org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto Maven / Gradle / Ivy
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// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: protobuf/opencb/variant_annotation.proto
package org.opencb.biodata.models.variant.protobuf;
public final class VariantAnnotationProto {
private VariantAnnotationProto() {}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistryLite registry) {
}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistry registry) {
registerAllExtensions(
(com.google.protobuf.ExtensionRegistryLite) registry);
}
public interface ClinVarOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.ClinVar)
com.google.protobuf.MessageOrBuilder {
/**
* string accession = 1;
* @return The accession.
*/
java.lang.String getAccession();
/**
* string accession = 1;
* @return The bytes for accession.
*/
com.google.protobuf.ByteString
getAccessionBytes();
/**
* string clinical_significance = 2;
* @return The clinicalSignificance.
*/
java.lang.String getClinicalSignificance();
/**
* string clinical_significance = 2;
* @return The bytes for clinicalSignificance.
*/
com.google.protobuf.ByteString
getClinicalSignificanceBytes();
/**
* repeated string traits = 3;
* @return A list containing the traits.
*/
java.util.List
getTraitsList();
/**
* repeated string traits = 3;
* @return The count of traits.
*/
int getTraitsCount();
/**
* repeated string traits = 3;
* @param index The index of the element to return.
* @return The traits at the given index.
*/
java.lang.String getTraits(int index);
/**
* repeated string traits = 3;
* @param index The index of the value to return.
* @return The bytes of the traits at the given index.
*/
com.google.protobuf.ByteString
getTraitsBytes(int index);
/**
* repeated string geneNames = 4;
* @return A list containing the geneNames.
*/
java.util.List
getGeneNamesList();
/**
* repeated string geneNames = 4;
* @return The count of geneNames.
*/
int getGeneNamesCount();
/**
* repeated string geneNames = 4;
* @param index The index of the element to return.
* @return The geneNames at the given index.
*/
java.lang.String getGeneNames(int index);
/**
* repeated string geneNames = 4;
* @param index The index of the value to return.
* @return The bytes of the geneNames at the given index.
*/
com.google.protobuf.ByteString
getGeneNamesBytes(int index);
/**
* string review_status = 5;
* @return The reviewStatus.
*/
java.lang.String getReviewStatus();
/**
* string review_status = 5;
* @return The bytes for reviewStatus.
*/
com.google.protobuf.ByteString
getReviewStatusBytes();
}
/**
* Protobuf type {@code protobuf.opencb.ClinVar}
*/
public static final class ClinVar extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.ClinVar)
ClinVarOrBuilder {
private static final long serialVersionUID = 0L;
// Use ClinVar.newBuilder() to construct.
private ClinVar(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private ClinVar() {
accession_ = "";
clinicalSignificance_ = "";
traits_ = com.google.protobuf.LazyStringArrayList.EMPTY;
geneNames_ = com.google.protobuf.LazyStringArrayList.EMPTY;
reviewStatus_ = "";
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new ClinVar();
}
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getUnknownFields() {
return this.unknownFields;
}
private ClinVar(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
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accession_ = s;
break;
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java.lang.String s = input.readStringRequireUtf8();
clinicalSignificance_ = s;
break;
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traits_.add(s);
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mutable_bitField0_ |= 0x00000002;
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geneNames_.add(s);
break;
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case 42: {
java.lang.String s = input.readStringRequireUtf8();
reviewStatus_ = s;
break;
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} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
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if (((mutable_bitField0_ & 0x00000001) != 0)) {
traits_ = traits_.getUnmodifiableView();
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
geneNames_ = geneNames_.getUnmodifiableView();
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ClinVar_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ClinVar_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder.class);
}
public static final int ACCESSION_FIELD_NUMBER = 1;
private volatile java.lang.Object accession_;
/**
* string accession = 1;
* @return The accession.
*/
public java.lang.String getAccession() {
java.lang.Object ref = accession_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
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com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
accession_ = s;
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/**
* string accession = 1;
* @return The bytes for accession.
*/
public com.google.protobuf.ByteString
getAccessionBytes() {
java.lang.Object ref = accession_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
accession_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int CLINICAL_SIGNIFICANCE_FIELD_NUMBER = 2;
private volatile java.lang.Object clinicalSignificance_;
/**
* string clinical_significance = 2;
* @return The clinicalSignificance.
*/
public java.lang.String getClinicalSignificance() {
java.lang.Object ref = clinicalSignificance_;
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();
clinicalSignificance_ = s;
return s;
}
}
/**
* string clinical_significance = 2;
* @return The bytes for clinicalSignificance.
*/
public com.google.protobuf.ByteString
getClinicalSignificanceBytes() {
java.lang.Object ref = clinicalSignificance_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
clinicalSignificance_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int TRAITS_FIELD_NUMBER = 3;
private com.google.protobuf.LazyStringList traits_;
/**
* repeated string traits = 3;
* @return A list containing the traits.
*/
public com.google.protobuf.ProtocolStringList
getTraitsList() {
return traits_;
}
/**
* repeated string traits = 3;
* @return The count of traits.
*/
public int getTraitsCount() {
return traits_.size();
}
/**
* repeated string traits = 3;
* @param index The index of the element to return.
* @return The traits at the given index.
*/
public java.lang.String getTraits(int index) {
return traits_.get(index);
}
/**
* repeated string traits = 3;
* @param index The index of the value to return.
* @return The bytes of the traits at the given index.
*/
public com.google.protobuf.ByteString
getTraitsBytes(int index) {
return traits_.getByteString(index);
}
public static final int GENENAMES_FIELD_NUMBER = 4;
private com.google.protobuf.LazyStringList geneNames_;
/**
* repeated string geneNames = 4;
* @return A list containing the geneNames.
*/
public com.google.protobuf.ProtocolStringList
getGeneNamesList() {
return geneNames_;
}
/**
* repeated string geneNames = 4;
* @return The count of geneNames.
*/
public int getGeneNamesCount() {
return geneNames_.size();
}
/**
* repeated string geneNames = 4;
* @param index The index of the element to return.
* @return The geneNames at the given index.
*/
public java.lang.String getGeneNames(int index) {
return geneNames_.get(index);
}
/**
* repeated string geneNames = 4;
* @param index The index of the value to return.
* @return The bytes of the geneNames at the given index.
*/
public com.google.protobuf.ByteString
getGeneNamesBytes(int index) {
return geneNames_.getByteString(index);
}
public static final int REVIEW_STATUS_FIELD_NUMBER = 5;
private volatile java.lang.Object reviewStatus_;
/**
* string review_status = 5;
* @return The reviewStatus.
*/
public java.lang.String getReviewStatus() {
java.lang.Object ref = reviewStatus_;
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();
reviewStatus_ = s;
return s;
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}
/**
* string review_status = 5;
* @return The bytes for reviewStatus.
