilesCount() {
return htsFiles_.size();
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index) {
return htsFiles_.get(index);
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public org.phenopackets.schema.v1.core.HtsFileOrBuilder getHtsFilesOrBuilder(
int index) {
return htsFiles_.get(index);
}
public static final int META_DATA_FIELD_NUMBER = 9;
private org.phenopackets.schema.v1.core.MetaData metaData_;
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public boolean hasMetaData() {
return metaData_ != null;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public org.phenopackets.schema.v1.core.MetaData getMetaData() {
return metaData_ == null ? org.phenopackets.schema.v1.core.MetaData.getDefaultInstance() : metaData_;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public org.phenopackets.schema.v1.core.MetaDataOrBuilder getMetaDataOrBuilder() {
return getMetaData();
}
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 (subject_ != null) {
output.writeMessage(2, getSubject());
}
for (int i = 0; i < phenotypicFeatures_.size(); i++) {
output.writeMessage(3, phenotypicFeatures_.get(i));
}
for (int i = 0; i < biosamples_.size(); i++) {
output.writeMessage(4, biosamples_.get(i));
}
for (int i = 0; i < genes_.size(); i++) {
output.writeMessage(5, genes_.get(i));
}
for (int i = 0; i < variants_.size(); i++) {
output.writeMessage(6, variants_.get(i));
}
for (int i = 0; i < diseases_.size(); i++) {
output.writeMessage(7, diseases_.get(i));
}
for (int i = 0; i < htsFiles_.size(); i++) {
output.writeMessage(8, htsFiles_.get(i));
}
if (metaData_ != null) {
output.writeMessage(9, getMetaData());
}
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 (subject_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(2, getSubject());
}
for (int i = 0; i < phenotypicFeatures_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(3, phenotypicFeatures_.get(i));
}
for (int i = 0; i < biosamples_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(4, biosamples_.get(i));
}
for (int i = 0; i < genes_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(5, genes_.get(i));
}
for (int i = 0; i < variants_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(6, variants_.get(i));
}
for (int i = 0; i < diseases_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(7, diseases_.get(i));
}
for (int i = 0; i < htsFiles_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(8, htsFiles_.get(i));
}
if (metaData_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, getMetaData());
}
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.Phenopacket)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.Phenopacket other = (org.phenopackets.schema.v1.Phenopacket) obj;
if (!getId()
.equals(other.getId())) return false;
if (hasSubject() != other.hasSubject()) return false;
if (hasSubject()) {
if (!getSubject()
.equals(other.getSubject())) return false;
}
if (!getPhenotypicFeaturesList()
.equals(other.getPhenotypicFeaturesList())) return false;
if (!getBiosamplesList()
.equals(other.getBiosamplesList())) return false;
if (!getGenesList()
.equals(other.getGenesList())) return false;
if (!getVariantsList()
.equals(other.getVariantsList())) return false;
if (!getDiseasesList()
.equals(other.getDiseasesList())) return false;
if (!getHtsFilesList()
.equals(other.getHtsFilesList())) return false;
if (hasMetaData() != other.hasMetaData()) return false;
if (hasMetaData()) {
if (!getMetaData()
.equals(other.getMetaData())) return false;
}
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();
if (hasSubject()) {
hash = (37 * hash) + SUBJECT_FIELD_NUMBER;
hash = (53 * hash) + getSubject().hashCode();
}
if (getPhenotypicFeaturesCount() > 0) {
hash = (37 * hash) + PHENOTYPIC_FEATURES_FIELD_NUMBER;
hash = (53 * hash) + getPhenotypicFeaturesList().hashCode();
}
if (getBiosamplesCount() > 0) {
hash = (37 * hash) + BIOSAMPLES_FIELD_NUMBER;
hash = (53 * hash) + getBiosamplesList().hashCode();
}
if (getGenesCount() > 0) {
hash = (37 * hash) + GENES_FIELD_NUMBER;
hash = (53 * hash) + getGenesList().hashCode();
}
if (getVariantsCount() > 0) {
hash = (37 * hash) + VARIANTS_FIELD_NUMBER;
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}
public static org.phenopackets.schema.v1.Phenopacket 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.Phenopacket parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.Phenopacket 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.Phenopacket parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.Phenopacket parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.Phenopacket parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.phenopackets.schema.v1.Phenopacket parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.phenopackets.schema.v1.Phenopacket parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.Phenopacket parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.Phenopacket parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.Phenopacket 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.Phenopacket 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;
}
/**
*
* An anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses.
