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A Protobuf schema for capturing clinical phenotypes
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: phenopackets.proto
package org.phenopackets.schema.v1;
/**
*
* Phenotype, sample and pedigree data required for a genomic diagnosis.
* Equivalent to the Genomics England InterpretationRequestRD
* https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl
*
*
* Protobuf type {@code org.phenopackets.schema.v1.Family}
*/
public final class Family extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.Family)
FamilyOrBuilder {
private static final long serialVersionUID = 0L;
// Use Family.newBuilder() to construct.
private Family(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private Family() {
id_ = "";
relatives_ = java.util.Collections.emptyList();
htsFiles_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new Family();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Family(
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;
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break;
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java.lang.String s = input.readStringRequireUtf8();
id_ = s;
break;
}
case 18: {
org.phenopackets.schema.v1.Phenopacket.Builder subBuilder = null;
if (proband_ != null) {
subBuilder = proband_.toBuilder();
}
proband_ = input.readMessage(org.phenopackets.schema.v1.Phenopacket.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(proband_);
proband_ = subBuilder.buildPartial();
}
break;
}
case 26: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
relatives_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
relatives_.add(
input.readMessage(org.phenopackets.schema.v1.Phenopacket.parser(), extensionRegistry));
break;
}
case 34: {
org.phenopackets.schema.v1.core.Pedigree.Builder subBuilder = null;
if (pedigree_ != null) {
subBuilder = pedigree_.toBuilder();
}
pedigree_ = input.readMessage(org.phenopackets.schema.v1.core.Pedigree.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(pedigree_);
pedigree_ = subBuilder.buildPartial();
}
break;
}
case 42: {
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
htsFiles_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
}
htsFiles_.add(
input.readMessage(org.phenopackets.schema.v1.core.HtsFile.parser(), extensionRegistry));
break;
}
case 50: {
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();
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throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
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} finally {
if (((mutable_bitField0_ & 0x00000001) != 0)) {
relatives_ = java.util.Collections.unmodifiableList(relatives_);
}
if (((mutable_bitField0_ & 0x00000002) != 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_Family_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Family_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.phenopackets.schema.v1.Family.class, org.phenopackets.schema.v1.Family.Builder.class);
}
public static final int ID_FIELD_NUMBER = 1;
private volatile java.lang.Object id_;
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
}
}
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int PROBAND_FIELD_NUMBER = 2;
private org.phenopackets.schema.v1.Phenopacket proband_;
/**
*
* 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;
*/
public boolean hasProband() {
return proband_ != null;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket getProband() {
return proband_ == null ? org.phenopackets.schema.v1.Phenopacket.getDefaultInstance() : proband_;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.PhenopacketOrBuilder getProbandOrBuilder() {
return getProband();
}
public static final int RELATIVES_FIELD_NUMBER = 3;
private java.util.List relatives_;
/**
*
* 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;
*/
public java.util.List getRelativesList() {
return relatives_;
}
/**
*
* 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;
*/
public java.util.List
getRelativesOrBuilderList() {
return relatives_;
}
/**
*
* 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;
*/
public int getRelativesCount() {
return relatives_.size();
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket getRelatives(int index) {
return relatives_.get(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;
*/
public org.phenopackets.schema.v1.PhenopacketOrBuilder getRelativesOrBuilder(
int index) {
return relatives_.get(index);
}
public static final int PEDIGREE_FIELD_NUMBER = 4;
private org.phenopackets.schema.v1.core.Pedigree pedigree_;
/**
*
* 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;
*/
public boolean hasPedigree() {
return pedigree_ != null;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.Pedigree getPedigree() {
return pedigree_ == null ? org.phenopackets.schema.v1.core.Pedigree.getDefaultInstance() : pedigree_;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.PedigreeOrBuilder getPedigreeOrBuilder() {
return getPedigree();
}
public static final int HTS_FILES_FIELD_NUMBER = 5;
private java.util.List htsFiles_;
/**
*
* 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;
*/
public java.util.List getHtsFilesList() {
return htsFiles_;
}
/**
*
* 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;
*/
public java.util.List
getHtsFilesOrBuilderList() {
return htsFiles_;
}
/**
*
* 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;
*/