*/
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getReviewStatusBytes() {
java.lang.Object ref = reviewStatus_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
reviewStatus_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
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@java.lang.Override
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byte isInitialized = memoizedIsInitialized;
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memoizedIsInitialized = 1;
return true;
}
@java.lang.Override
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if (!getAccessionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, accession_);
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if (!getClinicalSignificanceBytes().isEmpty()) {
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for (int i = 0; i < traits_.size(); i++) {
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if (!getReviewStatusBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, reviewStatus_);
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unknownFields.writeTo(output);
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if (obj == this) {
return true;
}
if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar) obj;
if (!getAccession()
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if (!getClinicalSignificance()
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if (!getTraitsList()
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if (!getGeneNamesList()
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if (!getReviewStatus()
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hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + ACCESSION_FIELD_NUMBER;
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
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@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code protobuf.opencb.ClinVar}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.ClinVar)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ClinVar_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ClinVar_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder.class);
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private Builder() {
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clinicalSignificance_ = "";
traits_ = com.google.protobuf.LazyStringArrayList.EMPTY;
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geneNames_ = com.google.protobuf.LazyStringArrayList.EMPTY;
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reviewStatus_ = "";
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar result = buildPartial();
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throw newUninitializedMessageException(result);
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return result;
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return this;
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public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.getDefaultInstance()) return this;
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onChanged();
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onChanged();
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
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java.lang.String value) {
if (value == null) {
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clinicalSignificance_ = value;
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onChanged();
return this;
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com.google.protobuf.ByteString value) {
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clinicalSignificance_ = value;
onChanged();
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traits_.set(index, value);
onChanged();
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java.lang.String value) {
if (value == null) {
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ensureTraitsIsMutable();
traits_.add(value);
onChanged();
return this;
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java.lang.Iterable values) {
ensureTraitsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, traits_);
onChanged();
return this;
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traits_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
return this;
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/**
* repeated string traits = 3;
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com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
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checkByteStringIsUtf8(value);
ensureTraitsIsMutable();
traits_.add(value);
onChanged();
return this;
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ensureGeneNamesIsMutable();
geneNames_.set(index, value);
onChanged();
return this;
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*/
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java.lang.String value) {
if (value == null) {
throw new NullPointerException();
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ensureGeneNamesIsMutable();
geneNames_.add(value);
onChanged();
return this;
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*/
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java.lang.Iterable values) {
ensureGeneNamesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, geneNames_);
onChanged();
return this;
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bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
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com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
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checkByteStringIsUtf8(value);
ensureGeneNamesIsMutable();
geneNames_.add(value);
onChanged();
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
reviewStatus_ = s;
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java.lang.Object ref = reviewStatus_;
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com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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java.lang.String value) {
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reviewStatus_ = getDefaultInstance().getReviewStatus();
onChanged();
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com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
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checkByteStringIsUtf8(value);
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onChanged();
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public final Builder setUnknownFields(
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@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
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// @@protoc_insertion_point(builder_scope:protobuf.opencb.ClinVar)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.ClinVar)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar();
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public ClinVar parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new ClinVar(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
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java.lang.String getSnpIdCurrent();
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com.google.protobuf.ByteString
getSnpIdCurrentBytes();
/**
* repeated string traits = 2;
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*/
java.util.List
getTraitsList();
/**
* repeated string traits = 2;
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*/
int getTraitsCount();
/**
* repeated string traits = 2;
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* @return The traits at the given index.
*/
java.lang.String getTraits(int index);
/**
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* @param index The index of the value to return.
* @return The bytes of the traits at the given index.
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com.google.protobuf.ByteString
getTraitsBytes(int index);
/**
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double getRiskAlleleFrequency();
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java.lang.String getReportedGenes();
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com.google.protobuf.ByteString
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public static final class Gwas extends
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riskAlleleFrequency_ = input.readDouble();
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java.lang.String s = input.readStringRequireUtf8();
reportedGenes_ = s;
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throw new com.google.protobuf.InvalidProtocolBufferException(
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if (((mutable_bitField0_ & 0x00000001) != 0)) {
traits_ = traits_.getUnmodifiableView();
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this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
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public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Gwas_descriptor;
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com.google.protobuf.ByteString b =
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snpIdCurrent_ = b;
return b;
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public static final int TRAITS_FIELD_NUMBER = 2;
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com.google.protobuf.ByteString b =
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return PARSER.parseFrom(data);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas parseFrom(
byte[] data,
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com.google.protobuf.ByteString b =
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mutationId_ = b;
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public static final int PRIMARY_SITE_FIELD_NUMBER = 2;
private volatile java.lang.Object primarySite_;
/**
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java.lang.Object ref = primarySite_;
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return (java.lang.String) ref;
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primarySite_ = s;
return s;
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getPrimarySiteBytes() {
java.lang.Object ref = primarySite_;
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com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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primarySite_ = b;
return b;
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public static final int SITE_SUBTYPE_FIELD_NUMBER = 3;
private volatile java.lang.Object siteSubtype_;
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public java.lang.String getSiteSubtype() {
java.lang.Object ref = siteSubtype_;
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();
siteSubtype_ = s;
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* string site_subtype = 3;
* @return The bytes for siteSubtype.
*/
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getSiteSubtypeBytes() {
java.lang.Object ref = siteSubtype_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
siteSubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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public static final int PRIMARY_HISTOLOGY_FIELD_NUMBER = 4;
private volatile java.lang.Object primaryHistology_;
/**
* string primary_histology = 4;
* @return The primaryHistology.
*/
public java.lang.String getPrimaryHistology() {
java.lang.Object ref = primaryHistology_;
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();
primaryHistology_ = s;
return s;
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* string primary_histology = 4;
* @return The bytes for primaryHistology.
*/
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getPrimaryHistologyBytes() {
java.lang.Object ref = primaryHistology_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primaryHistology_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int HISTOLOGY_SUBTYPE_FIELD_NUMBER = 5;
private volatile java.lang.Object histologySubtype_;
/**
* string histology_subtype = 5;
* @return The histologySubtype.
*/
public java.lang.String getHistologySubtype() {
java.lang.Object ref = histologySubtype_;
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();
histologySubtype_ = s;
return s;
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* string histology_subtype = 5;
* @return The bytes for histologySubtype.
*/
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getHistologySubtypeBytes() {
java.lang.Object ref = histologySubtype_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
histologySubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int SAMPLE_SOURCE_FIELD_NUMBER = 6;
private volatile java.lang.Object sampleSource_;
/**
* string sample_source = 6;
* @return The sampleSource.
*/
public java.lang.String getSampleSource() {
java.lang.Object ref = sampleSource_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
sampleSource_ = s;
return s;
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/**
* string sample_source = 6;
* @return The bytes for sampleSource.
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public com.google.protobuf.ByteString
getSampleSourceBytes() {
java.lang.Object ref = sampleSource_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
sampleSource_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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public static final int TUMOUR_ORIGIN_FIELD_NUMBER = 7;
private volatile java.lang.Object tumourOrigin_;
/**
* string tumour_origin = 7;
* @return The tumourOrigin.
*/
public java.lang.String getTumourOrigin() {
java.lang.Object ref = tumourOrigin_;
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();
tumourOrigin_ = s;
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/**
* string tumour_origin = 7;
* @return The bytes for tumourOrigin.
*/
public com.google.protobuf.ByteString
getTumourOriginBytes() {
java.lang.Object ref = tumourOrigin_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
tumourOrigin_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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public static final int GENE_NAME_FIELD_NUMBER = 8;
private volatile java.lang.Object geneName_;
/**
* string gene_name = 8;
* @return The geneName.
*/
public java.lang.String getGeneName() {
java.lang.Object ref = geneName_;
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();
geneName_ = s;
return s;
}
}
/**
* string gene_name = 8;
* @return The bytes for geneName.
*/
public com.google.protobuf.ByteString
getGeneNameBytes() {
java.lang.Object ref = geneName_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
geneName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int MUTATION_SOMATIC_STATUS_FIELD_NUMBER = 9;
private volatile java.lang.Object mutationSomaticStatus_;
/**
* string mutation_somatic_status = 9;
* @return The mutationSomaticStatus.
*/
public java.lang.String getMutationSomaticStatus() {
java.lang.Object ref = mutationSomaticStatus_;
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();
mutationSomaticStatus_ = s;
return s;
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* string mutation_somatic_status = 9;
* @return The bytes for mutationSomaticStatus.
