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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;
/**
*
* A single VCF allele.
* For structural variation the INFO field should contain the relevant information e.g.
* END=43500;SVTYPE=DUP;CHR2=1;SVLEN=29000;
* See https://samtools.github.io/hts-specs/VCFv4.3.pdf
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.VcfAllele}
*/
public final class VcfAllele extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.core.VcfAllele)
VcfAlleleOrBuilder {
private static final long serialVersionUID = 0L;
// Use VcfAllele.newBuilder() to construct.
private VcfAllele(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private VcfAllele() {
vcfVersion_ = "";
genomeAssembly_ = "";
id_ = "";
chr_ = "";
ref_ = "";
alt_ = "";
info_ = "";
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new VcfAllele();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private VcfAllele(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
}
com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
boolean done = false;
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int tag = input.readTag();
switch (tag) {
case 0:
done = true;
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case 10: {
java.lang.String s = input.readStringRequireUtf8();
vcfVersion_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
genomeAssembly_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
id_ = s;
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
chr_ = s;
break;
}
case 40: {
pos_ = input.readInt32();
break;
}
case 50: {
java.lang.String s = input.readStringRequireUtf8();
ref_ = s;
break;
}
case 58: {
java.lang.String s = input.readStringRequireUtf8();
alt_ = s;
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case 66: {
java.lang.String s = input.readStringRequireUtf8();
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this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
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}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_VcfAllele_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_VcfAllele_fieldAccessorTable
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org.phenopackets.schema.v1.core.VcfAllele.class, org.phenopackets.schema.v1.core.VcfAllele.Builder.class);
}
public static final int VCF_VERSION_FIELD_NUMBER = 1;
private volatile java.lang.Object vcfVersion_;
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public java.lang.String getVcfVersion() {
java.lang.Object ref = vcfVersion_;
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();
vcfVersion_ = s;
return s;
}
}
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public com.google.protobuf.ByteString
getVcfVersionBytes() {
java.lang.Object ref = vcfVersion_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
vcfVersion_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int GENOME_ASSEMBLY_FIELD_NUMBER = 2;
private volatile java.lang.Object genomeAssembly_;
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public java.lang.String getGenomeAssembly() {
java.lang.Object ref = genomeAssembly_;
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();
genomeAssembly_ = s;
return s;
}
}
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public com.google.protobuf.ByteString
getGenomeAssemblyBytes() {
java.lang.Object ref = genomeAssembly_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
genomeAssembly_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ID_FIELD_NUMBER = 3;
private volatile java.lang.Object id_;
/**
* string id = 3;
*/
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;
}
}
/**
* string id = 3;
*/
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;
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}
public static final int CHR_FIELD_NUMBER = 4;
private volatile java.lang.Object chr_;
/**
* string chr = 4;
*/
public java.lang.String getChr() {
java.lang.Object ref = chr_;
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();
chr_ = s;
return s;
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/**
* string chr = 4;
*/
public com.google.protobuf.ByteString
getChrBytes() {
java.lang.Object ref = chr_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chr_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int POS_FIELD_NUMBER = 5;
private int pos_;
/**
* int32 pos = 5;
*/
public int getPos() {
return pos_;
}
public static final int REF_FIELD_NUMBER = 6;
private volatile java.lang.Object ref_;
/**
* string ref = 6;
*/
public java.lang.String getRef() {
java.lang.Object ref = ref_;
if (ref instanceof java.lang.String) {
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com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
ref_ = s;
return s;
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/**
* string ref = 6;
*/
public com.google.protobuf.ByteString
getRefBytes() {
java.lang.Object ref = ref_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ref_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ALT_FIELD_NUMBER = 7;
private volatile java.lang.Object alt_;
/**
* string alt = 7;
*/
public java.lang.String getAlt() {
java.lang.Object ref = alt_;