* This is a bundle of high-level concepts with no specifically defined relational concepts. It is expected that the
* resources sharing the phenopackets will define and enforce their own semantics and level of requirements for included
* fields.
*
*
* Protobuf type {@code org.phenopackets.schema.v1.Phenopacket}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.Phenopacket)
org.phenopackets.schema.v1.PhenopacketOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Phenopacket_descriptor;
}
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protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Phenopacket_fieldAccessorTable
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org.phenopackets.schema.v1.Phenopacket.class, org.phenopackets.schema.v1.Phenopacket.Builder.class);
}
// Construct using org.phenopackets.schema.v1.Phenopacket.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getPhenotypicFeaturesFieldBuilder();
getBiosamplesFieldBuilder();
getGenesFieldBuilder();
getVariantsFieldBuilder();
getDiseasesFieldBuilder();
getHtsFilesFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
id_ = "";
if (subjectBuilder_ == null) {
subject_ = null;
} else {
subject_ = null;
subjectBuilder_ = null;
}
if (phenotypicFeaturesBuilder_ == null) {
phenotypicFeatures_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
phenotypicFeaturesBuilder_.clear();
}
if (biosamplesBuilder_ == null) {
biosamples_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
} else {
biosamplesBuilder_.clear();
}
if (genesBuilder_ == null) {
genes_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
genesBuilder_.clear();
}
if (variantsBuilder_ == null) {
variants_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
} else {
variantsBuilder_.clear();
}
if (diseasesBuilder_ == null) {
diseases_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
} else {
diseasesBuilder_.clear();
}
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000020);
} else {
htsFilesBuilder_.clear();
}
if (metaDataBuilder_ == null) {
metaData_ = null;
} else {
metaData_ = null;
metaDataBuilder_ = null;
}
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Phenopacket_descriptor;
}
@java.lang.Override
public org.phenopackets.schema.v1.Phenopacket getDefaultInstanceForType() {
return org.phenopackets.schema.v1.Phenopacket.getDefaultInstance();
}
@java.lang.Override
public org.phenopackets.schema.v1.Phenopacket build() {
org.phenopackets.schema.v1.Phenopacket result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.phenopackets.schema.v1.Phenopacket buildPartial() {
org.phenopackets.schema.v1.Phenopacket result = new org.phenopackets.schema.v1.Phenopacket(this);
int from_bitField0_ = bitField0_;
result.id_ = id_;
if (subjectBuilder_ == null) {
result.subject_ = subject_;
} else {
result.subject_ = subjectBuilder_.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 (biosamplesBuilder_ == null) {
if (((bitField0_ & 0x00000002) != 0)) {
biosamples_ = java.util.Collections.unmodifiableList(biosamples_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.biosamples_ = biosamples_;
} else {
result.biosamples_ = biosamplesBuilder_.build();
}
if (genesBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
genes_ = java.util.Collections.unmodifiableList(genes_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.genes_ = genes_;
} else {
result.genes_ = genesBuilder_.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();
}
if (diseasesBuilder_ == null) {
if (((bitField0_ & 0x00000010) != 0)) {
diseases_ = java.util.Collections.unmodifiableList(diseases_);
bitField0_ = (bitField0_ & ~0x00000010);
}
result.diseases_ = diseases_;
} else {
result.diseases_ = diseasesBuilder_.build();
}
if (htsFilesBuilder_ == null) {
if (((bitField0_ & 0x00000020) != 0)) {
htsFiles_ = java.util.Collections.unmodifiableList(htsFiles_);
bitField0_ = (bitField0_ & ~0x00000020);
}
result.htsFiles_ = htsFiles_;
} else {
result.htsFiles_ = htsFilesBuilder_.build();
}
if (metaDataBuilder_ == null) {
result.metaData_ = metaData_;
} else {
result.metaData_ = metaDataBuilder_.build();
}
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.Phenopacket) {
return mergeFrom((org.phenopackets.schema.v1.Phenopacket)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.phenopackets.schema.v1.Phenopacket other) {
if (other == org.phenopackets.schema.v1.Phenopacket.getDefaultInstance()) return this;
if (!other.getId().isEmpty()) {
id_ = other.id_;
onChanged();
}
if (other.hasSubject()) {
mergeSubject(other.getSubject());
}
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 (biosamplesBuilder_ == null) {
if (!other.biosamples_.isEmpty()) {
if (biosamples_.isEmpty()) {
biosamples_ = other.biosamples_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureBiosamplesIsMutable();
biosamples_.addAll(other.biosamples_);
}
onChanged();
}
} else {
if (!other.biosamples_.isEmpty()) {
if (biosamplesBuilder_.isEmpty()) {
biosamplesBuilder_.dispose();
biosamplesBuilder_ = null;
biosamples_ = other.biosamples_;
bitField0_ = (bitField0_ & ~0x00000002);
biosamplesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getBiosamplesFieldBuilder() : null;
} else {
biosamplesBuilder_.addAllMessages(other.biosamples_);
}
}
}
if (genesBuilder_ == null) {
if (!other.genes_.isEmpty()) {
if (genes_.isEmpty()) {
genes_ = other.genes_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureGenesIsMutable();
genes_.addAll(other.genes_);
}
onChanged();
}
} else {
if (!other.genes_.isEmpty()) {
if (genesBuilder_.isEmpty()) {
genesBuilder_.dispose();
genesBuilder_ = null;
genes_ = other.genes_;
bitField0_ = (bitField0_ & ~0x00000004);
genesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getGenesFieldBuilder() : null;
} else {
genesBuilder_.addAllMessages(other.genes_);
}
}
}
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 (diseasesBuilder_ == null) {
if (!other.diseases_.isEmpty()) {
if (diseases_.isEmpty()) {
diseases_ = other.diseases_;
bitField0_ = (bitField0_ & ~0x00000010);
} else {
ensureDiseasesIsMutable();
diseases_.addAll(other.diseases_);
}
onChanged();
}
} else {
if (!other.diseases_.isEmpty()) {
if (diseasesBuilder_.isEmpty()) {
diseasesBuilder_.dispose();
diseasesBuilder_ = null;
diseases_ = other.diseases_;
bitField0_ = (bitField0_ & ~0x00000010);
diseasesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getDiseasesFieldBuilder() : null;
} else {
diseasesBuilder_.addAllMessages(other.diseases_);
}
}
}
if (htsFilesBuilder_ == null) {
if (!other.htsFiles_.isEmpty()) {
if (htsFiles_.isEmpty()) {
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000020);
} else {
ensureHtsFilesIsMutable();
htsFiles_.addAll(other.htsFiles_);
}
onChanged();
}
} else {
if (!other.htsFiles_.isEmpty()) {
if (htsFilesBuilder_.isEmpty()) {
htsFilesBuilder_.dispose();
htsFilesBuilder_ = null;
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000020);
htsFilesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getHtsFilesFieldBuilder() : null;
} else {
htsFilesBuilder_.addAllMessages(other.htsFiles_);
}
}
}
if (other.hasMetaData()) {
mergeMetaData(other.getMetaData());
}
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.Phenopacket parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.phenopackets.schema.v1.Phenopacket) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object id_ = "";
/**
*
* An identifier specific for this phenopacket.
*
*
* 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;
}
}
/**
*
* An identifier specific for this phenopacket.
*
*
* 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;
}
}
/**
*
* An identifier specific for this phenopacket.
*
*
* string id = 1;
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
*
* An identifier specific for this phenopacket.
*
*
* string id = 1;
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
*
* An identifier specific for this phenopacket.
*
*
* 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 org.phenopackets.schema.v1.core.Individual subject_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Individual, org.phenopackets.schema.v1.core.Individual.Builder, org.phenopackets.schema.v1.core.IndividualOrBuilder> subjectBuilder_;
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public boolean hasSubject() {
return subjectBuilder_ != null || subject_ != null;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public org.phenopackets.schema.v1.core.Individual getSubject() {
if (subjectBuilder_ == null) {
return subject_ == null ? org.phenopackets.schema.v1.core.Individual.getDefaultInstance() : subject_;
} else {
return subjectBuilder_.getMessage();
}
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public Builder setSubject(org.phenopackets.schema.v1.core.Individual value) {
if (subjectBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
subject_ = value;
onChanged();
} else {
subjectBuilder_.setMessage(value);
}
return this;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public Builder setSubject(
org.phenopackets.schema.v1.core.Individual.Builder builderForValue) {
if (subjectBuilder_ == null) {
subject_ = builderForValue.build();
onChanged();
} else {
subjectBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public Builder mergeSubject(org.phenopackets.schema.v1.core.Individual value) {
if (subjectBuilder_ == null) {
if (subject_ != null) {
subject_ =
org.phenopackets.schema.v1.core.Individual.newBuilder(subject_).mergeFrom(value).buildPartial();
} else {
subject_ = value;
}
onChanged();
} else {
subjectBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public Builder clearSubject() {
if (subjectBuilder_ == null) {
subject_ = null;
onChanged();
} else {
subject_ = null;
subjectBuilder_ = null;
}
return this;
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public org.phenopackets.schema.v1.core.Individual.Builder getSubjectBuilder() {
onChanged();
return getSubjectFieldBuilder().getBuilder();
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
public org.phenopackets.schema.v1.core.IndividualOrBuilder getSubjectOrBuilder() {
if (subjectBuilder_ != null) {
return subjectBuilder_.getMessageOrBuilder();
} else {
return subject_ == null ?
