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A Protobuf schema for capturing clinical phenotypes
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: base.proto
package org.phenopackets.schema.v1.core;
/**
*
* An individual phenotypic feature, observed as either present or absent (negated), with possible onset, modifiers and
* frequency
* FHIR mapping: Condition (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.PhenotypicFeature}
*/
public final class PhenotypicFeature extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.core.PhenotypicFeature)
PhenotypicFeatureOrBuilder {
private static final long serialVersionUID = 0L;
// Use PhenotypicFeature.newBuilder() to construct.
private PhenotypicFeature(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private PhenotypicFeature() {
description_ = "";
modifiers_ = java.util.Collections.emptyList();
evidence_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new PhenotypicFeature();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private PhenotypicFeature(
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();
description_ = s;
break;
}
case 18: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (type_ != null) {
subBuilder = type_.toBuilder();
}
type_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(type_);
type_ = subBuilder.buildPartial();
}
break;
}
case 24: {
negated_ = input.readBool();
break;
}
case 34: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (severity_ != null) {
subBuilder = severity_.toBuilder();
}
severity_ = input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(severity_);
severity_ = subBuilder.buildPartial();
}
break;
}
case 42: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
modifiers_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
modifiers_.add(
input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry));
break;
}
case 50: {
org.phenopackets.schema.v1.core.Age.Builder subBuilder = null;
if (onsetCase_ == 6) {
subBuilder = ((org.phenopackets.schema.v1.core.Age) onset_).toBuilder();
}
onset_ =
input.readMessage(org.phenopackets.schema.v1.core.Age.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom((org.phenopackets.schema.v1.core.Age) onset_);
onset_ = subBuilder.buildPartial();
}
onsetCase_ = 6;
break;
}
case 58: {
org.phenopackets.schema.v1.core.AgeRange.Builder subBuilder = null;
if (onsetCase_ == 7) {
subBuilder = ((org.phenopackets.schema.v1.core.AgeRange) onset_).toBuilder();
}
onset_ =
input.readMessage(org.phenopackets.schema.v1.core.AgeRange.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom((org.phenopackets.schema.v1.core.AgeRange) onset_);
onset_ = subBuilder.buildPartial();
}
onsetCase_ = 7;
break;
}
case 74: {
org.phenopackets.schema.v1.core.OntologyClass.Builder subBuilder = null;
if (onsetCase_ == 9) {
subBuilder = ((org.phenopackets.schema.v1.core.OntologyClass) onset_).toBuilder();
}
onset_ =
input.readMessage(org.phenopackets.schema.v1.core.OntologyClass.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom((org.phenopackets.schema.v1.core.OntologyClass) onset_);
onset_ = subBuilder.buildPartial();
}
onsetCase_ = 9;
break;
}
case 82: {
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
evidence_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
}
evidence_.add(
input.readMessage(org.phenopackets.schema.v1.core.Evidence.parser(), extensionRegistry));
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
}
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000001) != 0)) {
modifiers_ = java.util.Collections.unmodifiableList(modifiers_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
evidence_ = java.util.Collections.unmodifiableList(evidence_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_PhenotypicFeature_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_PhenotypicFeature_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.phenopackets.schema.v1.core.PhenotypicFeature.class, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder.class);
}
private int onsetCase_ = 0;
private java.lang.Object onset_;
public enum OnsetCase
implements com.google.protobuf.Internal.EnumLite {
AGE_OF_ONSET(6),
AGE_RANGE_OF_ONSET(7),
CLASS_OF_ONSET(9),
ONSET_NOT_SET(0);
private final int value;
private OnsetCase(int value) {
this.value = value;
}
/**
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static OnsetCase valueOf(int value) {
return forNumber(value);
}
public static OnsetCase forNumber(int value) {
switch (value) {
case 6: return AGE_OF_ONSET;
case 7: return AGE_RANGE_OF_ONSET;
case 9: return CLASS_OF_ONSET;
case 0: return ONSET_NOT_SET;
default: return null;
}
}
public int getNumber() {
return this.value;
}
};
public OnsetCase
getOnsetCase() {
return OnsetCase.forNumber(
onsetCase_);
}
public static final int DESCRIPTION_FIELD_NUMBER = 1;
private volatile java.lang.Object description_;
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public java.lang.String getDescription() {
java.lang.Object ref = description_;
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();
description_ = s;
return s;
}
}
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public com.google.protobuf.ByteString
getDescriptionBytes() {
java.lang.Object ref = description_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
description_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int TYPE_FIELD_NUMBER = 2;
private org.phenopackets.schema.v1.core.OntologyClass type_;
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public boolean hasType() {
return type_ != null;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public org.phenopackets.schema.v1.core.OntologyClass getType() {
return type_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : type_;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTypeOrBuilder() {
return getType();
}
public static final int NEGATED_FIELD_NUMBER = 3;
private boolean negated_;
/**
*
* Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was
* observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be
* absent.
* More formally, this modifier indicates the logical negation of the OntologyClass used in the 'type' field.
* *CAUTION* It is imperative to check this field for correct interpretation of the phenotype!