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();
alt_ = s;
return s;
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/**
* string alt = 7;
*/
public com.google.protobuf.ByteString
getAltBytes() {
java.lang.Object ref = alt_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alt_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int INFO_FIELD_NUMBER = 8;
private volatile java.lang.Object info_;
/**
* string info = 8;
*/
public java.lang.String getInfo() {
java.lang.Object ref = info_;
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();
info_ = s;
return s;
}
}
/**
* string info = 8;
*/
public com.google.protobuf.ByteString
getInfoBytes() {
java.lang.Object ref = info_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
info_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
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 (!getVcfVersionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, vcfVersion_);
}
if (!getGenomeAssemblyBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, genomeAssembly_);
}
if (!getIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, id_);
}
if (!getChrBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, chr_);
}
if (pos_ != 0) {
output.writeInt32(5, pos_);
}
if (!getRefBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, ref_);
}
if (!getAltBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, alt_);
}
if (!getInfoBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 8, info_);
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getVcfVersionBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, vcfVersion_);
}
if (!getGenomeAssemblyBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, genomeAssembly_);
}
if (!getIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(3, id_);
}
if (!getChrBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(4, chr_);
}
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size += com.google.protobuf.CodedOutputStream
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if (!getRefBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, ref_);
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if (!getAltBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(7, alt_);
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if (!getInfoBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(8, info_);
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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.core.VcfAllele)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.core.VcfAllele other = (org.phenopackets.schema.v1.core.VcfAllele) obj;
if (!getVcfVersion()
.equals(other.getVcfVersion())) return false;
if (!getGenomeAssembly()
.equals(other.getGenomeAssembly())) return false;
if (!getId()
.equals(other.getId())) return false;
if (!getChr()
.equals(other.getChr())) return false;
if (getPos()
!= other.getPos()) return false;
if (!getRef()
.equals(other.getRef())) return false;
if (!getAlt()
.equals(other.getAlt())) return false;
if (!getInfo()
.equals(other.getInfo())) 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) + VCF_VERSION_FIELD_NUMBER;
hash = (53 * hash) + getVcfVersion().hashCode();
hash = (37 * hash) + GENOME_ASSEMBLY_FIELD_NUMBER;
hash = (53 * hash) + getGenomeAssembly().hashCode();
hash = (37 * hash) + ID_FIELD_NUMBER;
hash = (53 * hash) + getId().hashCode();
hash = (37 * hash) + CHR_FIELD_NUMBER;
hash = (53 * hash) + getChr().hashCode();
hash = (37 * hash) + POS_FIELD_NUMBER;
hash = (53 * hash) + getPos();
hash = (37 * hash) + REF_FIELD_NUMBER;
hash = (53 * hash) + getRef().hashCode();
hash = (37 * hash) + ALT_FIELD_NUMBER;
hash = (53 * hash) + getAlt().hashCode();
hash = (37 * hash) + INFO_FIELD_NUMBER;
hash = (53 * hash) + getInfo().hashCode();
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.phenopackets.schema.v1.core.VcfAllele parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.VcfAllele 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.VcfAllele parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.VcfAllele 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.VcfAllele parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.VcfAllele 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.VcfAllele parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.VcfAllele parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
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public static org.phenopackets.schema.v1.core.VcfAllele parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.VcfAllele parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.phenopackets.schema.v1.core.VcfAllele parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.phenopackets.schema.v1.core.VcfAllele parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
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();
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public static Builder newBuilder(org.phenopackets.schema.v1.core.VcfAllele 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;
}
/**
*
* A single VCF allele.
* For structural variation the INFO field should contain the relevant information e.g.