public int getHtsFilesCount() {
return htsFiles_.size();
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.HtsFile getHtsFiles(int index) {
return htsFiles_.get(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;
*/
public org.phenopackets.schema.v1.core.HtsFileOrBuilder getHtsFilesOrBuilder(
int index) {
return htsFiles_.get(index);
}
public static final int META_DATA_FIELD_NUMBER = 6;
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
public org.phenopackets.schema.v1.core.MetaDataOrBuilder getMetaDataOrBuilder() {
return getMetaData();
}
private byte memoizedIsInitialized = -1;
@java.lang.Override
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized == 1) return true;
if (isInitialized == 0) return false;
memoizedIsInitialized = 1;
return true;
}
@java.lang.Override
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
if (!getIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, id_);
}
if (proband_ != null) {
output.writeMessage(2, getProband());
}
for (int i = 0; i < relatives_.size(); i++) {
output.writeMessage(3, relatives_.get(i));
}
if (pedigree_ != null) {
output.writeMessage(4, getPedigree());
}
for (int i = 0; i < htsFiles_.size(); i++) {
output.writeMessage(5, htsFiles_.get(i));
}
if (metaData_ != null) {
output.writeMessage(6, getMetaData());
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, id_);
}
if (proband_ != null) {
size += com.google.protobuf.CodedOutputStream
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}
for (int i = 0; i < relatives_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
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}
if (pedigree_ != null) {
size += com.google.protobuf.CodedOutputStream
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}
for (int i = 0; i < htsFiles_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
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}
if (metaData_ != null) {
size += com.google.protobuf.CodedOutputStream
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}
size += unknownFields.getSerializedSize();
memoizedSize = size;
return size;
}
@java.lang.Override
public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.phenopackets.schema.v1.Family)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.Family other = (org.phenopackets.schema.v1.Family) obj;
if (!getId()
.equals(other.getId())) return false;
if (hasProband() != other.hasProband()) return false;
if (hasProband()) {
if (!getProband()
.equals(other.getProband())) return false;
}
if (!getRelativesList()
.equals(other.getRelativesList())) return false;
if (hasPedigree() != other.hasPedigree()) return false;
if (hasPedigree()) {
if (!getPedigree()
.equals(other.getPedigree())) return false;
}
if (!getHtsFilesList()
.equals(other.getHtsFilesList())) return false;
if (hasMetaData() != other.hasMetaData()) return false;
if (hasMetaData()) {
if (!getMetaData()
.equals(other.getMetaData())) return false;
}
if (!unknownFields.equals(other.unknownFields)) return false;
return true;
}
@java.lang.Override
public int hashCode() {
if (memoizedHashCode != 0) {
return memoizedHashCode;
}
int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + ID_FIELD_NUMBER;
hash = (53 * hash) + getId().hashCode();
if (hasProband()) {
hash = (37 * hash) + PROBAND_FIELD_NUMBER;
hash = (53 * hash) + getProband().hashCode();
}
if (getRelativesCount() > 0) {
hash = (37 * hash) + RELATIVES_FIELD_NUMBER;
hash = (53 * hash) + getRelativesList().hashCode();
}
if (hasPedigree()) {
hash = (37 * hash) + PEDIGREE_FIELD_NUMBER;
hash = (53 * hash) + getPedigree().hashCode();
}
if (getHtsFilesCount() > 0) {
hash = (37 * hash) + HTS_FILES_FIELD_NUMBER;
hash = (53 * hash) + getHtsFilesList().hashCode();
}
if (hasMetaData()) {
hash = (37 * hash) + META_DATA_FIELD_NUMBER;
hash = (53 * hash) + getMetaData().hashCode();
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.phenopackets.schema.v1.Family parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.Family parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.Family parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.Family parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.Family parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.Family parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
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public static org.phenopackets.schema.v1.Family parseFrom(
java.io.InputStream input,
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return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.Family parseDelimitedFrom(
java.io.InputStream input,
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return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.Family parseFrom(
com.google.protobuf.CodedInputStream input)
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return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.Family parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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return com.google.protobuf.GeneratedMessageV3
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@java.lang.Override
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.phenopackets.schema.v1.Family prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
? new Builder() : new Builder().mergeFrom(this);
}
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
*
* Phenotype, sample and pedigree data required for a genomic diagnosis.