*
*
* bool negated = 3;
*/
public boolean getNegated() {
return negated_;
}
public static final int SEVERITY_FIELD_NUMBER = 4;
private org.phenopackets.schema.v1.core.OntologyClass severity_;
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public boolean hasSeverity() {
return severity_ != null;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass getSeverity() {
return severity_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : severity_;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getSeverityOrBuilder() {
return getSeverity();
}
public static final int MODIFIERS_FIELD_NUMBER = 5;
private java.util.List modifiers_;
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public java.util.List getModifiersList() {
return modifiers_;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public java.util.List
getModifiersOrBuilderList() {
return modifiers_;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public int getModifiersCount() {
return modifiers_.size();
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClass getModifiers(int index) {
return modifiers_.get(index);
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getModifiersOrBuilder(
int index) {
return modifiers_.get(index);
}
public static final int AGE_OF_ONSET_FIELD_NUMBER = 6;
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public boolean hasAgeOfOnset() {
return onsetCase_ == 6;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public org.phenopackets.schema.v1.core.Age getAgeOfOnset() {
if (onsetCase_ == 6) {
return (org.phenopackets.schema.v1.core.Age) onset_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public org.phenopackets.schema.v1.core.AgeOrBuilder getAgeOfOnsetOrBuilder() {
if (onsetCase_ == 6) {
return (org.phenopackets.schema.v1.core.Age) onset_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
public static final int AGE_RANGE_OF_ONSET_FIELD_NUMBER = 7;
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public boolean hasAgeRangeOfOnset() {
return onsetCase_ == 7;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public org.phenopackets.schema.v1.core.AgeRange getAgeRangeOfOnset() {
if (onsetCase_ == 7) {
return (org.phenopackets.schema.v1.core.AgeRange) onset_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public org.phenopackets.schema.v1.core.AgeRangeOrBuilder getAgeRangeOfOnsetOrBuilder() {
if (onsetCase_ == 7) {
return (org.phenopackets.schema.v1.core.AgeRange) onset_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
public static final int CLASS_OF_ONSET_FIELD_NUMBER = 9;
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public boolean hasClassOfOnset() {
return onsetCase_ == 9;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass getClassOfOnset() {
if (onsetCase_ == 9) {
return (org.phenopackets.schema.v1.core.OntologyClass) onset_;
}
return org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getClassOfOnsetOrBuilder() {
if (onsetCase_ == 9) {
return (org.phenopackets.schema.v1.core.OntologyClass) onset_;
}
return org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
}
public static final int EVIDENCE_FIELD_NUMBER = 10;
private java.util.List evidence_;
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public java.util.List getEvidenceList() {
return evidence_;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public java.util.List
getEvidenceOrBuilderList() {
return evidence_;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public int getEvidenceCount() {
return evidence_.size();
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.Evidence getEvidence(int index) {
return evidence_.get(index);
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.EvidenceOrBuilder getEvidenceOrBuilder(
int index) {
return evidence_.get(index);
}
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 (!getDescriptionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, description_);
}
if (type_ != null) {
output.writeMessage(2, getType());
}
if (negated_ != false) {
output.writeBool(3, negated_);
}
if (severity_ != null) {
output.writeMessage(4, getSeverity());
}
for (int i = 0; i < modifiers_.size(); i++) {
output.writeMessage(5, modifiers_.get(i));
}
if (onsetCase_ == 6) {
output.writeMessage(6, (org.phenopackets.schema.v1.core.Age) onset_);
}
if (onsetCase_ == 7) {
output.writeMessage(7, (org.phenopackets.schema.v1.core.AgeRange) onset_);
}
if (onsetCase_ == 9) {
output.writeMessage(9, (org.phenopackets.schema.v1.core.OntologyClass) onset_);
}
for (int i = 0; i < evidence_.size(); i++) {
output.writeMessage(10, evidence_.get(i));
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getDescriptionBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, description_);
}
if (type_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(2, getType());
}
if (negated_ != false) {
size += com.google.protobuf.CodedOutputStream
.computeBoolSize(3, negated_);
}
if (severity_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(4, getSeverity());
}
for (int i = 0; i < modifiers_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(5, modifiers_.get(i));
}
if (onsetCase_ == 6) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(6, (org.phenopackets.schema.v1.core.Age) onset_);
}
if (onsetCase_ == 7) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(7, (org.phenopackets.schema.v1.core.AgeRange) onset_);
}
if (onsetCase_ == 9) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, (org.phenopackets.schema.v1.core.OntologyClass) onset_);
}
for (int i = 0; i < evidence_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(10, evidence_.get(i));
}
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.core.PhenotypicFeature)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.core.PhenotypicFeature other = (org.phenopackets.schema.v1.core.PhenotypicFeature) obj;
if (!getDescription()
.equals(other.getDescription())) return false;
if (hasType() != other.hasType()) return false;
if (hasType()) {
if (!getType()
.equals(other.getType())) return false;
}
if (getNegated()
!= other.getNegated()) return false;
if (hasSeverity() != other.hasSeverity()) return false;