* END=43500;SVTYPE=DUP;CHR2=1;SVLEN=29000;
* See https://samtools.github.io/hts-specs/VCFv4.3.pdf
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.VcfAllele}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.core.VcfAllele)
org.phenopackets.schema.v1.core.VcfAlleleOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_VcfAllele_descriptor;
}
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private Builder() {
maybeForceBuilderInitialization();
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private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
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maybeForceBuilderInitialization();
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private void maybeForceBuilderInitialization() {
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@java.lang.Override
public Builder clear() {
super.clear();
vcfVersion_ = "";
genomeAssembly_ = "";
id_ = "";
chr_ = "";
pos_ = 0;
ref_ = "";
alt_ = "";
info_ = "";
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_VcfAllele_descriptor;
}
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public org.phenopackets.schema.v1.core.VcfAllele getDefaultInstanceForType() {
return org.phenopackets.schema.v1.core.VcfAllele.getDefaultInstance();
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@java.lang.Override
public org.phenopackets.schema.v1.core.VcfAllele build() {
org.phenopackets.schema.v1.core.VcfAllele result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.VcfAllele buildPartial() {
org.phenopackets.schema.v1.core.VcfAllele result = new org.phenopackets.schema.v1.core.VcfAllele(this);
result.vcfVersion_ = vcfVersion_;
result.genomeAssembly_ = genomeAssembly_;
result.id_ = id_;
result.chr_ = chr_;
result.pos_ = pos_;
result.ref_ = ref_;
result.alt_ = alt_;
result.info_ = info_;
onBuilt();
return result;
}
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com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
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com.google.protobuf.Descriptors.FieldDescriptor field) {
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com.google.protobuf.Descriptors.OneofDescriptor oneof) {
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com.google.protobuf.Descriptors.FieldDescriptor field,
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@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
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@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.phenopackets.schema.v1.core.VcfAllele) {
return mergeFrom((org.phenopackets.schema.v1.core.VcfAllele)other);
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return this;
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}
public Builder mergeFrom(org.phenopackets.schema.v1.core.VcfAllele other) {
if (other == org.phenopackets.schema.v1.core.VcfAllele.getDefaultInstance()) return this;
if (!other.getVcfVersion().isEmpty()) {
vcfVersion_ = other.vcfVersion_;
onChanged();
}
if (!other.getGenomeAssembly().isEmpty()) {
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onChanged();
}
if (!other.getId().isEmpty()) {
id_ = other.id_;
onChanged();
}
if (!other.getChr().isEmpty()) {
chr_ = other.chr_;
onChanged();
}
if (other.getPos() != 0) {
setPos(other.getPos());
}
if (!other.getRef().isEmpty()) {
ref_ = other.ref_;
onChanged();
}
if (!other.getAlt().isEmpty()) {
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onChanged();
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onChanged();
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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.VcfAllele parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.phenopackets.schema.v1.core.VcfAllele) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
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mergeFrom(parsedMessage);
}
}
return this;
}
private java.lang.Object vcfVersion_ = "";
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public java.lang.String getVcfVersion() {
java.lang.Object ref = vcfVersion_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
vcfVersion_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public com.google.protobuf.ByteString
getVcfVersionBytes() {
java.lang.Object ref = vcfVersion_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
vcfVersion_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public Builder setVcfVersion(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
vcfVersion_ = value;
onChanged();
return this;
}
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public Builder clearVcfVersion() {
vcfVersion_ = getDefaultInstance().getVcfVersion();
onChanged();
return this;
}
/**
*
* The value of the VCF spec fileformat field: e.g VCFv4.1, VCFv4.2, VCFv4.3
*
*
* string vcf_version = 1;
*/
public Builder setVcfVersionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
vcfVersion_ = value;
onChanged();
return this;
}
private java.lang.Object genomeAssembly_ = "";
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public java.lang.String getGenomeAssembly() {
java.lang.Object ref = genomeAssembly_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
genomeAssembly_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public com.google.protobuf.ByteString
getGenomeAssemblyBytes() {
java.lang.Object ref = genomeAssembly_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