* Equivalent to the Genomics England InterpretationRequestRD
* https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl
*
*
* Protobuf type {@code org.phenopackets.schema.v1.Family}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.Family)
org.phenopackets.schema.v1.FamilyOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Family_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Family_fieldAccessorTable
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org.phenopackets.schema.v1.Family.class, org.phenopackets.schema.v1.Family.Builder.class);
}
// Construct using org.phenopackets.schema.v1.Family.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
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private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
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getRelativesFieldBuilder();
getHtsFilesFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
id_ = "";
if (probandBuilder_ == null) {
proband_ = null;
} else {
proband_ = null;
probandBuilder_ = null;
}
if (relativesBuilder_ == null) {
relatives_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
relativesBuilder_.clear();
}
if (pedigreeBuilder_ == null) {
pedigree_ = null;
} else {
pedigree_ = null;
pedigreeBuilder_ = null;
}
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
} else {
htsFilesBuilder_.clear();
}
if (metaDataBuilder_ == null) {
metaData_ = null;
} else {
metaData_ = null;
metaDataBuilder_ = null;
}
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.phenopackets.schema.v1.Phenopackets.internal_static_org_phenopackets_schema_v1_Family_descriptor;
}
@java.lang.Override
public org.phenopackets.schema.v1.Family getDefaultInstanceForType() {
return org.phenopackets.schema.v1.Family.getDefaultInstance();
}
@java.lang.Override
public org.phenopackets.schema.v1.Family build() {
org.phenopackets.schema.v1.Family result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.phenopackets.schema.v1.Family buildPartial() {
org.phenopackets.schema.v1.Family result = new org.phenopackets.schema.v1.Family(this);
int from_bitField0_ = bitField0_;
result.id_ = id_;
if (probandBuilder_ == null) {
result.proband_ = proband_;
} else {
result.proband_ = probandBuilder_.build();
}
if (relativesBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
relatives_ = java.util.Collections.unmodifiableList(relatives_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.relatives_ = relatives_;
} else {
result.relatives_ = relativesBuilder_.build();
}
if (pedigreeBuilder_ == null) {
result.pedigree_ = pedigree_;
} else {
result.pedigree_ = pedigreeBuilder_.build();
}
if (htsFilesBuilder_ == null) {
if (((bitField0_ & 0x00000002) != 0)) {
htsFiles_ = java.util.Collections.unmodifiableList(htsFiles_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.htsFiles_ = htsFiles_;
} else {
result.htsFiles_ = htsFilesBuilder_.build();
}
if (metaDataBuilder_ == null) {
result.metaData_ = metaData_;
} else {
result.metaData_ = metaDataBuilder_.build();
}
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
}
@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
}
@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
}
@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
}
@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
}
@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.phenopackets.schema.v1.Family) {
return mergeFrom((org.phenopackets.schema.v1.Family)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.phenopackets.schema.v1.Family other) {
if (other == org.phenopackets.schema.v1.Family.getDefaultInstance()) return this;
if (!other.getId().isEmpty()) {
id_ = other.id_;
onChanged();
}
if (other.hasProband()) {
mergeProband(other.getProband());
}
if (relativesBuilder_ == null) {
if (!other.relatives_.isEmpty()) {
if (relatives_.isEmpty()) {