if (hasSeverity()) {
if (!getSeverity()
.equals(other.getSeverity())) return false;
}
if (!getModifiersList()
.equals(other.getModifiersList())) return false;
if (!getEvidenceList()
.equals(other.getEvidenceList())) return false;
if (!getOnsetCase().equals(other.getOnsetCase())) return false;
switch (onsetCase_) {
case 6:
if (!getAgeOfOnset()
.equals(other.getAgeOfOnset())) return false;
break;
case 7:
if (!getAgeRangeOfOnset()
.equals(other.getAgeRangeOfOnset())) return false;
break;
case 9:
if (!getClassOfOnset()
.equals(other.getClassOfOnset())) return false;
break;
case 0:
default:
}
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) + DESCRIPTION_FIELD_NUMBER;
hash = (53 * hash) + getDescription().hashCode();
if (hasType()) {
hash = (37 * hash) + TYPE_FIELD_NUMBER;
hash = (53 * hash) + getType().hashCode();
}
hash = (37 * hash) + NEGATED_FIELD_NUMBER;
hash = (53 * hash) + com.google.protobuf.Internal.hashBoolean(
getNegated());
if (hasSeverity()) {
hash = (37 * hash) + SEVERITY_FIELD_NUMBER;
hash = (53 * hash) + getSeverity().hashCode();
}
if (getModifiersCount() > 0) {
hash = (37 * hash) + MODIFIERS_FIELD_NUMBER;
hash = (53 * hash) + getModifiersList().hashCode();
}
if (getEvidenceCount() > 0) {
hash = (37 * hash) + EVIDENCE_FIELD_NUMBER;
hash = (53 * hash) + getEvidenceList().hashCode();
}
switch (onsetCase_) {
case 6:
hash = (37 * hash) + AGE_OF_ONSET_FIELD_NUMBER;
hash = (53 * hash) + getAgeOfOnset().hashCode();
break;
case 7:
hash = (37 * hash) + AGE_RANGE_OF_ONSET_FIELD_NUMBER;
hash = (53 * hash) + getAgeRangeOfOnset().hashCode();
break;
case 9:
hash = (37 * hash) + CLASS_OF_ONSET_FIELD_NUMBER;
hash = (53 * hash) + getClassOfOnset().hashCode();
break;
case 0:
default:
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature 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.core.PhenotypicFeature parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature 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.core.PhenotypicFeature parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
@java.lang.Override
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.phenopackets.schema.v1.core.PhenotypicFeature prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
? new Builder() : new Builder().mergeFrom(this);
}
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
*
* An individual phenotypic feature, observed as either present or absent (negated), with possible onset, modifiers and
* frequency
* FHIR mapping: Condition (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.PhenotypicFeature}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.core.PhenotypicFeature)
org.phenopackets.schema.v1.core.PhenotypicFeatureOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_PhenotypicFeature_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_PhenotypicFeature_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.phenopackets.schema.v1.core.PhenotypicFeature.class, org.phenopackets.schema.v1.core.PhenotypicFeature.Builder.class);
}
// Construct using org.phenopackets.schema.v1.core.PhenotypicFeature.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getModifiersFieldBuilder();
getEvidenceFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
description_ = "";
if (typeBuilder_ == null) {
type_ = null;
} else {
type_ = null;
typeBuilder_ = null;
}
negated_ = false;
if (severityBuilder_ == null) {
severity_ = null;
} else {
severity_ = null;
severityBuilder_ = null;
}
if (modifiersBuilder_ == null) {
modifiers_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
modifiersBuilder_.clear();
}
if (evidenceBuilder_ == null) {
evidence_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
} else {
evidenceBuilder_.clear();
}
onsetCase_ = 0;
onset_ = null;
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_PhenotypicFeature_descriptor;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.PhenotypicFeature getDefaultInstanceForType() {
return org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance();
}
@java.lang.Override
public org.phenopackets.schema.v1.core.PhenotypicFeature build() {
org.phenopackets.schema.v1.core.PhenotypicFeature result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.PhenotypicFeature buildPartial() {
org.phenopackets.schema.v1.core.PhenotypicFeature result = new org.phenopackets.schema.v1.core.PhenotypicFeature(this);
int from_bitField0_ = bitField0_;
result.description_ = description_;
if (typeBuilder_ == null) {
result.type_ = type_;
} else {
result.type_ = typeBuilder_.build();
}
result.negated_ = negated_;
if (severityBuilder_ == null) {
result.severity_ = severity_;
} else {
result.severity_ = severityBuilder_.build();
}
if (modifiersBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
modifiers_ = java.util.Collections.unmodifiableList(modifiers_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.modifiers_ = modifiers_;
} else {
result.modifiers_ = modifiersBuilder_.build();
}
if (onsetCase_ == 6) {
if (ageOfOnsetBuilder_ == null) {
result.onset_ = onset_;
} else {
result.onset_ = ageOfOnsetBuilder_.build();
}
}
if (onsetCase_ == 7) {
if (ageRangeOfOnsetBuilder_ == null) {
result.onset_ = onset_;
} else {
result.onset_ = ageRangeOfOnsetBuilder_.build();
}
}
if (onsetCase_ == 9) {
if (classOfOnsetBuilder_ == null) {
result.onset_ = onset_;
} else {
result.onset_ = classOfOnsetBuilder_.build();
}
}
if (evidenceBuilder_ == null) {
if (((bitField0_ & 0x00000002) != 0)) {
evidence_ = java.util.Collections.unmodifiableList(evidence_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.evidence_ = evidence_;
} else {
result.evidence_ = evidenceBuilder_.build();
}
result.onsetCase_ = onsetCase_;
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.core.PhenotypicFeature) {
return mergeFrom((org.phenopackets.schema.v1.core.PhenotypicFeature)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.phenopackets.schema.v1.core.PhenotypicFeature other) {
if (other == org.phenopackets.schema.v1.core.PhenotypicFeature.getDefaultInstance()) return this;
if (!other.getDescription().isEmpty()) {