*/
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getMutationSomaticStatusBytes() {
java.lang.Object ref = mutationSomaticStatus_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
mutationSomaticStatus_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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byte isInitialized = memoizedIsInitialized;
if (isInitialized == 1) return true;
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memoizedIsInitialized = 1;
return true;
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if (!getMutationIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, mutationId_);
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if (!getPrimarySiteBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, primarySite_);
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if (!getSiteSubtypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, siteSubtype_);
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if (!getPrimaryHistologyBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, primaryHistology_);
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if (!getHistologySubtypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, histologySubtype_);
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if (!getSampleSourceBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, sampleSource_);
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if (!getTumourOriginBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, tumourOrigin_);
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if (!getGeneNameBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 8, geneName_);
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if (!getMutationSomaticStatusBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 9, mutationSomaticStatus_);
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unknownFields.writeTo(output);
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int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getMutationIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, mutationId_);
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if (!getHistologySubtypeBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, histologySubtype_);
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size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, sampleSource_);
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if (!getTumourOriginBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(7, tumourOrigin_);
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if (!getGeneNameBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(8, geneName_);
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if (!getMutationSomaticStatusBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(9, mutationSomaticStatus_);
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size += unknownFields.getSerializedSize();
memoizedSize = size;
return size;
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public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic) obj;
if (!getMutationId()
.equals(other.getMutationId())) return false;
if (!getPrimarySite()
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if (!getSiteSubtype()
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if (!getPrimaryHistology()
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if (!getHistologySubtype()
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if (!getSampleSource()
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if (!getTumourOrigin()
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if (!getGeneName()
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if (!getMutationSomaticStatus()
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if (!unknownFields.equals(other.unknownFields)) return false;
return true;
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if (memoizedHashCode != 0) {
return memoizedHashCode;
}
int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + MUTATION_ID_FIELD_NUMBER;
hash = (53 * hash) + getMutationId().hashCode();
hash = (37 * hash) + PRIMARY_SITE_FIELD_NUMBER;
hash = (53 * hash) + getPrimarySite().hashCode();
hash = (37 * hash) + SITE_SUBTYPE_FIELD_NUMBER;
hash = (53 * hash) + getSiteSubtype().hashCode();
hash = (37 * hash) + PRIMARY_HISTOLOGY_FIELD_NUMBER;
hash = (53 * hash) + getPrimaryHistology().hashCode();
hash = (37 * hash) + HISTOLOGY_SUBTYPE_FIELD_NUMBER;
hash = (53 * hash) + getHistologySubtype().hashCode();
hash = (37 * hash) + SAMPLE_SOURCE_FIELD_NUMBER;
hash = (53 * hash) + getSampleSource().hashCode();
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hash = (53 * hash) + getTumourOrigin().hashCode();
hash = (37 * hash) + GENE_NAME_FIELD_NUMBER;
hash = (53 * hash) + getGeneName().hashCode();
hash = (37 * hash) + MUTATION_SOMATIC_STATUS_FIELD_NUMBER;
hash = (53 * hash) + getMutationSomaticStatus().hashCode();
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
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}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
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@java.lang.Override
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic 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;
}
/**
* Protobuf type {@code protobuf.opencb.Cosmic}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.Cosmic)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Cosmic_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Cosmic_fieldAccessorTable
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// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
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private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
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}
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@java.lang.Override
public Builder clear() {
super.clear();
mutationId_ = "";
primarySite_ = "";
siteSubtype_ = "";
primaryHistology_ = "";
histologySubtype_ = "";
sampleSource_ = "";
tumourOrigin_ = "";
geneName_ = "";
mutationSomaticStatus_ = "";
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Cosmic_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic(this);
result.mutationId_ = mutationId_;
result.primarySite_ = primarySite_;
result.siteSubtype_ = siteSubtype_;
result.primaryHistology_ = primaryHistology_;
result.histologySubtype_ = histologySubtype_;
result.sampleSource_ = sampleSource_;
result.tumourOrigin_ = tumourOrigin_;
result.geneName_ = geneName_;
result.mutationSomaticStatus_ = mutationSomaticStatus_;
onBuilt();
return result;
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@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);
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@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
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@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
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@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
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@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
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@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic)other);
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super.mergeFrom(other);
return this;
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public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.getDefaultInstance()) return this;
if (!other.getMutationId().isEmpty()) {
mutationId_ = other.mutationId_;
onChanged();
}
if (!other.getPrimarySite().isEmpty()) {
primarySite_ = other.primarySite_;
onChanged();
}
if (!other.getSiteSubtype().isEmpty()) {
siteSubtype_ = other.siteSubtype_;
onChanged();
}
if (!other.getPrimaryHistology().isEmpty()) {
primaryHistology_ = other.primaryHistology_;
onChanged();
}
if (!other.getHistologySubtype().isEmpty()) {
histologySubtype_ = other.histologySubtype_;
onChanged();
}
if (!other.getSampleSource().isEmpty()) {
sampleSource_ = other.sampleSource_;
onChanged();
}
if (!other.getTumourOrigin().isEmpty()) {
tumourOrigin_ = other.tumourOrigin_;
onChanged();
}
if (!other.getGeneName().isEmpty()) {
geneName_ = other.geneName_;
onChanged();
}
if (!other.getMutationSomaticStatus().isEmpty()) {
mutationSomaticStatus_ = other.mutationSomaticStatus_;
onChanged();
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private java.lang.Object mutationId_ = "";
/**
* string mutation_id = 1;
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*/
public java.lang.String getMutationId() {
java.lang.Object ref = mutationId_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
mutationId_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string mutation_id = 1;
* @return The bytes for mutationId.
*/
public com.google.protobuf.ByteString
getMutationIdBytes() {
java.lang.Object ref = mutationId_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
mutationId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string mutation_id = 1;
* @param value The mutationId to set.
* @return This builder for chaining.
*/
public Builder setMutationId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
mutationId_ = value;
onChanged();
return this;
}
/**
* string mutation_id = 1;
* @return This builder for chaining.
*/
public Builder clearMutationId() {
mutationId_ = getDefaultInstance().getMutationId();
onChanged();
return this;
}
/**
* string mutation_id = 1;
* @param value The bytes for mutationId to set.
* @return This builder for chaining.
*/
public Builder setMutationIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
mutationId_ = value;
onChanged();
return this;
}
private java.lang.Object primarySite_ = "";
/**
* string primary_site = 2;
* @return The primarySite.
*/
public java.lang.String getPrimarySite() {
java.lang.Object ref = primarySite_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primarySite_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string primary_site = 2;
* @return The bytes for primarySite.
*/
public com.google.protobuf.ByteString
getPrimarySiteBytes() {
java.lang.Object ref = primarySite_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primarySite_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string primary_site = 2;
* @param value The primarySite to set.
* @return This builder for chaining.
*/
public Builder setPrimarySite(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
primarySite_ = value;
onChanged();
return this;
}
/**
* string primary_site = 2;
* @return This builder for chaining.
*/
public Builder clearPrimarySite() {
primarySite_ = getDefaultInstance().getPrimarySite();
onChanged();
return this;
}
/**
* string primary_site = 2;
* @param value The bytes for primarySite to set.
* @return This builder for chaining.
*/
public Builder setPrimarySiteBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
primarySite_ = value;
onChanged();
return this;
}
private java.lang.Object siteSubtype_ = "";
/**
* string site_subtype = 3;
* @return The siteSubtype.
*/
public java.lang.String getSiteSubtype() {
java.lang.Object ref = siteSubtype_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
siteSubtype_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string site_subtype = 3;
* @return The bytes for siteSubtype.
*/
public com.google.protobuf.ByteString
getSiteSubtypeBytes() {
java.lang.Object ref = siteSubtype_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
siteSubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string site_subtype = 3;
* @param value The siteSubtype to set.
* @return This builder for chaining.
*/
public Builder setSiteSubtype(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
siteSubtype_ = value;
onChanged();
return this;
}
/**
* string site_subtype = 3;
* @return This builder for chaining.
*/
public Builder clearSiteSubtype() {
siteSubtype_ = getDefaultInstance().getSiteSubtype();
onChanged();
return this;
}
/**
* string site_subtype = 3;
* @param value The bytes for siteSubtype to set.
* @return This builder for chaining.
*/
public Builder setSiteSubtypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
siteSubtype_ = value;
onChanged();
return this;
}
private java.lang.Object primaryHistology_ = "";
/**
* string primary_histology = 4;
* @return The primaryHistology.
*/
public java.lang.String getPrimaryHistology() {
java.lang.Object ref = primaryHistology_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primaryHistology_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string primary_histology = 4;
* @return The bytes for primaryHistology.
*/
public com.google.protobuf.ByteString
getPrimaryHistologyBytes() {
java.lang.Object ref = primaryHistology_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primaryHistology_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string primary_histology = 4;
* @param value The primaryHistology to set.
* @return This builder for chaining.
*/
public Builder setPrimaryHistology(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
primaryHistology_ = value;
onChanged();
return this;
}
/**
* string primary_histology = 4;
* @return This builder for chaining.
*/
public Builder clearPrimaryHistology() {
primaryHistology_ = getDefaultInstance().getPrimaryHistology();
onChanged();
return this;
}
/**
* string primary_histology = 4;
* @param value The bytes for primaryHistology to set.
* @return This builder for chaining.
*/
public Builder setPrimaryHistologyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
primaryHistology_ = value;
onChanged();
return this;
}
private java.lang.Object histologySubtype_ = "";
/**
* string histology_subtype = 5;
* @return The histologySubtype.
*/
public java.lang.String getHistologySubtype() {
java.lang.Object ref = histologySubtype_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
histologySubtype_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string histology_subtype = 5;
* @return The bytes for histologySubtype.
*/
public com.google.protobuf.ByteString
getHistologySubtypeBytes() {
java.lang.Object ref = histologySubtype_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
histologySubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string histology_subtype = 5;
* @param value The histologySubtype to set.
* @return This builder for chaining.
*/
public Builder setHistologySubtype(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
histologySubtype_ = value;
onChanged();
return this;
}
/**
* string histology_subtype = 5;
* @return This builder for chaining.