relatives_ = other.relatives_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureRelativesIsMutable();
relatives_.addAll(other.relatives_);
}
onChanged();
}
} else {
if (!other.relatives_.isEmpty()) {
if (relativesBuilder_.isEmpty()) {
relativesBuilder_.dispose();
relativesBuilder_ = null;
relatives_ = other.relatives_;
bitField0_ = (bitField0_ & ~0x00000001);
relativesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getRelativesFieldBuilder() : null;
} else {
relativesBuilder_.addAllMessages(other.relatives_);
}
}
}
if (other.hasPedigree()) {
mergePedigree(other.getPedigree());
}
if (htsFilesBuilder_ == null) {
if (!other.htsFiles_.isEmpty()) {
if (htsFiles_.isEmpty()) {
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureHtsFilesIsMutable();
htsFiles_.addAll(other.htsFiles_);
}
onChanged();
}
} else {
if (!other.htsFiles_.isEmpty()) {
if (htsFilesBuilder_.isEmpty()) {
htsFilesBuilder_.dispose();
htsFilesBuilder_ = null;
htsFiles_ = other.htsFiles_;
bitField0_ = (bitField0_ & ~0x00000002);
htsFilesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getHtsFilesFieldBuilder() : null;
} else {
htsFilesBuilder_.addAllMessages(other.htsFiles_);
}
}
}
if (other.hasMetaData()) {
mergeMetaData(other.getMetaData());
}
this.mergeUnknownFields(other.unknownFields);
onChanged();
return this;
}
@java.lang.Override
public final boolean isInitialized() {
return true;
}
@java.lang.Override
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.phenopackets.schema.v1.Family parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.phenopackets.schema.v1.Family) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object id_ = "";
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
*
* An identifier specific for this family.
*
*
* string id = 1;
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
private org.phenopackets.schema.v1.Phenopacket proband_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder> probandBuilder_;
/**
*
* 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;
*/
public boolean hasProband() {
return probandBuilder_ != null || proband_ != null;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket getProband() {
if (probandBuilder_ == null) {
return proband_ == null ? org.phenopackets.schema.v1.Phenopacket.getDefaultInstance() : proband_;
} else {
return probandBuilder_.getMessage();
}
}
/**
*
* 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;
*/
public Builder setProband(org.phenopackets.schema.v1.Phenopacket value) {
if (probandBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
proband_ = value;
onChanged();
} else {
probandBuilder_.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.Phenopacket proband = 2;
*/
public Builder setProband(
org.phenopackets.schema.v1.Phenopacket.Builder builderForValue) {
if (probandBuilder_ == null) {
proband_ = builderForValue.build();
onChanged();
} else {
probandBuilder_.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.Phenopacket proband = 2;
*/
public Builder mergeProband(org.phenopackets.schema.v1.Phenopacket value) {
if (probandBuilder_ == null) {
if (proband_ != null) {
proband_ =
org.phenopackets.schema.v1.Phenopacket.newBuilder(proband_).mergeFrom(value).buildPartial();
} else {
proband_ = value;
}
onChanged();
} else {
probandBuilder_.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.Phenopacket proband = 2;
*/
public Builder clearProband() {
if (probandBuilder_ == null) {
proband_ = null;
onChanged();
} else {
proband_ = null;
probandBuilder_ = 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.Phenopacket proband = 2;
*/
public org.phenopackets.schema.v1.Phenopacket.Builder getProbandBuilder() {
onChanged();
return getProbandFieldBuilder().getBuilder();
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.PhenopacketOrBuilder getProbandOrBuilder() {
if (probandBuilder_ != null) {
return probandBuilder_.getMessageOrBuilder();
} else {
return proband_ == null ?