description_ = other.description_;
onChanged();
}
if (other.hasType()) {
mergeType(other.getType());
}
if (other.getNegated() != false) {
setNegated(other.getNegated());
}
if (other.hasSeverity()) {
mergeSeverity(other.getSeverity());
}
if (modifiersBuilder_ == null) {
if (!other.modifiers_.isEmpty()) {
if (modifiers_.isEmpty()) {
modifiers_ = other.modifiers_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureModifiersIsMutable();
modifiers_.addAll(other.modifiers_);
}
onChanged();
}
} else {
if (!other.modifiers_.isEmpty()) {
if (modifiersBuilder_.isEmpty()) {
modifiersBuilder_.dispose();
modifiersBuilder_ = null;
modifiers_ = other.modifiers_;
bitField0_ = (bitField0_ & ~0x00000001);
modifiersBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getModifiersFieldBuilder() : null;
} else {
modifiersBuilder_.addAllMessages(other.modifiers_);
}
}
}
if (evidenceBuilder_ == null) {
if (!other.evidence_.isEmpty()) {
if (evidence_.isEmpty()) {
evidence_ = other.evidence_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureEvidenceIsMutable();
evidence_.addAll(other.evidence_);
}
onChanged();
}
} else {
if (!other.evidence_.isEmpty()) {
if (evidenceBuilder_.isEmpty()) {
evidenceBuilder_.dispose();
evidenceBuilder_ = null;
evidence_ = other.evidence_;
bitField0_ = (bitField0_ & ~0x00000002);
evidenceBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getEvidenceFieldBuilder() : null;
} else {
evidenceBuilder_.addAllMessages(other.evidence_);
}
}
}
switch (other.getOnsetCase()) {
case AGE_OF_ONSET: {
mergeAgeOfOnset(other.getAgeOfOnset());
break;
}
case AGE_RANGE_OF_ONSET: {
mergeAgeRangeOfOnset(other.getAgeRangeOfOnset());
break;
}
case CLASS_OF_ONSET: {
mergeClassOfOnset(other.getClassOfOnset());
break;
}
case ONSET_NOT_SET: {
break;
}
}
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.core.PhenotypicFeature parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.phenopackets.schema.v1.core.PhenotypicFeature) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int onsetCase_ = 0;
private java.lang.Object onset_;
public OnsetCase
getOnsetCase() {
return OnsetCase.forNumber(
onsetCase_);
}
public Builder clearOnset() {
onsetCase_ = 0;
onset_ = null;
onChanged();
return this;
}
private int bitField0_;
private java.lang.Object description_ = "";
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public java.lang.String getDescription() {
java.lang.Object ref = description_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
description_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public com.google.protobuf.ByteString
getDescriptionBytes() {
java.lang.Object ref = description_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
description_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public Builder setDescription(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
description_ = value;
onChanged();
return this;
}
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public Builder clearDescription() {
description_ = getDefaultInstance().getDescription();
onChanged();
return this;
}
/**
*
* Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype -
* the type and onset etc... fields should be used for this purpose.
*
*
* string description = 1;
*/
public Builder setDescriptionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
description_ = value;
onChanged();
return this;
}
private org.phenopackets.schema.v1.core.OntologyClass type_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> typeBuilder_;
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public boolean hasType() {
return typeBuilder_ != null || type_ != null;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public org.phenopackets.schema.v1.core.OntologyClass getType() {
if (typeBuilder_ == null) {
return type_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : type_;
} else {
return typeBuilder_.getMessage();
}
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public Builder setType(org.phenopackets.schema.v1.core.OntologyClass value) {
if (typeBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
type_ = value;
onChanged();
} else {
typeBuilder_.setMessage(value);
}
return this;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public Builder setType(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (typeBuilder_ == null) {
type_ = builderForValue.build();
onChanged();
} else {
typeBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public Builder mergeType(org.phenopackets.schema.v1.core.OntologyClass value) {
if (typeBuilder_ == null) {
if (type_ != null) {
type_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(type_).mergeFrom(value).buildPartial();
} else {
type_ = value;
}
onChanged();
} else {
typeBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public Builder clearType() {
if (typeBuilder_ == null) {
type_ = null;
onChanged();
} else {
type_ = null;
typeBuilder_ = null;
}
return this;
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getTypeBuilder() {
onChanged();
return getTypeFieldBuilder().getBuilder();
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getTypeOrBuilder() {
if (typeBuilder_ != null) {
return typeBuilder_.getMessageOrBuilder();
} else {
return type_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : type_;
}
}
/**
*
* The primary ontology class which describes the phenotype. For example "HP:0001363" "Craniosynostosis"
* FHIR mapping: Condition.identifier
*
*
* .org.phenopackets.schema.v1.core.OntologyClass type = 2;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getTypeFieldBuilder() {
if (typeBuilder_ == null) {
typeBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getType(),
getParentForChildren(),
isClean());
type_ = null;
}
return typeBuilder_;
}
private boolean negated_ ;
/**
*
* Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was
* observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be
* absent.
* More formally, this modifier indicates the logical negation of the OntologyClass used in the 'type' field.
* *CAUTION* It is imperative to check this field for correct interpretation of the phenotype!