*/
public Builder clearHistologySubtype() {
histologySubtype_ = getDefaultInstance().getHistologySubtype();
onChanged();
return this;
}
/**
* string histology_subtype = 5;
* @param value The bytes for histologySubtype to set.
* @return This builder for chaining.
*/
public Builder setHistologySubtypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
histologySubtype_ = value;
onChanged();
return this;
}
private java.lang.Object sampleSource_ = "";
/**
* string sample_source = 6;
* @return The sampleSource.
*/
public java.lang.String getSampleSource() {
java.lang.Object ref = sampleSource_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
sampleSource_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string sample_source = 6;
* @return The bytes for sampleSource.
*/
public com.google.protobuf.ByteString
getSampleSourceBytes() {
java.lang.Object ref = sampleSource_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
sampleSource_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string sample_source = 6;
* @param value The sampleSource to set.
* @return This builder for chaining.
*/
public Builder setSampleSource(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
sampleSource_ = value;
onChanged();
return this;
}
/**
* string sample_source = 6;
* @return This builder for chaining.
*/
public Builder clearSampleSource() {
sampleSource_ = getDefaultInstance().getSampleSource();
onChanged();
return this;
}
/**
* string sample_source = 6;
* @param value The bytes for sampleSource to set.
* @return This builder for chaining.
*/
public Builder setSampleSourceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
sampleSource_ = value;
onChanged();
return this;
}
private java.lang.Object tumourOrigin_ = "";
/**
* string tumour_origin = 7;
* @return The tumourOrigin.
*/
public java.lang.String getTumourOrigin() {
java.lang.Object ref = tumourOrigin_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
tumourOrigin_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string tumour_origin = 7;
* @return The bytes for tumourOrigin.
*/
public com.google.protobuf.ByteString
getTumourOriginBytes() {
java.lang.Object ref = tumourOrigin_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
tumourOrigin_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string tumour_origin = 7;
* @param value The tumourOrigin to set.
* @return This builder for chaining.
*/
public Builder setTumourOrigin(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
tumourOrigin_ = value;
onChanged();
return this;
}
/**
* string tumour_origin = 7;
* @return This builder for chaining.
*/
public Builder clearTumourOrigin() {
tumourOrigin_ = getDefaultInstance().getTumourOrigin();
onChanged();
return this;
}
/**
* string tumour_origin = 7;
* @param value The bytes for tumourOrigin to set.
* @return This builder for chaining.
*/
public Builder setTumourOriginBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
tumourOrigin_ = value;
onChanged();
return this;
}
private java.lang.Object geneName_ = "";
/**
* string gene_name = 8;
* @return The geneName.
*/
public java.lang.String getGeneName() {
java.lang.Object ref = geneName_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
geneName_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string gene_name = 8;
* @return The bytes for geneName.
*/
public com.google.protobuf.ByteString
getGeneNameBytes() {
java.lang.Object ref = geneName_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
geneName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string gene_name = 8;
* @param value The geneName to set.
* @return This builder for chaining.
*/
public Builder setGeneName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
geneName_ = value;
onChanged();
return this;
}
/**
* string gene_name = 8;
* @return This builder for chaining.
*/
public Builder clearGeneName() {
geneName_ = getDefaultInstance().getGeneName();
onChanged();
return this;
}
/**
* string gene_name = 8;
* @param value The bytes for geneName to set.
* @return This builder for chaining.
*/
public Builder setGeneNameBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
geneName_ = value;
onChanged();
return this;
}
private java.lang.Object mutationSomaticStatus_ = "";
/**
* string mutation_somatic_status = 9;
* @return The mutationSomaticStatus.
*/
public java.lang.String getMutationSomaticStatus() {
java.lang.Object ref = mutationSomaticStatus_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
mutationSomaticStatus_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string mutation_somatic_status = 9;
* @return The bytes for mutationSomaticStatus.
*/
public com.google.protobuf.ByteString
getMutationSomaticStatusBytes() {
java.lang.Object ref = mutationSomaticStatus_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
mutationSomaticStatus_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string mutation_somatic_status = 9;
* @param value The mutationSomaticStatus to set.
* @return This builder for chaining.
*/
public Builder setMutationSomaticStatus(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
mutationSomaticStatus_ = value;
onChanged();
return this;
}
/**
* string mutation_somatic_status = 9;
* @return This builder for chaining.
*/
public Builder clearMutationSomaticStatus() {
mutationSomaticStatus_ = getDefaultInstance().getMutationSomaticStatus();
onChanged();
return this;
}
/**
* string mutation_somatic_status = 9;
* @param value The bytes for mutationSomaticStatus to set.
* @return This builder for chaining.
*/
public Builder setMutationSomaticStatusBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
mutationSomaticStatus_ = 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:protobuf.opencb.Cosmic)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.Cosmic)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Cosmic parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Cosmic(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface VariantTraitAssociationOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.VariantTraitAssociation)
com.google.protobuf.MessageOrBuilder {
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
java.util.List
getClinvarList();
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar getClinvar(int index);
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
int getClinvarCount();
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
java.util.List
getClinvarOrBuilderList();
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder getClinvarOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
java.util.List
getGwasList();
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas getGwas(int index);
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
int getGwasCount();
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
java.util.List
getGwasOrBuilderList();
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder getGwasOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
java.util.List
getCosmicList();
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getCosmic(int index);
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
int getCosmicCount();
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
java.util.List
getCosmicOrBuilderList();
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder getCosmicOrBuilder(
int index);
}
/**
* Protobuf type {@code protobuf.opencb.VariantTraitAssociation}
*/
public static final class VariantTraitAssociation extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.VariantTraitAssociation)
VariantTraitAssociationOrBuilder {
private static final long serialVersionUID = 0L;
// Use VariantTraitAssociation.newBuilder() to construct.
private VariantTraitAssociation(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private VariantTraitAssociation() {
clinvar_ = java.util.Collections.emptyList();
gwas_ = java.util.Collections.emptyList();
cosmic_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new VariantTraitAssociation();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private VariantTraitAssociation(
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: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
clinvar_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
clinvar_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.parser(), extensionRegistry));
break;
}
case 18: {
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
gwas_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
}
gwas_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.parser(), extensionRegistry));
break;
}
case 26: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
cosmic_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
cosmic_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.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)) {
clinvar_ = java.util.Collections.unmodifiableList(clinvar_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
gwas_ = java.util.Collections.unmodifiableList(gwas_);
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
cosmic_ = java.util.Collections.unmodifiableList(cosmic_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantTraitAssociation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantTraitAssociation_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.Builder.class);
}
public static final int CLINVAR_FIELD_NUMBER = 1;
private java.util.List clinvar_;
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public java.util.List getClinvarList() {
return clinvar_;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public java.util.List
getClinvarOrBuilderList() {
return clinvar_;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public int getClinvarCount() {
return clinvar_.size();
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar getClinvar(int index) {
return clinvar_.get(index);
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder getClinvarOrBuilder(
int index) {
return clinvar_.get(index);
}
public static final int GWAS_FIELD_NUMBER = 2;
private java.util.List gwas_;
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public java.util.List getGwasList() {
return gwas_;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public java.util.List
getGwasOrBuilderList() {
return gwas_;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public int getGwasCount() {
return gwas_.size();
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas getGwas(int index) {
return gwas_.get(index);
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder getGwasOrBuilder(
int index) {
return gwas_.get(index);
}
public static final int COSMIC_FIELD_NUMBER = 3;
private java.util.List cosmic_;
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public java.util.List getCosmicList() {
return cosmic_;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public java.util.List
getCosmicOrBuilderList() {
return cosmic_;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public int getCosmicCount() {
return cosmic_.size();
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getCosmic(int index) {
return cosmic_.get(index);
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder getCosmicOrBuilder(
int index) {
return cosmic_.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 {
for (int i = 0; i < clinvar_.size(); i++) {
output.writeMessage(1, clinvar_.get(i));
}
for (int i = 0; i < gwas_.size(); i++) {
output.writeMessage(2, gwas_.get(i));
}
for (int i = 0; i < cosmic_.size(); i++) {