org.phenopackets.schema.v1.core.Individual.getDefaultInstance() : subject_;
}
}
/**
*
* The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
*
*
* .org.phenopackets.schema.v1.core.Individual subject = 2;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Individual, org.phenopackets.schema.v1.core.Individual.Builder, org.phenopackets.schema.v1.core.IndividualOrBuilder>
getSubjectFieldBuilder() {
if (subjectBuilder_ == null) {
subjectBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Individual, org.phenopackets.schema.v1.core.Individual.Builder, org.phenopackets.schema.v1.core.IndividualOrBuilder>(
getSubject(),
getParentForChildren(),
isClean());
subject_ = null;
}
return subjectBuilder_;
}
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public java.util.List getPhenotypicFeaturesList() {
if (phenotypicFeaturesBuilder_ == null) {
return java.util.Collections.unmodifiableList(phenotypicFeatures_);
} else {
return phenotypicFeaturesBuilder_.getMessageList();
}
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public int getPhenotypicFeaturesCount() {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.size();
} else {
return phenotypicFeaturesBuilder_.getCount();
}
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature getPhenotypicFeatures(int index) {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.get(index);
} else {
return phenotypicFeaturesBuilder_.getMessage(index);
}
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public Builder clearPhenotypicFeatures() {
if (phenotypicFeaturesBuilder_ == null) {
phenotypicFeatures_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
phenotypicFeaturesBuilder_.clear();
}
return this;
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public Builder removePhenotypicFeatures(int index) {
if (phenotypicFeaturesBuilder_ == null) {
ensurePhenotypicFeaturesIsMutable();
phenotypicFeatures_.remove(index);
onChanged();
} else {
phenotypicFeaturesBuilder_.remove(index);
}
return this;
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder getPhenotypicFeaturesBuilder(
int index) {
return getPhenotypicFeaturesFieldBuilder().getBuilder(index);
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder getPhenotypicFeaturesOrBuilder(
int index) {
if (phenotypicFeaturesBuilder_ == null) {
return phenotypicFeatures_.get(index); } else {
return phenotypicFeaturesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public java.util.List
getPhenotypicFeaturesOrBuilderList() {
if (phenotypicFeaturesBuilder_ != null) {
return phenotypicFeaturesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(phenotypicFeatures_);
}
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder addPhenotypicFeaturesBuilder() {
return getPhenotypicFeaturesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance());
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
public org.phenopackets.schema.v1.core.PhenotypicFeature.Builder addPhenotypicFeaturesBuilder(
int index) {
return getPhenotypicFeaturesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance());
}
/**
*
* Phenotypic features relating to the subject of the phenopacket
*
*
* repeated .org.phenopackets.schema.v1.core.PhenotypicFeature phenotypic_features = 3;
*/
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 java.util.List biosamples_ =
java.util.Collections.emptyList();
private void ensureBiosamplesIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
biosamples_ = new java.util.ArrayList(biosamples_);
bitField0_ |= 0x00000002;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Biosample, org.phenopackets.schema.v1.core.Biosample.Builder, org.phenopackets.schema.v1.core.BiosampleOrBuilder> biosamplesBuilder_;
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public java.util.List getBiosamplesList() {
if (biosamplesBuilder_ == null) {
return java.util.Collections.unmodifiableList(biosamples_);
} else {
return biosamplesBuilder_.getMessageList();
}
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public int getBiosamplesCount() {
if (biosamplesBuilder_ == null) {
return biosamples_.size();
} else {
return biosamplesBuilder_.getCount();
}
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.Biosample getBiosamples(int index) {
if (biosamplesBuilder_ == null) {
return biosamples_.get(index);
} else {
return biosamplesBuilder_.getMessage(index);
}
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder setBiosamples(
int index, org.phenopackets.schema.v1.core.Biosample value) {
if (biosamplesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureBiosamplesIsMutable();
biosamples_.set(index, value);
onChanged();
} else {
biosamplesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder setBiosamples(
int index, org.phenopackets.schema.v1.core.Biosample.Builder builderForValue) {
if (biosamplesBuilder_ == null) {
ensureBiosamplesIsMutable();
biosamples_.set(index, builderForValue.build());
onChanged();
} else {
biosamplesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder addBiosamples(org.phenopackets.schema.v1.core.Biosample value) {
if (biosamplesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureBiosamplesIsMutable();