org.phenopackets.schema.v1.Phenopacket.getDefaultInstance() : proband_;
}
}
/**
*
* 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;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder>
getProbandFieldBuilder() {
if (probandBuilder_ == null) {
probandBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder>(
getProband(),
getParentForChildren(),
isClean());
proband_ = null;
}
return probandBuilder_;
}
private java.util.List relatives_ =
java.util.Collections.emptyList();
private void ensureRelativesIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
relatives_ = new java.util.ArrayList(relatives_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder> relativesBuilder_;
/**
*
* 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;
*/
public java.util.List getRelativesList() {
if (relativesBuilder_ == null) {
return java.util.Collections.unmodifiableList(relatives_);
} else {
return relativesBuilder_.getMessageList();
}
}
/**
*
* 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;
*/
public int getRelativesCount() {
if (relativesBuilder_ == null) {
return relatives_.size();
} else {
return relativesBuilder_.getCount();
}
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket getRelatives(int index) {
if (relativesBuilder_ == null) {
return relatives_.get(index);
} else {
return relativesBuilder_.getMessage(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;
*/
public Builder setRelatives(
int index, org.phenopackets.schema.v1.Phenopacket value) {
if (relativesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRelativesIsMutable();
relatives_.set(index, value);
onChanged();
} else {
relativesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* 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;
*/
public Builder setRelatives(
int index, org.phenopackets.schema.v1.Phenopacket.Builder builderForValue) {
if (relativesBuilder_ == null) {
ensureRelativesIsMutable();
relatives_.set(index, builderForValue.build());
onChanged();
} else {
relativesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* 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;
*/
public Builder addRelatives(org.phenopackets.schema.v1.Phenopacket value) {
if (relativesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRelativesIsMutable();
relatives_.add(value);
onChanged();
} else {
relativesBuilder_.addMessage(value);
}
return this;
}
/**
*
* 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;
*/
public Builder addRelatives(
int index, org.phenopackets.schema.v1.Phenopacket value) {
if (relativesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRelativesIsMutable();
relatives_.add(index, value);
onChanged();
} else {
relativesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* 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;
*/
public Builder addRelatives(
org.phenopackets.schema.v1.Phenopacket.Builder builderForValue) {
if (relativesBuilder_ == null) {
ensureRelativesIsMutable();
relatives_.add(builderForValue.build());
onChanged();
} else {
relativesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* 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;
*/
public Builder addRelatives(
int index, org.phenopackets.schema.v1.Phenopacket.Builder builderForValue) {
if (relativesBuilder_ == null) {
ensureRelativesIsMutable();
relatives_.add(index, builderForValue.build());
onChanged();
} else {
relativesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* 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;
*/
public Builder addAllRelatives(
java.lang.Iterable values) {
if (relativesBuilder_ == null) {
ensureRelativesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, relatives_);
onChanged();
} else {
relativesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* 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;
*/
public Builder clearRelatives() {
if (relativesBuilder_ == null) {
relatives_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
relativesBuilder_.clear();
}
return this;
}
/**
*
* 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;
*/
public Builder removeRelatives(int index) {
if (relativesBuilder_ == null) {
ensureRelativesIsMutable();
relatives_.remove(index);
onChanged();
} else {
relativesBuilder_.remove(index);
}
return this;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket.Builder getRelativesBuilder(
int index) {
return getRelativesFieldBuilder().getBuilder(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;
*/
public org.phenopackets.schema.v1.PhenopacketOrBuilder getRelativesOrBuilder(
int index) {
if (relativesBuilder_ == null) {
return relatives_.get(index); } else {
return relativesBuilder_.getMessageOrBuilder(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;
*/
public java.util.List
getRelativesOrBuilderList() {
if (relativesBuilder_ != null) {
return relativesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(relatives_);
}
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket.Builder addRelativesBuilder() {
return getRelativesFieldBuilder().addBuilder(
org.phenopackets.schema.v1.Phenopacket.getDefaultInstance());
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.Phenopacket.Builder addRelativesBuilder(
int index) {
return getRelativesFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.Phenopacket.getDefaultInstance());
}
/**
*
* 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;
*/
public java.util.List
getRelativesBuilderList() {
return getRelativesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder>
