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

Show more of this group Show more artifacts with this name
Show all versions of phenopacket-schema Show documentation
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: phenopackets.proto

package org.phenopackets.schema.v1;

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

  /**
   *    * An identifier specific for this family.
   * 
   *
   * string id = 1;
   */
  java.lang.String getId();
  /**
   *    * An identifier specific for this family.
   * 
   *
   * 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.Phenopacket proband = 2;
   */
  boolean hasProband();
  /**
   *    * The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
   * 
   *
   * .org.phenopackets.schema.v1.Phenopacket proband = 2;
   */
  org.phenopackets.schema.v1.Phenopacket getProband();
  /**
   *    * The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
   * 
   *
   * .org.phenopackets.schema.v1.Phenopacket proband = 2;
   */
  org.phenopackets.schema.v1.PhenopacketOrBuilder getProbandOrBuilder();

  /**
   *    * Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
   * be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
   * genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
   * describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
   * the cohort.
   * 
   *
   * repeated .org.phenopackets.schema.v1.Phenopacket relatives = 3;
   */
  java.util.List 
      getRelativesList();
  /**
   *    * Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
   * be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
   * genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
   * describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
   * the cohort.
   * 
   *
   * repeated .org.phenopackets.schema.v1.Phenopacket relatives = 3;
   */
  org.phenopackets.schema.v1.Phenopacket getRelatives(int index);
  /**
   *    * Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
   * be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
   * genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
   * describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
   * the cohort.
   * 
   *
   * repeated .org.phenopackets.schema.v1.Phenopacket relatives = 3;
   */
  int getRelativesCount();
  /**
   *    * Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
   * be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
   * genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
   * describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
   * the cohort.
   * 
   *
   * repeated .org.phenopackets.schema.v1.Phenopacket relatives = 3;
   */
  java.util.List 
      getRelativesOrBuilderList();
  /**
   *    * Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
   * be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
   * genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
   * describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
   * the cohort.
   * 
   *
   * repeated .org.phenopackets.schema.v1.Phenopacket relatives = 3;
   */
  org.phenopackets.schema.v1.PhenopacketOrBuilder getRelativesOrBuilder(
      int index);

  /**
   *    * The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should
   * map to the PhenoPacket.Individual.id
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  boolean hasPedigree();
  /**
   *    * The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should
   * map to the PhenoPacket.Individual.id
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  org.phenopackets.schema.v1.core.Pedigree getPedigree();
  /**
   *    * The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should
   * map to the PhenoPacket.Individual.id
   * 
   *
   * .org.phenopackets.schema.v1.core.Pedigree pedigree = 4;
   */
  org.phenopackets.schema.v1.core.PedigreeOrBuilder getPedigreeOrBuilder();

  /**
   *    * Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
   * members e.g a multi-sample VCF
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 5;
   */
  java.util.List 
      getHtsFilesList();
  /**
   *    * Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
   * members e.g a multi-sample VCF
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 5;
   */
  org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index);
  /**
   *    * Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
   * members e.g a multi-sample VCF
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 5;
   */
  int getHtsFilesCount();
  /**
   *    * Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
   * members e.g a multi-sample VCF
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 5;
   */
  java.util.List 
      getHtsFilesOrBuilderList();
  /**
   *    * Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
   * members e.g a multi-sample VCF
   * 
   *
   * repeated .org.phenopackets.schema.v1.core.HtsFile hts_files = 5;
   */
  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 meta_data = 6;
   */
  boolean hasMetaData();
  /**
   *    * Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
   * 
   *
   * .org.phenopackets.schema.v1.core.MetaData meta_data = 6;
   */
  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 meta_data = 6;
   */
  org.phenopackets.schema.v1.core.MetaDataOrBuilder getMetaDataOrBuilder();
}