*
*
* bool negated = 3;
*/
public boolean getNegated() {
return negated_;
}
/**
*
* Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was
* observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be
* absent.
* More formally, this modifier indicates the logical negation of the OntologyClass used in the 'type' field.
* *CAUTION* It is imperative to check this field for correct interpretation of the phenotype!
*
*
* bool negated = 3;
*/
public Builder setNegated(boolean value) {
negated_ = value;
onChanged();
return this;
}
/**
*
* Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was
* observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be
* absent.
* More formally, this modifier indicates the logical negation of the OntologyClass used in the 'type' field.
* *CAUTION* It is imperative to check this field for correct interpretation of the phenotype!
*
*
* bool negated = 3;
*/
public Builder clearNegated() {
negated_ = false;
onChanged();
return this;
}
private org.phenopackets.schema.v1.core.OntologyClass severity_;
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> severityBuilder_;
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public boolean hasSeverity() {
return severityBuilder_ != null || severity_ != null;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass getSeverity() {
if (severityBuilder_ == null) {
return severity_ == null ? org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : severity_;
} else {
return severityBuilder_.getMessage();
}
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public Builder setSeverity(org.phenopackets.schema.v1.core.OntologyClass value) {
if (severityBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
severity_ = value;
onChanged();
} else {
severityBuilder_.setMessage(value);
}
return this;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public Builder setSeverity(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (severityBuilder_ == null) {
severity_ = builderForValue.build();
onChanged();
} else {
severityBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public Builder mergeSeverity(org.phenopackets.schema.v1.core.OntologyClass value) {
if (severityBuilder_ == null) {
if (severity_ != null) {
severity_ =
org.phenopackets.schema.v1.core.OntologyClass.newBuilder(severity_).mergeFrom(value).buildPartial();
} else {
severity_ = value;
}
onChanged();
} else {
severityBuilder_.mergeFrom(value);
}
return this;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public Builder clearSeverity() {
if (severityBuilder_ == null) {
severity_ = null;
onChanged();
} else {
severity_ = null;
severityBuilder_ = null;
}
return this;
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getSeverityBuilder() {
onChanged();
return getSeverityFieldBuilder().getBuilder();
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getSeverityOrBuilder() {
if (severityBuilder_ != null) {
return severityBuilder_.getMessageOrBuilder();
} else {
return severity_ == null ?
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance() : severity_;
}
}
/**
*
* Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities
* FHIR mapping: Condition.severity
*
*
* .org.phenopackets.schema.v1.core.OntologyClass severity = 4;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getSeverityFieldBuilder() {
if (severityBuilder_ == null) {
severityBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
getSeverity(),
getParentForChildren(),
isClean());
severity_ = null;
}
return severityBuilder_;
}
private java.util.List modifiers_ =
java.util.Collections.emptyList();
private void ensureModifiersIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
modifiers_ = new java.util.ArrayList(modifiers_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> modifiersBuilder_;
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public java.util.List getModifiersList() {
if (modifiersBuilder_ == null) {
return java.util.Collections.unmodifiableList(modifiers_);
} else {
return modifiersBuilder_.getMessageList();
}
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public int getModifiersCount() {
if (modifiersBuilder_ == null) {
return modifiers_.size();
} else {
return modifiersBuilder_.getCount();
}
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClass getModifiers(int index) {
if (modifiersBuilder_ == null) {
return modifiers_.get(index);
} else {
return modifiersBuilder_.getMessage(index);
}
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder setModifiers(
int index, org.phenopackets.schema.v1.core.OntologyClass value) {
if (modifiersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureModifiersIsMutable();
modifiers_.set(index, value);
onChanged();
} else {
modifiersBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder setModifiers(
int index, org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (modifiersBuilder_ == null) {
ensureModifiersIsMutable();
modifiers_.set(index, builderForValue.build());
onChanged();
} else {
modifiersBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder addModifiers(org.phenopackets.schema.v1.core.OntologyClass value) {
if (modifiersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureModifiersIsMutable();
modifiers_.add(value);
onChanged();
} else {
modifiersBuilder_.addMessage(value);
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder addModifiers(
int index, org.phenopackets.schema.v1.core.OntologyClass value) {
if (modifiersBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureModifiersIsMutable();
modifiers_.add(index, value);
onChanged();
} else {
modifiersBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder addModifiers(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (modifiersBuilder_ == null) {
ensureModifiersIsMutable();
modifiers_.add(builderForValue.build());
onChanged();
} else {
modifiersBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder addModifiers(
int index, org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (modifiersBuilder_ == null) {