getRelativesFieldBuilder() {
if (relativesBuilder_ == null) {
relativesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.Phenopacket, org.phenopackets.schema.v1.Phenopacket.Builder, org.phenopackets.schema.v1.PhenopacketOrBuilder>(
relatives_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
relatives_ = null;
}
return relativesBuilder_;
}
private org.phenopackets.schema.v1.core.Pedigree pedigree_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Pedigree, org.phenopackets.schema.v1.core.Pedigree.Builder, org.phenopackets.schema.v1.core.PedigreeOrBuilder> pedigreeBuilder_;
/**
*
* 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;
*/
public boolean hasPedigree() {
return pedigreeBuilder_ != null || pedigree_ != null;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.Pedigree getPedigree() {
if (pedigreeBuilder_ == null) {
return pedigree_ == null ? org.phenopackets.schema.v1.core.Pedigree.getDefaultInstance() : pedigree_;
} else {
return pedigreeBuilder_.getMessage();
}
}
/**
*
* 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;
*/
public Builder setPedigree(org.phenopackets.schema.v1.core.Pedigree value) {
if (pedigreeBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
pedigree_ = value;
onChanged();
} else {
pedigreeBuilder_.setMessage(value);
}
return this;
}
/**
*
* 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;
*/
public Builder setPedigree(
org.phenopackets.schema.v1.core.Pedigree.Builder builderForValue) {
if (pedigreeBuilder_ == null) {
pedigree_ = builderForValue.build();
onChanged();
} else {
pedigreeBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* 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;
*/
public Builder mergePedigree(org.phenopackets.schema.v1.core.Pedigree value) {
if (pedigreeBuilder_ == null) {
if (pedigree_ != null) {
pedigree_ =
org.phenopackets.schema.v1.core.Pedigree.newBuilder(pedigree_).mergeFrom(value).buildPartial();
} else {
pedigree_ = value;
}
onChanged();
} else {
pedigreeBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* 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;
*/
public Builder clearPedigree() {
if (pedigreeBuilder_ == null) {
pedigree_ = null;
onChanged();
} else {
pedigree_ = null;
pedigreeBuilder_ = null;
}
return this;
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.Pedigree.Builder getPedigreeBuilder() {
onChanged();
return getPedigreeFieldBuilder().getBuilder();
}
/**
*
* 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;
*/
public org.phenopackets.schema.v1.core.PedigreeOrBuilder getPedigreeOrBuilder() {
if (pedigreeBuilder_ != null) {
return pedigreeBuilder_.getMessageOrBuilder();
} else {
return pedigree_ == null ?
org.phenopackets.schema.v1.core.Pedigree.getDefaultInstance() : pedigree_;
}
}
/**
*
* 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;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Pedigree, org.phenopackets.schema.v1.core.Pedigree.Builder, org.phenopackets.schema.v1.core.PedigreeOrBuilder>
getPedigreeFieldBuilder() {
if (pedigreeBuilder_ == null) {
pedigreeBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Pedigree, org.phenopackets.schema.v1.core.Pedigree.Builder, org.phenopackets.schema.v1.core.PedigreeOrBuilder>(
getPedigree(),
getParentForChildren(),
isClean());
pedigree_ = null;
}
return pedigreeBuilder_;
}
private java.util.List htsFiles_ =
java.util.Collections.emptyList();
private void ensureHtsFilesIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
htsFiles_ = new java.util.ArrayList(htsFiles_);
bitField0_ |= 0x00000002;
}
}
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 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;
*/
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 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;
*/
public int getHtsFilesCount() {
if (htsFilesBuilder_ == null) {
return htsFiles_.size();
} else {
return htsFilesBuilder_.getCount();
}
}
/**
*
* 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
public Builder clearHtsFiles() {
if (htsFilesBuilder_ == null) {
htsFiles_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
} else {
htsFilesBuilder_.clear();
}
return this;
}
/**
*
* 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;
*/
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 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;
*/
public org.phenopackets.schema.v1.core.HtsFile.Builder getHtsFilesBuilder(
int index) {
return getHtsFilesFieldBuilder().getBuilder(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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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 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;
*/
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_ & 0x00000002) != 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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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 = 6;
*/
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.Family)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.Family)
private static final org.phenopackets.schema.v1.Family DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.Family();
}
public static org.phenopackets.schema.v1.Family getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Family parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Family(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.Family getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}