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

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A Protobuf schema for capturing clinical phenotypes
There is a newer version: 2.0.2
// Generated by the protocol buffer compiler.  DO NOT EDIT!
// source: org/phenopackets/schema/v1/phenopackets.proto

package org.phenopackets.schema.v1;

public interface PhenoPacketOrBuilder extends
    // @@protoc_insertion_point(interface_extends:org.phenopackets.schema.v1.PhenoPacket)
    com.google.protobuf.MessageOrBuilder {

  /**
   *    * An identifier specific for this phenopacket.
   * 
   *
   * string id = 1;
   */
  java.lang.String getId();
  /**
   *    * An identifier specific for this phenopacket.
   * 
   *
   * string id = 1;
   */
  com.google.protobuf.ByteString
      getIdBytes();

  /**
   *    * 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;
   */
  boolean hasSubject();
  /**
   *    * 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;
   */
  org.phenopackets.schema.v1.core.Individual getSubject();
  /**
   *    * 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;
   */
  org.phenopackets.schema.v1.core.IndividualOrBuilder getSubjectOrBuilder();

  /**
   *    * Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort.
   * It is expected that a pedigree be included if this and the patient fields are included.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Individual individuals = 3;
   */
  java.util.List 
      getIndividualsList();
  /**
   *    * Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort.
   * It is expected that a pedigree be included if this and the patient fields are included.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Individual individuals = 3;
   */
  org.phenopackets.schema.v1.core.Individual getIndividuals(int index);
  /**
   *    * Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort.
   * It is expected that a pedigree be included if this and the patient fields are included.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Individual individuals = 3;
   */
  int getIndividualsCount();
  /**
   *    * Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort.
   * It is expected that a pedigree be included if this and the patient fields are included.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Individual individuals = 3;
   */
  java.util.List 
      getIndividualsOrBuilderList();
  /**
   *    * Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort.
   * It is expected that a pedigree be included if this and the patient fields are included.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Individual individuals = 3;
   */
  org.phenopackets.schema.v1.core.IndividualOrBuilder getIndividualsOrBuilder(
      int index);

  /**
   *    * The pedigree defining the relations between the patient and their relatives.
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  boolean hasPedigree();
  /**
   *    * The pedigree defining the relations between the patient and their relatives.
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  org.phenopackets.schema.v1.core.Pedigree getPedigree();
  /**
   *    * The pedigree defining the relations between the patient and their relatives.
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  org.phenopackets.schema.v1.core.PedigreeOrBuilder getPedigreeOrBuilder();

  /**
   *    * Biosample(s) derived from the patient or a collection of biosamples in isolation
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 5;
   */
  java.util.List 
      getBiosamplesList();
  /**
   *    * Biosample(s) derived from the patient or a collection of biosamples in isolation
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 5;
   */
  org.phenopackets.schema.v1.core.Biosample getBiosamples(int index);
  /**
   *    * Biosample(s) derived from the patient or a collection of biosamples in isolation
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 5;
   */
  int getBiosamplesCount();
  /**
   *    * Biosample(s) derived from the patient or a collection of biosamples in isolation
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 5;
   */
  java.util.List 
      getBiosamplesOrBuilderList();
  /**
   *    * Biosample(s) derived from the patient or a collection of biosamples in isolation
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Biosample biosamples = 5;
   */
  org.phenopackets.schema.v1.core.BiosampleOrBuilder getBiosamplesOrBuilder(
      int index);

  /**
   *    * Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Gene genes = 6;
   */
  java.util.List 
      getGenesList();
  /**
   *    * Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Gene genes = 6;
   */
  org.phenopackets.schema.v1.core.Gene getGenes(int index);
  /**
   *    * Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Gene genes = 6;
   */
  int getGenesCount();
  /**
   *    * Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Gene genes = 6;
   */
  java.util.List 
      getGenesOrBuilderList();
  /**
   *    * Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Gene genes = 6;
   */
  org.phenopackets.schema.v1.core.GeneOrBuilder getGenesOrBuilder(
      int index);

  /**
   *    * Placeholder for genetic variants - could be used for either describing 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 = 7;
   */
  java.util.List 
      getVariantsList();
  /**
   *    * Placeholder for genetic variants - could be used for either describing 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 = 7;
   */
  org.phenopackets.schema.v1.core.Variant getVariants(int index);
  /**
   *    * Placeholder for genetic variants - could be used for either describing 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 = 7;
   */
  int getVariantsCount();
  /**
   *    * Placeholder for genetic variants - could be used for either describing 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 = 7;
   */
  java.util.List 
      getVariantsOrBuilderList();
  /**
   *    * Placeholder for genetic variants - could be used for either describing 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 = 7;
   */
  org.phenopackets.schema.v1.core.VariantOrBuilder getVariantsOrBuilder(
      int index);

  /**
   *    * Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Disease diseases = 8;
   */
  java.util.List 
      getDiseasesList();
  /**
   *    * Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Disease diseases = 8;
   */
  org.phenopackets.schema.v1.core.Disease getDiseases(int index);
  /**
   *    * Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Disease diseases = 8;
   */
  int getDiseasesCount();
  /**
   *    * Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Disease diseases = 8;
   */
  java.util.List 
      getDiseasesOrBuilderList();
  /**
   *    * Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The
   * resources using these fields should define what this represents in their context.
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.Disease diseases = 8;
   */
  org.phenopackets.schema.v1.core.DiseaseOrBuilder getDiseasesOrBuilder(
      int index);

  /**
   *    * Pointer to the relevant HTS file(s) for the patient
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 9;
   */
  java.util.List 
      getHtsFilesList();
  /**
   *    * Pointer to the relevant HTS file(s) for the patient
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 9;
   */
  org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index);
  /**
   *    * Pointer to the relevant HTS file(s) for the patient
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 9;
   */
  int getHtsFilesCount();
  /**
   *    * Pointer to the relevant HTS file(s) for the patient
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 9;
   */
  java.util.List 
      getHtsFilesOrBuilderList();
  /**
   *    * Pointer to the relevant HTS file(s) for the patient
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 9;
   */
  org.phenopackets.schema.v1.core.HtsFileOrBuilder getHtsFilesOrBuilder(
      int index);

  /**
   *    * Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
   * 
   *
   * .org.phenopackets.schema.v1.core.MetaData metaData = 10;
   */
  boolean hasMetaData();
  /**
   *    * Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
   * 
   *
   * .org.phenopackets.schema.v1.core.MetaData metaData = 10;
   */
  org.phenopackets.schema.v1.core.MetaData getMetaData();
  /**
   *    * Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
   * 
   *
   * .org.phenopackets.schema.v1.core.MetaData metaData = 10;
   */
  org.phenopackets.schema.v1.core.MetaDataOrBuilder getMetaDataOrBuilder();
}