ensureModifiersIsMutable();
modifiers_.add(index, builderForValue.build());
onChanged();
} else {
modifiersBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder addAllModifiers(
java.lang.Iterable values) {
if (modifiersBuilder_ == null) {
ensureModifiersIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, modifiers_);
onChanged();
} else {
modifiersBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder clearModifiers() {
if (modifiersBuilder_ == null) {
modifiers_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
modifiersBuilder_.clear();
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public Builder removeModifiers(int index) {
if (modifiersBuilder_ == null) {
ensureModifiersIsMutable();
modifiers_.remove(index);
onChanged();
} else {
modifiersBuilder_.remove(index);
}
return this;
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getModifiersBuilder(
int index) {
return getModifiersFieldBuilder().getBuilder(index);
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getModifiersOrBuilder(
int index) {
if (modifiersBuilder_ == null) {
return modifiers_.get(index); } else {
return modifiersBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public java.util.List
getModifiersOrBuilderList() {
if (modifiersBuilder_ != null) {
return modifiersBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(modifiers_);
}
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder addModifiersBuilder() {
return getModifiersFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance());
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder addModifiersBuilder(
int index) {
return getModifiersFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance());
}
/**
*
* subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity
*
*
* repeated .org.phenopackets.schema.v1.core.OntologyClass modifiers = 5;
*/
public java.util.List
getModifiersBuilderList() {
return getModifiersFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getModifiersFieldBuilder() {
if (modifiersBuilder_ == null) {
modifiersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
modifiers_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
modifiers_ = null;
}
return modifiersBuilder_;
}
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder> ageOfOnsetBuilder_;
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public boolean hasAgeOfOnset() {
return onsetCase_ == 6;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public org.phenopackets.schema.v1.core.Age getAgeOfOnset() {
if (ageOfOnsetBuilder_ == null) {
if (onsetCase_ == 6) {
return (org.phenopackets.schema.v1.core.Age) onset_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
} else {
if (onsetCase_ == 6) {
return ageOfOnsetBuilder_.getMessage();
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public Builder setAgeOfOnset(org.phenopackets.schema.v1.core.Age value) {
if (ageOfOnsetBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
onset_ = value;
onChanged();
} else {
ageOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 6;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public Builder setAgeOfOnset(
org.phenopackets.schema.v1.core.Age.Builder builderForValue) {
if (ageOfOnsetBuilder_ == null) {
onset_ = builderForValue.build();
onChanged();
} else {
ageOfOnsetBuilder_.setMessage(builderForValue.build());
}
onsetCase_ = 6;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public Builder mergeAgeOfOnset(org.phenopackets.schema.v1.core.Age value) {
if (ageOfOnsetBuilder_ == null) {
if (onsetCase_ == 6 &&
onset_ != org.phenopackets.schema.v1.core.Age.getDefaultInstance()) {
onset_ = org.phenopackets.schema.v1.core.Age.newBuilder((org.phenopackets.schema.v1.core.Age) onset_)
.mergeFrom(value).buildPartial();
} else {
onset_ = value;
}
onChanged();
} else {
if (onsetCase_ == 6) {
ageOfOnsetBuilder_.mergeFrom(value);
}
ageOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 6;
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public Builder clearAgeOfOnset() {
if (ageOfOnsetBuilder_ == null) {
if (onsetCase_ == 6) {
onsetCase_ = 0;
onset_ = null;
onChanged();
}
} else {
if (onsetCase_ == 6) {
onsetCase_ = 0;
onset_ = null;
}
ageOfOnsetBuilder_.clear();
}
return this;
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public org.phenopackets.schema.v1.core.Age.Builder getAgeOfOnsetBuilder() {
return getAgeOfOnsetFieldBuilder().getBuilder();
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
public org.phenopackets.schema.v1.core.AgeOrBuilder getAgeOfOnsetOrBuilder() {
if ((onsetCase_ == 6) && (ageOfOnsetBuilder_ != null)) {
return ageOfOnsetBuilder_.getMessageOrBuilder();
} else {
if (onsetCase_ == 6) {
return (org.phenopackets.schema.v1.core.Age) onset_;
}
return org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.Age age_of_onset = 6;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder>
getAgeOfOnsetFieldBuilder() {
if (ageOfOnsetBuilder_ == null) {
if (!(onsetCase_ == 6)) {
onset_ = org.phenopackets.schema.v1.core.Age.getDefaultInstance();
}
ageOfOnsetBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.Age, org.phenopackets.schema.v1.core.Age.Builder, org.phenopackets.schema.v1.core.AgeOrBuilder>(
(org.phenopackets.schema.v1.core.Age) onset_,
getParentForChildren(),
isClean());
onset_ = null;
}
onsetCase_ = 6;
onChanged();;
return ageOfOnsetBuilder_;
}
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder> ageRangeOfOnsetBuilder_;
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public boolean hasAgeRangeOfOnset() {
return onsetCase_ == 7;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public org.phenopackets.schema.v1.core.AgeRange getAgeRangeOfOnset() {
if (ageRangeOfOnsetBuilder_ == null) {
if (onsetCase_ == 7) {
return (org.phenopackets.schema.v1.core.AgeRange) onset_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
} else {
if (onsetCase_ == 7) {
return ageRangeOfOnsetBuilder_.getMessage();
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public Builder setAgeRangeOfOnset(org.phenopackets.schema.v1.core.AgeRange value) {