genomeAssembly_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public Builder setGenomeAssembly(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
genomeAssembly_ = value;
onChanged();
return this;
}
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public Builder clearGenomeAssembly() {
genomeAssembly_ = getDefaultInstance().getGenomeAssembly();
onChanged();
return this;
}
/**
*
* Genome assembly the allele was called against. We recommend using the Genome Reference Consortium
* nomenclature e.g. GRCh37, GRCh38
*
*
* string genome_assembly = 2;
*/
public Builder setGenomeAssemblyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
genomeAssembly_ = value;
onChanged();
return this;
}
private java.lang.Object id_ = "";
/**
* string id = 3;
*/
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;
}
}
/**
* string id = 3;
*/
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;
}
}
/**
* string id = 3;
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
* string id = 3;
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
* string id = 3;
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
private java.lang.Object chr_ = "";
/**
* string chr = 4;
*/
public java.lang.String getChr() {
java.lang.Object ref = chr_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
chr_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string chr = 4;
*/
public com.google.protobuf.ByteString
getChrBytes() {
java.lang.Object ref = chr_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chr_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string chr = 4;
*/
public Builder setChr(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
chr_ = value;
onChanged();
return this;
}
/**
* string chr = 4;
*/
public Builder clearChr() {
chr_ = getDefaultInstance().getChr();
onChanged();
return this;
}
/**
* string chr = 4;
*/
public Builder setChrBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
chr_ = value;
onChanged();
return this;
}
private int pos_ ;
/**
* int32 pos = 5;
*/
public int getPos() {
return pos_;
}
/**
* int32 pos = 5;
*/
public Builder setPos(int value) {
pos_ = value;
onChanged();
return this;
}
/**
* int32 pos = 5;
*/
public Builder clearPos() {
pos_ = 0;
onChanged();
return this;
}
private java.lang.Object ref_ = "";
/**
* string ref = 6;
*/
public java.lang.String getRef() {
java.lang.Object ref = ref_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
ref_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string ref = 6;
*/
public com.google.protobuf.ByteString
getRefBytes() {
java.lang.Object ref = ref_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ref_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string ref = 6;
*/
public Builder setRef(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ref_ = value;
onChanged();
return this;
}
/**
* string ref = 6;
*/
public Builder clearRef() {
ref_ = getDefaultInstance().getRef();
onChanged();
return this;
}
/**
* string ref = 6;
*/
public Builder setRefBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ref_ = value;
onChanged();
return this;
}
private java.lang.Object alt_ = "";
/**
* string alt = 7;
*/
public java.lang.String getAlt() {
java.lang.Object ref = alt_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
alt_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string alt = 7;
*/
public com.google.protobuf.ByteString
getAltBytes() {
java.lang.Object ref = alt_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alt_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string alt = 7;
*/
public Builder setAlt(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
alt_ = value;
onChanged();
return this;
}
/**
* string alt = 7;
*/
public Builder clearAlt() {
alt_ = getDefaultInstance().getAlt();
onChanged();
return this;
}
/**
* string alt = 7;
*/
public Builder setAltBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
alt_ = value;
onChanged();
return this;
}
private java.lang.Object info_ = "";
/**
* string info = 8;
*/
public java.lang.String getInfo() {
java.lang.Object ref = info_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
info_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string info = 8;
*/
public com.google.protobuf.ByteString
getInfoBytes() {
java.lang.Object ref = info_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
info_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string info = 8;
*/
public Builder setInfo(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
info_ = value;
onChanged();
return this;
}
/**
* string info = 8;
*/
public Builder clearInfo() {
info_ = getDefaultInstance().getInfo();
onChanged();
return this;
}
/**
* string info = 8;
*/
public Builder setInfoBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
info_ = value;
onChanged();
return this;
}
@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.VcfAllele)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.VcfAllele)
private static final org.phenopackets.schema.v1.core.VcfAllele DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.core.VcfAllele();
}
public static org.phenopackets.schema.v1.core.VcfAllele getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public VcfAllele parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new VcfAllele(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.VcfAllele getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}