output.writeMessage(3, cosmic_.get(i));
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
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public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation) obj;
if (!getClinvarList()
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if (!getGwasList()
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if (!getCosmicList()
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if (!unknownFields.equals(other.unknownFields)) return false;
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@java.lang.Override
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if (memoizedHashCode != 0) {
return memoizedHashCode;
}
int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
if (getClinvarCount() > 0) {
hash = (37 * hash) + CLINVAR_FIELD_NUMBER;
hash = (53 * hash) + getClinvarList().hashCode();
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hash = (53 * hash) + getGwasList().hashCode();
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if (getCosmicCount() > 0) {
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hash = (53 * hash) + getCosmicList().hashCode();
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation 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();
}
public static Builder newBuilder(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation 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;
}
/**
* Protobuf type {@code protobuf.opencb.VariantTraitAssociation}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.VariantTraitAssociation)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociationOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantTraitAssociation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantTraitAssociation_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.Builder.class);
}
// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getClinvarFieldBuilder();
getGwasFieldBuilder();
getCosmicFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
if (clinvarBuilder_ == null) {
clinvar_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
clinvarBuilder_.clear();
}
if (gwasBuilder_ == null) {
gwas_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
} else {
gwasBuilder_.clear();
}
if (cosmicBuilder_ == null) {
cosmic_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
cosmicBuilder_.clear();
}
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantTraitAssociation_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation(this);
int from_bitField0_ = bitField0_;
if (clinvarBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
clinvar_ = java.util.Collections.unmodifiableList(clinvar_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.clinvar_ = clinvar_;
} else {
result.clinvar_ = clinvarBuilder_.build();
}
if (gwasBuilder_ == null) {
if (((bitField0_ & 0x00000002) != 0)) {
gwas_ = java.util.Collections.unmodifiableList(gwas_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.gwas_ = gwas_;
} else {
result.gwas_ = gwasBuilder_.build();
}
if (cosmicBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
cosmic_ = java.util.Collections.unmodifiableList(cosmic_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.cosmic_ = cosmic_;
} else {
result.cosmic_ = cosmicBuilder_.build();
}
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
}
@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
}
@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
}
@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
}
@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
}
@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.getDefaultInstance()) return this;
if (clinvarBuilder_ == null) {
if (!other.clinvar_.isEmpty()) {
if (clinvar_.isEmpty()) {
clinvar_ = other.clinvar_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureClinvarIsMutable();
clinvar_.addAll(other.clinvar_);
}
onChanged();
}
} else {
if (!other.clinvar_.isEmpty()) {
if (clinvarBuilder_.isEmpty()) {
clinvarBuilder_.dispose();
clinvarBuilder_ = null;
clinvar_ = other.clinvar_;
bitField0_ = (bitField0_ & ~0x00000001);
clinvarBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getClinvarFieldBuilder() : null;
} else {
clinvarBuilder_.addAllMessages(other.clinvar_);
}
}
}
if (gwasBuilder_ == null) {
if (!other.gwas_.isEmpty()) {
if (gwas_.isEmpty()) {
gwas_ = other.gwas_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureGwasIsMutable();
gwas_.addAll(other.gwas_);
}
onChanged();
}
} else {
if (!other.gwas_.isEmpty()) {
if (gwasBuilder_.isEmpty()) {
gwasBuilder_.dispose();
gwasBuilder_ = null;
gwas_ = other.gwas_;
bitField0_ = (bitField0_ & ~0x00000002);
gwasBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getGwasFieldBuilder() : null;
} else {
gwasBuilder_.addAllMessages(other.gwas_);
}
}
}
if (cosmicBuilder_ == null) {
if (!other.cosmic_.isEmpty()) {
if (cosmic_.isEmpty()) {
cosmic_ = other.cosmic_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureCosmicIsMutable();
cosmic_.addAll(other.cosmic_);
}
onChanged();
}
} else {
if (!other.cosmic_.isEmpty()) {
if (cosmicBuilder_.isEmpty()) {
cosmicBuilder_.dispose();
cosmicBuilder_ = null;
cosmic_ = other.cosmic_;
bitField0_ = (bitField0_ & ~0x00000004);
cosmicBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getCosmicFieldBuilder() : null;
} else {
cosmicBuilder_.addAllMessages(other.cosmic_);
}
}
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.util.List clinvar_ =
java.util.Collections.emptyList();
private void ensureClinvarIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
clinvar_ = new java.util.ArrayList(clinvar_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder> clinvarBuilder_;
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public java.util.List getClinvarList() {
if (clinvarBuilder_ == null) {
return java.util.Collections.unmodifiableList(clinvar_);
} else {
return clinvarBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public int getClinvarCount() {
if (clinvarBuilder_ == null) {
return clinvar_.size();
} else {
return clinvarBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar getClinvar(int index) {
if (clinvarBuilder_ == null) {
return clinvar_.get(index);
} else {
return clinvarBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder setClinvar(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar value) {
if (clinvarBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureClinvarIsMutable();
clinvar_.set(index, value);
onChanged();
} else {
clinvarBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder setClinvar(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder builderForValue) {
if (clinvarBuilder_ == null) {
ensureClinvarIsMutable();
clinvar_.set(index, builderForValue.build());
onChanged();
} else {
clinvarBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder addClinvar(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar value) {
if (clinvarBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureClinvarIsMutable();
clinvar_.add(value);
onChanged();
} else {
clinvarBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder addClinvar(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar value) {
if (clinvarBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureClinvarIsMutable();
clinvar_.add(index, value);
onChanged();
} else {
clinvarBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder addClinvar(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder builderForValue) {
if (clinvarBuilder_ == null) {
ensureClinvarIsMutable();
clinvar_.add(builderForValue.build());
onChanged();
} else {
clinvarBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder addClinvar(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder builderForValue) {
if (clinvarBuilder_ == null) {
ensureClinvarIsMutable();
clinvar_.add(index, builderForValue.build());
onChanged();
} else {
clinvarBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder addAllClinvar(
java.lang.Iterable values) {
if (clinvarBuilder_ == null) {
ensureClinvarIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, clinvar_);
onChanged();
} else {
clinvarBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder clearClinvar() {
if (clinvarBuilder_ == null) {
clinvar_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
clinvarBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public Builder removeClinvar(int index) {
if (clinvarBuilder_ == null) {
ensureClinvarIsMutable();
clinvar_.remove(index);
onChanged();
} else {
clinvarBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder getClinvarBuilder(
int index) {
return getClinvarFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder getClinvarOrBuilder(
int index) {
if (clinvarBuilder_ == null) {
return clinvar_.get(index); } else {
return clinvarBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public java.util.List
getClinvarOrBuilderList() {
if (clinvarBuilder_ != null) {
return clinvarBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(clinvar_);
}
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder addClinvarBuilder() {
return getClinvarFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder addClinvarBuilder(
int index) {
return getClinvarFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ClinVar clinvar = 1;
*/
public java.util.List
getClinvarBuilderList() {
return getClinvarFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder>
getClinvarFieldBuilder() {
if (clinvarBuilder_ == null) {
clinvarBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVar.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ClinVarOrBuilder>(
clinvar_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
clinvar_ = null;
}
return clinvarBuilder_;
}
private java.util.List gwas_ =
java.util.Collections.emptyList();
private void ensureGwasIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
gwas_ = new java.util.ArrayList(gwas_);
bitField0_ |= 0x00000002;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder> gwasBuilder_;
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public java.util.List getGwasList() {
if (gwasBuilder_ == null) {
return java.util.Collections.unmodifiableList(gwas_);
} else {
return gwasBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public int getGwasCount() {
if (gwasBuilder_ == null) {
return gwas_.size();
} else {
return gwasBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas getGwas(int index) {
if (gwasBuilder_ == null) {
return gwas_.get(index);
} else {
return gwasBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder setGwas(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas value) {
if (gwasBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGwasIsMutable();
gwas_.set(index, value);
onChanged();
} else {
gwasBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder setGwas(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder builderForValue) {
if (gwasBuilder_ == null) {
ensureGwasIsMutable();
gwas_.set(index, builderForValue.build());
onChanged();
} else {
gwasBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder addGwas(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas value) {
if (gwasBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGwasIsMutable();
gwas_.add(value);
onChanged();
} else {
gwasBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder addGwas(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas value) {
if (gwasBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGwasIsMutable();
gwas_.add(index, value);
onChanged();