if (ageRangeOfOnsetBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
onset_ = value;
onChanged();
} else {
ageRangeOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public Builder setAgeRangeOfOnset(
org.phenopackets.schema.v1.core.AgeRange.Builder builderForValue) {
if (ageRangeOfOnsetBuilder_ == null) {
onset_ = builderForValue.build();
onChanged();
} else {
ageRangeOfOnsetBuilder_.setMessage(builderForValue.build());
}
onsetCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public Builder mergeAgeRangeOfOnset(org.phenopackets.schema.v1.core.AgeRange value) {
if (ageRangeOfOnsetBuilder_ == null) {
if (onsetCase_ == 7 &&
onset_ != org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance()) {
onset_ = org.phenopackets.schema.v1.core.AgeRange.newBuilder((org.phenopackets.schema.v1.core.AgeRange) onset_)
.mergeFrom(value).buildPartial();
} else {
onset_ = value;
}
onChanged();
} else {
if (onsetCase_ == 7) {
ageRangeOfOnsetBuilder_.mergeFrom(value);
}
ageRangeOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 7;
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public Builder clearAgeRangeOfOnset() {
if (ageRangeOfOnsetBuilder_ == null) {
if (onsetCase_ == 7) {
onsetCase_ = 0;
onset_ = null;
onChanged();
}
} else {
if (onsetCase_ == 7) {
onsetCase_ = 0;
onset_ = null;
}
ageRangeOfOnsetBuilder_.clear();
}
return this;
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public org.phenopackets.schema.v1.core.AgeRange.Builder getAgeRangeOfOnsetBuilder() {
return getAgeRangeOfOnsetFieldBuilder().getBuilder();
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
public org.phenopackets.schema.v1.core.AgeRangeOrBuilder getAgeRangeOfOnsetOrBuilder() {
if ((onsetCase_ == 7) && (ageRangeOfOnsetBuilder_ != null)) {
return ageRangeOfOnsetBuilder_.getMessageOrBuilder();
} else {
if (onsetCase_ == 7) {
return (org.phenopackets.schema.v1.core.AgeRange) onset_;
}
return org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.AgeRange age_range_of_onset = 7;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder>
getAgeRangeOfOnsetFieldBuilder() {
if (ageRangeOfOnsetBuilder_ == null) {
if (!(onsetCase_ == 7)) {
onset_ = org.phenopackets.schema.v1.core.AgeRange.getDefaultInstance();
}
ageRangeOfOnsetBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.AgeRange, org.phenopackets.schema.v1.core.AgeRange.Builder, org.phenopackets.schema.v1.core.AgeRangeOrBuilder>(
(org.phenopackets.schema.v1.core.AgeRange) onset_,
getParentForChildren(),
isClean());
onset_ = null;
}
onsetCase_ = 7;
onChanged();;
return ageRangeOfOnsetBuilder_;
}
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder> classOfOnsetBuilder_;
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public boolean hasClassOfOnset() {
return onsetCase_ == 9;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass getClassOfOnset() {
if (classOfOnsetBuilder_ == null) {
if (onsetCase_ == 9) {
return (org.phenopackets.schema.v1.core.OntologyClass) onset_;
}
return org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
} else {
if (onsetCase_ == 9) {
return classOfOnsetBuilder_.getMessage();
}
return org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public Builder setClassOfOnset(org.phenopackets.schema.v1.core.OntologyClass value) {
if (classOfOnsetBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
onset_ = value;
onChanged();
} else {
classOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 9;
return this;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public Builder setClassOfOnset(
org.phenopackets.schema.v1.core.OntologyClass.Builder builderForValue) {
if (classOfOnsetBuilder_ == null) {
onset_ = builderForValue.build();
onChanged();
} else {
classOfOnsetBuilder_.setMessage(builderForValue.build());
}
onsetCase_ = 9;
return this;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public Builder mergeClassOfOnset(org.phenopackets.schema.v1.core.OntologyClass value) {
if (classOfOnsetBuilder_ == null) {
if (onsetCase_ == 9 &&
onset_ != org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance()) {
onset_ = org.phenopackets.schema.v1.core.OntologyClass.newBuilder((org.phenopackets.schema.v1.core.OntologyClass) onset_)
.mergeFrom(value).buildPartial();
} else {
onset_ = value;
}
onChanged();
} else {
if (onsetCase_ == 9) {
classOfOnsetBuilder_.mergeFrom(value);
}
classOfOnsetBuilder_.setMessage(value);
}
onsetCase_ = 9;
return this;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public Builder clearClassOfOnset() {
if (classOfOnsetBuilder_ == null) {
if (onsetCase_ == 9) {
onsetCase_ = 0;
onset_ = null;
onChanged();
}
} else {
if (onsetCase_ == 9) {
onsetCase_ = 0;
onset_ = null;
}
classOfOnsetBuilder_.clear();
}
return this;
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClass.Builder getClassOfOnsetBuilder() {
return getClassOfOnsetFieldBuilder().getBuilder();
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
public org.phenopackets.schema.v1.core.OntologyClassOrBuilder getClassOfOnsetOrBuilder() {
if ((onsetCase_ == 9) && (classOfOnsetBuilder_ != null)) {
return classOfOnsetBuilder_.getMessageOrBuilder();
} else {
if (onsetCase_ == 9) {
return (org.phenopackets.schema.v1.core.OntologyClass) onset_;
}
return org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
}
}
/**
* .org.phenopackets.schema.v1.core.OntologyClass class_of_onset = 9;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>
getClassOfOnsetFieldBuilder() {
if (classOfOnsetBuilder_ == null) {
if (!(onsetCase_ == 9)) {
onset_ = org.phenopackets.schema.v1.core.OntologyClass.getDefaultInstance();
}
classOfOnsetBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.phenopackets.schema.v1.core.OntologyClass, org.phenopackets.schema.v1.core.OntologyClass.Builder, org.phenopackets.schema.v1.core.OntologyClassOrBuilder>(
(org.phenopackets.schema.v1.core.OntologyClass) onset_,
getParentForChildren(),
isClean());
onset_ = null;
}
onsetCase_ = 9;
onChanged();;
return classOfOnsetBuilder_;
}
