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• phenopacket-schema
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• Phenopacket.java

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org.phenopackets.schema.v1.Phenopacket Maven / Gradle / Ivy

// Generated by the protocol buffer compiler.  DO NOT EDIT!
// source: phenopackets/schema/v1/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 (com.google.protobuf.UninitializedMessageException e) {
      throw e.asInvalidProtocolBufferException().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;
   * @return The id.
   */
  @java.lang.Override
  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;
   * @return The bytes for id.
   */
  @java.lang.Override
  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;
   * @return Whether the subject field is set.
   */
  @java.lang.Override
  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;
   * @return The subject.
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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;
   * @return Whether the metaData field is set.
   */
  @java.lang.Override
  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;
   * @return The metaData.
   */
  @java.lang.Override
  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;
   */
  @java.lang.Override
  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 (!com.google.protobuf.GeneratedMessageV3.isStringEmpty(id_)) {
      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 (!com.google.protobuf.GeneratedMessageV3.isStringEmpty(id_)) {
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  public static org.phenopackets.schema.v1.Phenopacket parseFrom(
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  public static org.phenopackets.schema.v1.Phenopacket parseFrom(
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  @java.lang.Override
  public Builder newBuilderForType() { return newBuilder(); }
  public static Builder newBuilder() {
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  public static Builder newBuilder(org.phenopackets.schema.v1.Phenopacket prototype) {
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  public Builder toBuilder() {
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  protected Builder newBuilderForType(
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  /**
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   *
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      }
      if (metaDataBuilder_ == null) {
        result.metaData_ = metaData_;
      } else {
        result.metaData_ = metaDataBuilder_.build();
      }
      onBuilt();
      return result;
    }

    @java.lang.Override
    public Builder clone() {
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    @java.lang.Override
    public Builder setField(
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    @java.lang.Override
    public final boolean isInitialized() {
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    @java.lang.Override
    public Builder mergeFrom(
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        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
        throws java.io.IOException {
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      try {
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        parsedMessage = (org.phenopackets.schema.v1.Phenopacket) e.getUnfinishedMessage();
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    private int bitField0_;

    private java.lang.Object id_ = "";
    /**
     * 
     * An identifier specific for this phenopacket.
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     *
     * string id = 1;
     * @return The id.
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    /**
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        return b;
      } else {
        return (com.google.protobuf.ByteString) ref;
      }
    }
    /**
     * 
     * An identifier specific for this phenopacket.
     * 
     *
     * string id = 1;
     * @param value The id to set.
     * @return This builder for chaining.
     */
    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;
     * @return This builder for chaining.
     */
    public Builder clearId() {
      
      id_ = getDefaultInstance().getId();
      onChanged();
      return this;
    }
    /**
     * 
     * An identifier specific for this phenopacket.
     * 
     *
     * string id = 1;
     * @param value The bytes for id to set.
     * @return This builder for chaining.
     */
    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;
     * @return Whether the subject field is set.
     */
    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;
     * @return The subject.
     */
    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;
     * @return Whether the metaData field is set.
     */
    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;
     * @return The metaData.
     */
    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;
  }

}