} else {
gwasBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder addGwas(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder builderForValue) {
if (gwasBuilder_ == null) {
ensureGwasIsMutable();
gwas_.add(builderForValue.build());
onChanged();
} else {
gwasBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder addGwas(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder builderForValue) {
if (gwasBuilder_ == null) {
ensureGwasIsMutable();
gwas_.add(index, builderForValue.build());
onChanged();
} else {
gwasBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder addAllGwas(
java.lang.Iterable values) {
if (gwasBuilder_ == null) {
ensureGwasIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, gwas_);
onChanged();
} else {
gwasBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder clearGwas() {
if (gwasBuilder_ == null) {
gwas_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
} else {
gwasBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public Builder removeGwas(int index) {
if (gwasBuilder_ == null) {
ensureGwasIsMutable();
gwas_.remove(index);
onChanged();
} else {
gwasBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder getGwasBuilder(
int index) {
return getGwasFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder getGwasOrBuilder(
int index) {
if (gwasBuilder_ == null) {
return gwas_.get(index); } else {
return gwasBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public java.util.List
getGwasOrBuilderList() {
if (gwasBuilder_ != null) {
return gwasBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(gwas_);
}
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder addGwasBuilder() {
return getGwasFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder addGwasBuilder(
int index) {
return getGwasFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Gwas gwas = 2;
*/
public java.util.List
getGwasBuilderList() {
return getGwasFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder>
getGwasFieldBuilder() {
if (gwasBuilder_ == null) {
gwasBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Gwas.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.GwasOrBuilder>(
gwas_,
((bitField0_ & 0x00000002) != 0),
getParentForChildren(),
isClean());
gwas_ = null;
}
return gwasBuilder_;
}
private java.util.List cosmic_ =
java.util.Collections.emptyList();
private void ensureCosmicIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
cosmic_ = new java.util.ArrayList(cosmic_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder> cosmicBuilder_;
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public java.util.List getCosmicList() {
if (cosmicBuilder_ == null) {
return java.util.Collections.unmodifiableList(cosmic_);
} else {
return cosmicBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public int getCosmicCount() {
if (cosmicBuilder_ == null) {
return cosmic_.size();
} else {
return cosmicBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic getCosmic(int index) {
if (cosmicBuilder_ == null) {
return cosmic_.get(index);
} else {
return cosmicBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder setCosmic(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic value) {
if (cosmicBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureCosmicIsMutable();
cosmic_.set(index, value);
onChanged();
} else {
cosmicBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder setCosmic(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder builderForValue) {
if (cosmicBuilder_ == null) {
ensureCosmicIsMutable();
cosmic_.set(index, builderForValue.build());
onChanged();
} else {
cosmicBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder addCosmic(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic value) {
if (cosmicBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureCosmicIsMutable();
cosmic_.add(value);
onChanged();
} else {
cosmicBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder addCosmic(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic value) {
if (cosmicBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureCosmicIsMutable();
cosmic_.add(index, value);
onChanged();
} else {
cosmicBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder addCosmic(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder builderForValue) {
if (cosmicBuilder_ == null) {
ensureCosmicIsMutable();
cosmic_.add(builderForValue.build());
onChanged();
} else {
cosmicBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder addCosmic(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder builderForValue) {
if (cosmicBuilder_ == null) {
ensureCosmicIsMutable();
cosmic_.add(index, builderForValue.build());
onChanged();
} else {
cosmicBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder addAllCosmic(
java.lang.Iterable values) {
if (cosmicBuilder_ == null) {
ensureCosmicIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, cosmic_);
onChanged();
} else {
cosmicBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder clearCosmic() {
if (cosmicBuilder_ == null) {
cosmic_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
cosmicBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public Builder removeCosmic(int index) {
if (cosmicBuilder_ == null) {
ensureCosmicIsMutable();
cosmic_.remove(index);
onChanged();
} else {
cosmicBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder getCosmicBuilder(
int index) {
return getCosmicFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder getCosmicOrBuilder(
int index) {
if (cosmicBuilder_ == null) {
return cosmic_.get(index); } else {
return cosmicBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public java.util.List
getCosmicOrBuilderList() {
if (cosmicBuilder_ != null) {
return cosmicBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(cosmic_);
}
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder addCosmicBuilder() {
return getCosmicFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder addCosmicBuilder(
int index) {
return getCosmicFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Cosmic cosmic = 3;
*/
public java.util.List
getCosmicBuilderList() {
return getCosmicFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder>
getCosmicFieldBuilder() {
if (cosmicBuilder_ == null) {
cosmicBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cosmic.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CosmicOrBuilder>(
cosmic_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
cosmic_ = null;
}
return cosmicBuilder_;
}
@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:protobuf.opencb.VariantTraitAssociation)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.VariantTraitAssociation)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public VariantTraitAssociation parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new VariantTraitAssociation(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface PopulationFrequencyOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.PopulationFrequency)
com.google.protobuf.MessageOrBuilder {
/**
* string study = 1;
* @return The study.
*/
java.lang.String getStudy();
/**
* string study = 1;
* @return The bytes for study.
*/
com.google.protobuf.ByteString
getStudyBytes();
/**
* string population = 2;
* @return The population.
*/
java.lang.String getPopulation();
/**
* string population = 2;
* @return The bytes for population.
*/
com.google.protobuf.ByteString
getPopulationBytes();
/**
* string ref_allele = 3;
* @return The refAllele.
*/
java.lang.String getRefAllele();
/**
* string ref_allele = 3;
* @return The bytes for refAllele.
*/
com.google.protobuf.ByteString
getRefAlleleBytes();
/**
* string alt_allele = 4;
* @return The altAllele.
*/
java.lang.String getAltAllele();
/**
* string alt_allele = 4;
* @return The bytes for altAllele.
*/
com.google.protobuf.ByteString
getAltAlleleBytes();
/**
* float ref_allele_freq = 5;
* @return The refAlleleFreq.
*/
float getRefAlleleFreq();
/**
* float alt_allele_freq = 6;
* @return The altAlleleFreq.
*/
float getAltAlleleFreq();
/**
* float ref_hom_genotype_freq = 7;
* @return The refHomGenotypeFreq.
*/
float getRefHomGenotypeFreq();
/**
* float het_genotype_freq = 8;
* @return The hetGenotypeFreq.
*/
float getHetGenotypeFreq();
/**
* float alt_hom_genotype_freq = 9;
* @return The altHomGenotypeFreq.
*/
float getAltHomGenotypeFreq();
}
/**
* Protobuf type {@code protobuf.opencb.PopulationFrequency}
*/
public static final class PopulationFrequency extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.PopulationFrequency)
PopulationFrequencyOrBuilder {
private static final long serialVersionUID = 0L;
// Use PopulationFrequency.newBuilder() to construct.
private PopulationFrequency(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private PopulationFrequency() {
study_ = "";
population_ = "";
refAllele_ = "";
altAllele_ = "";
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new PopulationFrequency();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private PopulationFrequency(
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;
while (!done) {
int tag = input.readTag();
switch (tag) {
case 0:
done = true;
break;
case 10: {
java.lang.String s = input.readStringRequireUtf8();
study_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
population_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
refAllele_ = s;
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
altAllele_ = s;
break;
}
case 45: {
refAlleleFreq_ = input.readFloat();
break;
}
case 53: {
altAlleleFreq_ = input.readFloat();
break;
}
case 61: {
refHomGenotypeFreq_ = input.readFloat();
break;
}
case 69: {
hetGenotypeFreq_ = input.readFloat();
break;
}
case 77: {
altHomGenotypeFreq_ = input.readFloat();
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 {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_PopulationFrequency_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_PopulationFrequency_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder.class);
}
public static final int STUDY_FIELD_NUMBER = 1;
private volatile java.lang.Object study_;
/**
* string study = 1;
* @return The study.
*/
public java.lang.String getStudy() {
java.lang.Object ref = study_;
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();
study_ = s;
return s;
}
}
/**
* string study = 1;
* @return The bytes for study.
*/
public com.google.protobuf.ByteString
getStudyBytes() {
java.lang.Object ref = study_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
study_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int POPULATION_FIELD_NUMBER = 2;
private volatile java.lang.Object population_;
/**
* string population = 2;
* @return The population.
*/
public java.lang.String getPopulation() {
java.lang.Object ref = population_;
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();
population_ = s;
return s;
}
}
/**
* string population = 2;
* @return The bytes for population.
*/
public com.google.protobuf.ByteString
getPopulationBytes() {
java.lang.Object ref = population_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
population_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int REF_ALLELE_FIELD_NUMBER = 3;
private volatile java.lang.Object refAllele_;
/**
* string ref_allele = 3;
* @return The refAllele.
*/
public java.lang.String getRefAllele() {
java.lang.Object ref = refAllele_;
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();
refAllele_ = s;
return s;
}
}
/**
* string ref_allele = 3;
* @return The bytes for refAllele.