biosamples_.add(value);
onChanged();
} else {
biosamplesBuilder_.addMessage(value);
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder addBiosamples(
int index, org.phenopackets.schema.v1.core.Biosample value) {
if (biosamplesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureBiosamplesIsMutable();
biosamples_.add(index, value);
onChanged();
} else {
biosamplesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder addBiosamples(
org.phenopackets.schema.v1.core.Biosample.Builder builderForValue) {
if (biosamplesBuilder_ == null) {
ensureBiosamplesIsMutable();
biosamples_.add(builderForValue.build());
onChanged();
} else {
biosamplesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder addBiosamples(
int index, org.phenopackets.schema.v1.core.Biosample.Builder builderForValue) {
if (biosamplesBuilder_ == null) {
ensureBiosamplesIsMutable();
biosamples_.add(index, builderForValue.build());
onChanged();
} else {
biosamplesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder addAllBiosamples(
java.lang.Iterable values) {
if (biosamplesBuilder_ == null) {
ensureBiosamplesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, biosamples_);
onChanged();
} else {
biosamplesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder clearBiosamples() {
if (biosamplesBuilder_ == null) {
biosamples_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
} else {
biosamplesBuilder_.clear();
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public Builder removeBiosamples(int index) {
if (biosamplesBuilder_ == null) {
ensureBiosamplesIsMutable();
biosamples_.remove(index);
onChanged();
} else {
biosamplesBuilder_.remove(index);
}
return this;
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.Biosample.Builder getBiosamplesBuilder(
int index) {
return getBiosamplesFieldBuilder().getBuilder(index);
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.BiosampleOrBuilder getBiosamplesOrBuilder(
int index) {
if (biosamplesBuilder_ == null) {
return biosamples_.get(index); } else {
return biosamplesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public java.util.List
getBiosamplesOrBuilderList() {
if (biosamplesBuilder_ != null) {
return biosamplesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(biosamples_);
}
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.Biosample.Builder addBiosamplesBuilder() {
return getBiosamplesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Biosample.getDefaultInstance());
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public org.phenopackets.schema.v1.core.Biosample.Builder addBiosamplesBuilder(
int index) {
return getBiosamplesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Biosample.getDefaultInstance());
}
/**
*
* Biosample(s) derived from the patient or a collection of biosamples in isolation
*
*
* repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 4;
*/
public java.util.List
getBiosamplesBuilderList() {
return getBiosamplesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Biosample, org.phenopackets.schema.v1.core.Biosample.Builder, org.phenopackets.schema.v1.core.BiosampleOrBuilder>
getBiosamplesFieldBuilder() {
if (biosamplesBuilder_ == null) {
biosamplesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Biosample, org.phenopackets.schema.v1.core.Biosample.Builder, org.phenopackets.schema.v1.core.BiosampleOrBuilder>(
biosamples_,
((bitField0_ & 0x00000002) != 0),
getParentForChildren(),
isClean());
biosamples_ = null;
}
return biosamplesBuilder_;
}
private java.util.List genes_ =
java.util.Collections.emptyList();
private void ensureGenesIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
genes_ = new java.util.ArrayList(genes_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Gene, org.phenopackets.schema.v1.core.Gene.Builder, org.phenopackets.schema.v1.core.GeneOrBuilder> genesBuilder_;
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public java.util.List getGenesList() {
if (genesBuilder_ == null) {
return java.util.Collections.unmodifiableList(genes_);
} else {
return genesBuilder_.getMessageList();
}
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public int getGenesCount() {
if (genesBuilder_ == null) {
return genes_.size();
} else {
return genesBuilder_.getCount();
}
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.Gene getGenes(int index) {
if (genesBuilder_ == null) {
return genes_.get(index);
} else {
return genesBuilder_.getMessage(index);
}
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder setGenes(
int index, org.phenopackets.schema.v1.core.Gene value) {
if (genesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenesIsMutable();
genes_.set(index, value);
onChanged();
} else {
genesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder setGenes(
int index, org.phenopackets.schema.v1.core.Gene.Builder builderForValue) {
if (genesBuilder_ == null) {
ensureGenesIsMutable();
genes_.set(index, builderForValue.build());
onChanged();
} else {
genesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder addGenes(org.phenopackets.schema.v1.core.Gene value) {
if (genesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenesIsMutable();