private java.util.List evidence_ =
java.util.Collections.emptyList();
private void ensureEvidenceIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
evidence_ = new java.util.ArrayList(evidence_);
bitField0_ |= 0x00000002;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Evidence, org.phenopackets.schema.v1.core.Evidence.Builder, org.phenopackets.schema.v1.core.EvidenceOrBuilder> evidenceBuilder_;
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public java.util.List getEvidenceList() {
if (evidenceBuilder_ == null) {
return java.util.Collections.unmodifiableList(evidence_);
} else {
return evidenceBuilder_.getMessageList();
}
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public int getEvidenceCount() {
if (evidenceBuilder_ == null) {
return evidence_.size();
} else {
return evidenceBuilder_.getCount();
}
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.Evidence getEvidence(int index) {
if (evidenceBuilder_ == null) {
return evidence_.get(index);
} else {
return evidenceBuilder_.getMessage(index);
}
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder setEvidence(
int index, org.phenopackets.schema.v1.core.Evidence value) {
if (evidenceBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureEvidenceIsMutable();
evidence_.set(index, value);
onChanged();
} else {
evidenceBuilder_.setMessage(index, value);
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder setEvidence(
int index, org.phenopackets.schema.v1.core.Evidence.Builder builderForValue) {
if (evidenceBuilder_ == null) {
ensureEvidenceIsMutable();
evidence_.set(index, builderForValue.build());
onChanged();
} else {
evidenceBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder addEvidence(org.phenopackets.schema.v1.core.Evidence value) {
if (evidenceBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureEvidenceIsMutable();
evidence_.add(value);
onChanged();
} else {
evidenceBuilder_.addMessage(value);
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder addEvidence(
int index, org.phenopackets.schema.v1.core.Evidence value) {
if (evidenceBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureEvidenceIsMutable();
evidence_.add(index, value);
onChanged();
} else {
evidenceBuilder_.addMessage(index, value);
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder addEvidence(
org.phenopackets.schema.v1.core.Evidence.Builder builderForValue) {
if (evidenceBuilder_ == null) {
ensureEvidenceIsMutable();
evidence_.add(builderForValue.build());
onChanged();
} else {
evidenceBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder addEvidence(
int index, org.phenopackets.schema.v1.core.Evidence.Builder builderForValue) {
if (evidenceBuilder_ == null) {
ensureEvidenceIsMutable();
evidence_.add(index, builderForValue.build());
onChanged();
} else {
evidenceBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder addAllEvidence(
java.lang.Iterable values) {
if (evidenceBuilder_ == null) {
ensureEvidenceIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, evidence_);
onChanged();
} else {
evidenceBuilder_.addAllMessages(values);
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder clearEvidence() {
if (evidenceBuilder_ == null) {
evidence_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
} else {
evidenceBuilder_.clear();
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public Builder removeEvidence(int index) {
if (evidenceBuilder_ == null) {
ensureEvidenceIsMutable();
evidence_.remove(index);
onChanged();
} else {
evidenceBuilder_.remove(index);
}
return this;
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.Evidence.Builder getEvidenceBuilder(
int index) {
return getEvidenceFieldBuilder().getBuilder(index);
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.EvidenceOrBuilder getEvidenceOrBuilder(
int index) {
if (evidenceBuilder_ == null) {
return evidence_.get(index); } else {
return evidenceBuilder_.getMessageOrBuilder(index);
}
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public java.util.List
getEvidenceOrBuilderList() {
if (evidenceBuilder_ != null) {
return evidenceBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(evidence_);
}
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.Evidence.Builder addEvidenceBuilder() {
return getEvidenceFieldBuilder().addBuilder(
org.phenopackets.schema.v1.core.Evidence.getDefaultInstance());
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public org.phenopackets.schema.v1.core.Evidence.Builder addEvidenceBuilder(
int index) {
return getEvidenceFieldBuilder().addBuilder(
index, org.phenopackets.schema.v1.core.Evidence.getDefaultInstance());
}
/**
*
* Evidences for how the phenotype was determined.
*
*
* repeated .org.phenopackets.schema.v1.core.Evidence evidence = 10;
*/
public java.util.List
getEvidenceBuilderList() {
return getEvidenceFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Evidence, org.phenopackets.schema.v1.core.Evidence.Builder, org.phenopackets.schema.v1.core.EvidenceOrBuilder>
getEvidenceFieldBuilder() {
if (evidenceBuilder_ == null) {
evidenceBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.phenopackets.schema.v1.core.Evidence, org.phenopackets.schema.v1.core.Evidence.Builder, org.phenopackets.schema.v1.core.EvidenceOrBuilder>(
evidence_,
((bitField0_ & 0x00000002) != 0),
getParentForChildren(),
isClean());
evidence_ = null;
}
return evidenceBuilder_;
}
@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.core.PhenotypicFeature)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.PhenotypicFeature)
private static final org.phenopackets.schema.v1.core.PhenotypicFeature DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.core.PhenotypicFeature();
}
public static org.phenopackets.schema.v1.core.PhenotypicFeature getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public PhenotypicFeature parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new PhenotypicFeature(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.core.PhenotypicFeature getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}