*/
public com.google.protobuf.ByteString
getRefAlleleBytes() {
java.lang.Object ref = refAllele_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
refAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ALT_ALLELE_FIELD_NUMBER = 4;
private volatile java.lang.Object altAllele_;
/**
* string alt_allele = 4;
* @return The altAllele.
*/
public java.lang.String getAltAllele() {
java.lang.Object ref = altAllele_;
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();
altAllele_ = s;
return s;
}
}
/**
* string alt_allele = 4;
* @return The bytes for altAllele.
*/
public com.google.protobuf.ByteString
getAltAlleleBytes() {
java.lang.Object ref = altAllele_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
altAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int REF_ALLELE_FREQ_FIELD_NUMBER = 5;
private float refAlleleFreq_;
/**
* float ref_allele_freq = 5;
* @return The refAlleleFreq.
*/
public float getRefAlleleFreq() {
return refAlleleFreq_;
}
public static final int ALT_ALLELE_FREQ_FIELD_NUMBER = 6;
private float altAlleleFreq_;
/**
* float alt_allele_freq = 6;
* @return The altAlleleFreq.
*/
public float getAltAlleleFreq() {
return altAlleleFreq_;
}
public static final int REF_HOM_GENOTYPE_FREQ_FIELD_NUMBER = 7;
private float refHomGenotypeFreq_;
/**
* float ref_hom_genotype_freq = 7;
* @return The refHomGenotypeFreq.
*/
public float getRefHomGenotypeFreq() {
return refHomGenotypeFreq_;
}
public static final int HET_GENOTYPE_FREQ_FIELD_NUMBER = 8;
private float hetGenotypeFreq_;
/**
* float het_genotype_freq = 8;
* @return The hetGenotypeFreq.
*/
public float getHetGenotypeFreq() {
return hetGenotypeFreq_;
}
public static final int ALT_HOM_GENOTYPE_FREQ_FIELD_NUMBER = 9;
private float altHomGenotypeFreq_;
/**
* float alt_hom_genotype_freq = 9;
* @return The altHomGenotypeFreq.
*/
public float getAltHomGenotypeFreq() {
return altHomGenotypeFreq_;
}
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 (!getStudyBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, study_);
}
if (!getPopulationBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, population_);
}
if (!getRefAlleleBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, refAllele_);
}
if (!getAltAlleleBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, altAllele_);
}
if (refAlleleFreq_ != 0F) {
output.writeFloat(5, refAlleleFreq_);
}
if (altAlleleFreq_ != 0F) {
output.writeFloat(6, altAlleleFreq_);
}
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if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency)) {
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency) obj;
if (!getStudy()
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if (!getPopulation()
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if (!getRefAllele()
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if (java.lang.Float.floatToIntBits(getAltHomGenotypeFreq())
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if (!unknownFields.equals(other.unknownFields)) return false;
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@java.lang.Override
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if (memoizedHashCode != 0) {
return memoizedHashCode;
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int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + STUDY_FIELD_NUMBER;
hash = (53 * hash) + getStudy().hashCode();
hash = (37 * hash) + POPULATION_FIELD_NUMBER;
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hash = (53 * hash) + java.lang.Float.floatToIntBits(
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hash = (29 * hash) + unknownFields.hashCode();
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return hash;
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency 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;
}
/**
* Protobuf type {@code protobuf.opencb.PopulationFrequency}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.PopulationFrequency)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_PopulationFrequency_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_PopulationFrequency_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder.class);
}
// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
}
}
@java.lang.Override
public Builder clear() {
super.clear();
study_ = "";
population_ = "";
refAllele_ = "";
altAllele_ = "";
refAlleleFreq_ = 0F;
altAlleleFreq_ = 0F;
refHomGenotypeFreq_ = 0F;
hetGenotypeFreq_ = 0F;
altHomGenotypeFreq_ = 0F;
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_PopulationFrequency_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency(this);
result.study_ = study_;
result.population_ = population_;
result.refAllele_ = refAllele_;
result.altAllele_ = altAllele_;
result.refAlleleFreq_ = refAlleleFreq_;
result.altAlleleFreq_ = altAlleleFreq_;
result.refHomGenotypeFreq_ = refHomGenotypeFreq_;
result.hetGenotypeFreq_ = hetGenotypeFreq_;
result.altHomGenotypeFreq_ = altHomGenotypeFreq_;
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.getDefaultInstance()) return this;
if (!other.getStudy().isEmpty()) {
study_ = other.study_;
onChanged();
}
if (!other.getPopulation().isEmpty()) {
population_ = other.population_;
onChanged();
}
if (!other.getRefAllele().isEmpty()) {
refAllele_ = other.refAllele_;
onChanged();
}
if (!other.getAltAllele().isEmpty()) {
altAllele_ = other.altAllele_;
onChanged();
}
if (other.getRefAlleleFreq() != 0F) {
setRefAlleleFreq(other.getRefAlleleFreq());
}
if (other.getAltAlleleFreq() != 0F) {
setAltAlleleFreq(other.getAltAlleleFreq());
}
if (other.getRefHomGenotypeFreq() != 0F) {
setRefHomGenotypeFreq(other.getRefHomGenotypeFreq());
}
if (other.getHetGenotypeFreq() != 0F) {
setHetGenotypeFreq(other.getHetGenotypeFreq());
}
if (other.getAltHomGenotypeFreq() != 0F) {
setAltHomGenotypeFreq(other.getAltHomGenotypeFreq());
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private java.lang.Object study_ = "";
/**
* string study = 1;
* @return The study.
*/
public java.lang.String getStudy() {
java.lang.Object ref = study_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
study_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string study = 1;
* @return The bytes for study.
*/
public com.google.protobuf.ByteString
getStudyBytes() {
java.lang.Object ref = study_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
study_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string study = 1;
* @param value The study to set.
* @return This builder for chaining.
*/
public Builder setStudy(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
study_ = value;
onChanged();
return this;
}
/**
* string study = 1;
* @return This builder for chaining.
*/
public Builder clearStudy() {
study_ = getDefaultInstance().getStudy();
onChanged();
return this;
}
/**
* string study = 1;
* @param value The bytes for study to set.
* @return This builder for chaining.
*/
public Builder setStudyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
study_ = value;
onChanged();
return this;
}
private java.lang.Object population_ = "";
/**
* string population = 2;
* @return The population.
*/
public java.lang.String getPopulation() {
java.lang.Object ref = population_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
population_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string population = 2;
* @return The bytes for population.
*/
public com.google.protobuf.ByteString
getPopulationBytes() {
java.lang.Object ref = population_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
population_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string population = 2;
* @param value The population to set.
* @return This builder for chaining.
*/
public Builder setPopulation(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
population_ = value;
onChanged();
return this;
}
/**
* string population = 2;
* @return This builder for chaining.
*/
public Builder clearPopulation() {
population_ = getDefaultInstance().getPopulation();
onChanged();
return this;
}
/**
* string population = 2;
* @param value The bytes for population to set.
* @return This builder for chaining.
*/
public Builder setPopulationBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
population_ = value;
onChanged();
return this;
}
private java.lang.Object refAllele_ = "";
/**
* string ref_allele = 3;
* @return The refAllele.
*/
public java.lang.String getRefAllele() {
java.lang.Object ref = refAllele_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
refAllele_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string ref_allele = 3;
* @return The bytes for refAllele.
*/
public com.google.protobuf.ByteString
getRefAlleleBytes() {
java.lang.Object ref = refAllele_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
refAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string ref_allele = 3;
* @param value The refAllele to set.
* @return This builder for chaining.
*/
public Builder setRefAllele(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
refAllele_ = value;
onChanged();
return this;
}
/**
* string ref_allele = 3;
* @return This builder for chaining.
*/
public Builder clearRefAllele() {
refAllele_ = getDefaultInstance().getRefAllele();
onChanged();
return this;
}
/**
* string ref_allele = 3;
* @param value The bytes for refAllele to set.
* @return This builder for chaining.
*/
public Builder setRefAlleleBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
refAllele_ = value;
onChanged();
return this;
}
private java.lang.Object altAllele_ = "";
/**
* string alt_allele = 4;
* @return The altAllele.
*/
public java.lang.String getAltAllele() {
java.lang.Object ref = altAllele_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
altAllele_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string alt_allele = 4;
* @return The bytes for altAllele.