genes_.add(value);
onChanged();
} else {
genesBuilder_.addMessage(value);
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder addGenes(
int index, org.phenopackets.schema.v1.core.Gene value) {
if (genesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenesIsMutable();
genes_.add(index, value);
onChanged();
} else {
genesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder addGenes(
org.phenopackets.schema.v1.core.Gene.Builder builderForValue) {
if (genesBuilder_ == null) {
ensureGenesIsMutable();
genes_.add(builderForValue.build());
onChanged();
} else {
genesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder addGenes(
int index, org.phenopackets.schema.v1.core.Gene.Builder builderForValue) {
if (genesBuilder_ == null) {
ensureGenesIsMutable();
genes_.add(index, builderForValue.build());
onChanged();
} else {
genesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder addAllGenes(
java.lang.Iterable values) {
if (genesBuilder_ == null) {
ensureGenesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, genes_);
onChanged();
} else {
genesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder clearGenes() {
if (genesBuilder_ == null) {
genes_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
genesBuilder_.clear();
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public Builder removeGenes(int index) {
if (genesBuilder_ == null) {
ensureGenesIsMutable();
genes_.remove(index);
onChanged();
} else {
genesBuilder_.remove(index);
}
return this;
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.Gene.Builder getGenesBuilder(
int index) {
return getGenesFieldBuilder().getBuilder(index);
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.GeneOrBuilder getGenesOrBuilder(
int index) {
if (genesBuilder_ == null) {
return genes_.get(index); } else {
return genesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public java.util.List
getGenesOrBuilderList() {
if (genesBuilder_ != null) {
return genesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(genes_);
}
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.Gene.Builder addGenesBuilder() {
return getGenesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Gene.getDefaultInstance());
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public org.phenopackets.schema.v1.core.Gene.Builder addGenesBuilder(
int index) {
return getGenesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Gene.getDefaultInstance());
}
/**
*
* Field for gene identifiers - could be used for listing either candidate genes or causative genes. The
* resources using these fields should define what this represents in their context. This could be used in order to
* obfuscate the specific causative/candidate variant.
*
*
* repeated .org.phenopackets.schema.v1.core.Gene genes = 5;
*/
public java.util.List
getGenesBuilderList() {
return getGenesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Gene, org.phenopackets.schema.v1.core.Gene.Builder, org.phenopackets.schema.v1.core.GeneOrBuilder>
getGenesFieldBuilder() {
if (genesBuilder_ == null) {
genesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Gene, org.phenopackets.schema.v1.core.Gene.Builder, org.phenopackets.schema.v1.core.GeneOrBuilder>(
genes_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
genes_ = null;
}
return genesBuilder_;
}
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public java.util.List getVariantsList() {
if (variantsBuilder_ == null) {
return java.util.Collections.unmodifiableList(variants_);
} else {
return variantsBuilder_.getMessageList();
}
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public int getVariantsCount() {
if (variantsBuilder_ == null) {
return variants_.size();
} else {
return variantsBuilder_.getCount();
}
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.Variant getVariants(int index) {
if (variantsBuilder_ == null) {
return variants_.get(index);
} else {
return variantsBuilder_.getMessage(index);
}
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public Builder clearVariants() {
if (variantsBuilder_ == null) {
variants_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
onChanged();
} else {
variantsBuilder_.clear();
}
return this;
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public Builder removeVariants(int index) {
if (variantsBuilder_ == null) {
ensureVariantsIsMutable();
variants_.remove(index);
onChanged();
} else {
variantsBuilder_.remove(index);
}
return this;
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.Variant.Builder getVariantsBuilder(
int index) {
return getVariantsFieldBuilder().getBuilder(index);
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.VariantOrBuilder getVariantsOrBuilder(
int index) {
if (variantsBuilder_ == null) {
return variants_.get(index); } else {
return variantsBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public java.util.List
getVariantsOrBuilderList() {
if (variantsBuilder_ != null) {
return variantsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(variants_);
}
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.Variant.Builder addVariantsBuilder() {
return getVariantsFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Variant.getDefaultInstance());
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
public org.phenopackets.schema.v1.core.Variant.Builder addVariantsBuilder(
int index) {
return getVariantsFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Variant.getDefaultInstance());
}
/**
*
* Field for genetic variants - could be used for listing either candidate variants or diagnosed causative
* variants. The resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Variant variants = 6;
*/
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 java.util.List diseases_ =
java.util.Collections.emptyList();
private void ensureDiseasesIsMutable() {
if (!((bitField0_ & 0x00000010) != 0)) {
diseases_ = new java.util.ArrayList(diseases_);
bitField0_ |= 0x00000010;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Disease, org.phenopackets.schema.v1.core.Disease.Builder, org.phenopackets.schema.v1.core.DiseaseOrBuilder> diseasesBuilder_;
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public java.util.List getDiseasesList() {
if (diseasesBuilder_ == null) {
return java.util.Collections.unmodifiableList(diseases_);
} else {
return diseasesBuilder_.getMessageList();
}
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public int getDiseasesCount() {
if (diseasesBuilder_ == null) {
return diseases_.size();
} else {
return diseasesBuilder_.getCount();
}
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.Disease getDiseases(int index) {
if (diseasesBuilder_ == null) {
return diseases_.get(index);
} else {
return diseasesBuilder_.getMessage(index);
}
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder setDiseases(
int index, org.phenopackets.schema.v1.core.Disease value) {
if (diseasesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiseasesIsMutable();
diseases_.set(index, value);
onChanged();
} else {
diseasesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder setDiseases(
int index, org.phenopackets.schema.v1.core.Disease.Builder builderForValue) {
if (diseasesBuilder_ == null) {
ensureDiseasesIsMutable();
diseases_.set(index, builderForValue.build());
onChanged();
} else {
diseasesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder addDiseases(org.phenopackets.schema.v1.core.Disease value) {
if (diseasesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiseasesIsMutable();
diseases_.add(value);
onChanged();
} else {
diseasesBuilder_.addMessage(value);
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder addDiseases(
int index, org.phenopackets.schema.v1.core.Disease value) {
if (diseasesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiseasesIsMutable();
diseases_.add(index, value);
onChanged();
} else {
diseasesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder addDiseases(
org.phenopackets.schema.v1.core.Disease.Builder builderForValue) {
if (diseasesBuilder_ == null) {
ensureDiseasesIsMutable();
diseases_.add(builderForValue.build());
onChanged();
} else {
diseasesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder addDiseases(
int index, org.phenopackets.schema.v1.core.Disease.Builder builderForValue) {
if (diseasesBuilder_ == null) {
ensureDiseasesIsMutable();
diseases_.add(index, builderForValue.build());
onChanged();
} else {
diseasesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder addAllDiseases(
java.lang.Iterable values) {
if (diseasesBuilder_ == null) {
ensureDiseasesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, diseases_);
onChanged();
} else {
diseasesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder clearDiseases() {
if (diseasesBuilder_ == null) {
diseases_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
onChanged();
} else {
diseasesBuilder_.clear();
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public Builder removeDiseases(int index) {
if (diseasesBuilder_ == null) {
ensureDiseasesIsMutable();
diseases_.remove(index);
onChanged();
} else {
diseasesBuilder_.remove(index);
}
return this;
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.Disease.Builder getDiseasesBuilder(
int index) {
return getDiseasesFieldBuilder().getBuilder(index);
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.DiseaseOrBuilder getDiseasesOrBuilder(
int index) {
if (diseasesBuilder_ == null) {
return diseases_.get(index); } else {
return diseasesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public java.util.List
getDiseasesOrBuilderList() {
if (diseasesBuilder_ != null) {
return diseasesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(diseases_);
}
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.Disease.Builder addDiseasesBuilder() {
return getDiseasesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Disease.getDefaultInstance());
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public org.phenopackets.schema.v1.core.Disease.Builder addDiseasesBuilder(
int index) {
return getDiseasesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Disease.getDefaultInstance());
}
/**
*
* Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
* resources using these fields should define what this represents in their context.
*
*
* repeated .org.phenopackets.schema.v1.core.Disease diseases = 7;
*/
public java.util.List
getDiseasesBuilderList() {
return getDiseasesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Disease, org.phenopackets.schema.v1.core.Disease.Builder, org.phenopackets.schema.v1.core.DiseaseOrBuilder>
getDiseasesFieldBuilder() {
if (diseasesBuilder_ == null) {
diseasesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Disease, org.phenopackets.schema.v1.core.Disease.Builder, org.phenopackets.schema.v1.core.DiseaseOrBuilder>(
diseases_,
((bitField0_ & 0x00000010) != 0),
getParentForChildren(),
isClean());
diseases_ = null;
}
return diseasesBuilder_;
}
private java.util.List htsFiles_ =
java.util.Collections.emptyList();
private void ensureHtsFilesIsMutable() {
if (!((bitField0_ & 0x00000020) != 0)) {
htsFiles_ = new java.util.ArrayList(htsFiles_);
bitField0_ |= 0x00000020;
}
}
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public int getHtsFilesCount() {
if (htsFilesBuilder_ == null) {
return htsFiles_.size();
} else {
return htsFilesBuilder_.getCount();
}
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public Builder clearHtsFiles() {
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000020);
onChanged();
} else {
htsFilesBuilder_.clear();
}
return this;
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
public org.phenopackets.schema.v1.core.HtsFile.Builder getHtsFilesBuilder(
int index) {
return getHtsFilesFieldBuilder().getBuilder(index);
}
/**
*
* Pointer to the relevant HTS file(s) for the patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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 patient
*
*
* repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 8;
*/
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_ & 0x00000020) != 0),
getParentForChildren(),
isClean());
htsFiles_ = null;
}
return htsFilesBuilder_;
}
private org.phenopackets.schema.v1.core.MetaData metaData_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.MetaData, org.phenopackets.schema.v1.core.MetaData.Builder, org.phenopackets.schema.v1.core.MetaDataOrBuilder> metaDataBuilder_;
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public boolean hasMetaData() {
return metaDataBuilder_ != null || metaData_ != null;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public org.phenopackets.schema.v1.core.MetaData getMetaData() {
if (metaDataBuilder_ == null) {
return metaData_ == null ? org.phenopackets.schema.v1.core.MetaData.getDefaultInstance() : metaData_;
} else {
return metaDataBuilder_.getMessage();
}
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public Builder setMetaData(org.phenopackets.schema.v1.core.MetaData value) {
if (metaDataBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
metaData_ = value;
onChanged();
} else {
metaDataBuilder_.setMessage(value);
}
return this;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public Builder setMetaData(
org.phenopackets.schema.v1.core.MetaData.Builder builderForValue) {
if (metaDataBuilder_ == null) {
metaData_ = builderForValue.build();
onChanged();
} else {
metaDataBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public Builder mergeMetaData(org.phenopackets.schema.v1.core.MetaData value) {
if (metaDataBuilder_ == null) {
if (metaData_ != null) {
metaData_ =
org.phenopackets.schema.v1.core.MetaData.newBuilder(metaData_).mergeFrom(value).buildPartial();
} else {
metaData_ = value;
}
onChanged();
} else {
metaDataBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public Builder clearMetaData() {
if (metaDataBuilder_ == null) {
metaData_ = null;
onChanged();
} else {
metaData_ = null;
metaDataBuilder_ = null;
}
return this;
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public org.phenopackets.schema.v1.core.MetaData.Builder getMetaDataBuilder() {
onChanged();
return getMetaDataFieldBuilder().getBuilder();
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
public org.phenopackets.schema.v1.core.MetaDataOrBuilder getMetaDataOrBuilder() {
if (metaDataBuilder_ != null) {
return metaDataBuilder_.getMessageOrBuilder();
} else {
return metaData_ == null ?
org.phenopackets.schema.v1.core.MetaData.getDefaultInstance() : metaData_;
}
}
/**
*
* Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
*
*
* .org.phenopackets.schema.v1.core.MetaData meta_data = 9;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.MetaData, org.phenopackets.schema.v1.core.MetaData.Builder, org.phenopackets.schema.v1.core.MetaDataOrBuilder>
getMetaDataFieldBuilder() {
if (metaDataBuilder_ == null) {
metaDataBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.MetaData, org.phenopackets.schema.v1.core.MetaData.Builder, org.phenopackets.schema.v1.core.MetaDataOrBuilder>(
getMetaData(),
getParentForChildren(),
isClean());
metaData_ = null;
}
return metaDataBuilder_;
}
@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.Phenopacket)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.Phenopacket)
private static final org.phenopackets.schema.v1.Phenopacket DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.Phenopacket();
}
public static org.phenopackets.schema.v1.Phenopacket getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Phenopacket parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Phenopacket(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.Phenopacket getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}