*/
public com.google.protobuf.ByteString
getAltAlleleBytes() {
java.lang.Object ref = altAllele_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
altAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string alt_allele = 4;
* @param value The altAllele to set.
* @return This builder for chaining.
*/
public Builder setAltAllele(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
altAllele_ = value;
onChanged();
return this;
}
/**
* string alt_allele = 4;
* @return This builder for chaining.
*/
public Builder clearAltAllele() {
altAllele_ = getDefaultInstance().getAltAllele();
onChanged();
return this;
}
/**
* string alt_allele = 4;
* @param value The bytes for altAllele to set.
* @return This builder for chaining.
*/
public Builder setAltAlleleBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
altAllele_ = value;
onChanged();
return this;
}
private float refAlleleFreq_ ;
/**
* float ref_allele_freq = 5;
* @return The refAlleleFreq.
*/
public float getRefAlleleFreq() {
return refAlleleFreq_;
}
/**
* float ref_allele_freq = 5;
* @param value The refAlleleFreq to set.
* @return This builder for chaining.
*/
public Builder setRefAlleleFreq(float value) {
refAlleleFreq_ = value;
onChanged();
return this;
}
/**
* float ref_allele_freq = 5;
* @return This builder for chaining.
*/
public Builder clearRefAlleleFreq() {
refAlleleFreq_ = 0F;
onChanged();
return this;
}
private float altAlleleFreq_ ;
/**
* float alt_allele_freq = 6;
* @return The altAlleleFreq.
*/
public float getAltAlleleFreq() {
return altAlleleFreq_;
}
/**
* float alt_allele_freq = 6;
* @param value The altAlleleFreq to set.
* @return This builder for chaining.
*/
public Builder setAltAlleleFreq(float value) {
altAlleleFreq_ = value;
onChanged();
return this;
}
/**
* float alt_allele_freq = 6;
* @return This builder for chaining.
*/
public Builder clearAltAlleleFreq() {
altAlleleFreq_ = 0F;
onChanged();
return this;
}
private float refHomGenotypeFreq_ ;
/**
* float ref_hom_genotype_freq = 7;
* @return The refHomGenotypeFreq.
*/
public float getRefHomGenotypeFreq() {
return refHomGenotypeFreq_;
}
/**
* float ref_hom_genotype_freq = 7;
* @param value The refHomGenotypeFreq to set.
* @return This builder for chaining.
*/
public Builder setRefHomGenotypeFreq(float value) {
refHomGenotypeFreq_ = value;
onChanged();
return this;
}
/**
* float ref_hom_genotype_freq = 7;
* @return This builder for chaining.
*/
public Builder clearRefHomGenotypeFreq() {
refHomGenotypeFreq_ = 0F;
onChanged();
return this;
}
private float hetGenotypeFreq_ ;
/**
* float het_genotype_freq = 8;
* @return The hetGenotypeFreq.
*/
public float getHetGenotypeFreq() {
return hetGenotypeFreq_;
}
/**
* float het_genotype_freq = 8;
* @param value The hetGenotypeFreq to set.
* @return This builder for chaining.
*/
public Builder setHetGenotypeFreq(float value) {
hetGenotypeFreq_ = value;
onChanged();
return this;
}
/**
* float het_genotype_freq = 8;
* @return This builder for chaining.
*/
public Builder clearHetGenotypeFreq() {
hetGenotypeFreq_ = 0F;
onChanged();
return this;
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score parseFrom(
com.google.protobuf.ByteString data)
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return PARSER.parseFrom(data);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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/**
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder {
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onChanged();
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source_ = value;
onChanged();
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onChanged();
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getSubstitutionScoresOrBuilder(
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* repeated string keywords = 10;
* @param index The index of the element to return.
* @return The keywords at the given index.
*/
java.lang.String getKeywords(int index);
/**
* repeated string keywords = 10;
* @param index The index of the value to return.
* @return The bytes of the keywords at the given index.
*/
com.google.protobuf.ByteString
getKeywordsBytes(int index);
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
java.util.List
getFeaturesList();
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature getFeatures(int index);
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
int getFeaturesCount();
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
java.util.List
getFeaturesOrBuilderList();
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder getFeaturesOrBuilder(
int index);
}
/**
* Protobuf type {@code protobuf.opencb.ProteinVariantAnnotation}
*/
public static final class ProteinVariantAnnotation extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.ProteinVariantAnnotation)
ProteinVariantAnnotationOrBuilder {
private static final long serialVersionUID = 0L;
// Use ProteinVariantAnnotation.newBuilder() to construct.
private ProteinVariantAnnotation(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private ProteinVariantAnnotation() {
uniprotAccession_ = "";
uniprotName_ = "";
reference_ = "";
alternate_ = "";
uniprotVariantId_ = "";
functionalDescription_ = "";
substitutionScores_ = java.util.Collections.emptyList();
keywords_ = com.google.protobuf.LazyStringArrayList.EMPTY;
features_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new ProteinVariantAnnotation();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private ProteinVariantAnnotation(
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();
uniprotAccession_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
uniprotName_ = s;
break;
}
case 24: {
position_ = input.readInt32();
break;
}
case 42: {
java.lang.String s = input.readStringRequireUtf8();
reference_ = s;
break;
}
case 50: {
java.lang.String s = input.readStringRequireUtf8();
alternate_ = s;
break;
}
case 58: {
java.lang.String s = input.readStringRequireUtf8();
uniprotVariantId_ = s;
break;
}
case 66: {
java.lang.String s = input.readStringRequireUtf8();
functionalDescription_ = s;
break;
}
case 74: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
substitutionScores_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
substitutionScores_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.parser(), extensionRegistry));
break;
}
case 82: {
java.lang.String s = input.readStringRequireUtf8();
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
keywords_ = new com.google.protobuf.LazyStringArrayList();
mutable_bitField0_ |= 0x00000002;
}
keywords_.add(s);
break;
}
case 90: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
features_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
features_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.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)) {
substitutionScores_ = java.util.Collections.unmodifiableList(substitutionScores_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
keywords_ = keywords_.getUnmodifiableView();
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
features_ = java.util.Collections.unmodifiableList(features_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ProteinVariantAnnotation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ProteinVariantAnnotation_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder.class);
}
public static final int UNIPROT_ACCESSION_FIELD_NUMBER = 1;
private volatile java.lang.Object uniprotAccession_;
/**
* string uniprot_accession = 1;
* @return The uniprotAccession.
*/
public java.lang.String getUniprotAccession() {
java.lang.Object ref = uniprotAccession_;
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();
uniprotAccession_ = s;
return s;
}
}
/**
* string uniprot_accession = 1;
* @return The bytes for uniprotAccession.
*/
public com.google.protobuf.ByteString
getUniprotAccessionBytes() {
java.lang.Object ref = uniprotAccession_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotAccession_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int UNIPROT_NAME_FIELD_NUMBER = 2;
private volatile java.lang.Object uniprotName_;
/**
* string uniprot_name = 2;
* @return The uniprotName.
*/
public java.lang.String getUniprotName() {
java.lang.Object ref = uniprotName_;
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();
uniprotName_ = s;
return s;
}
}
/**
* string uniprot_name = 2;
* @return The bytes for uniprotName.
*/
public com.google.protobuf.ByteString
getUniprotNameBytes() {
java.lang.Object ref = uniprotName_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int POSITION_FIELD_NUMBER = 3;
private int position_;
/**
* int32 position = 3;
* @return The position.
*/
public int getPosition() {
return position_;
}
public static final int REFERENCE_FIELD_NUMBER = 5;
private volatile java.lang.Object reference_;
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @return The reference.
*/
public java.lang.String getReference() {
java.lang.Object ref = reference_;
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();
reference_ = s;
return s;
}
}
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @return The bytes for reference.
*/
public com.google.protobuf.ByteString
getReferenceBytes() {
java.lang.Object ref = reference_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
reference_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ALTERNATE_FIELD_NUMBER = 6;
private volatile java.lang.Object alternate_;
/**
* string alternate = 6;
* @return The alternate.
*/
public java.lang.String getAlternate() {
java.lang.Object ref = alternate_;
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();
alternate_ = s;
return s;
}
}
/**
* string alternate = 6;
* @return The bytes for alternate.
*/
public com.google.protobuf.ByteString
getAlternateBytes() {
java.lang.Object ref = alternate_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alternate_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int UNIPROT_VARIANT_ID_FIELD_NUMBER = 7;
private volatile java.lang.Object uniprotVariantId_;
/**
* string uniprot_variant_id = 7;
* @return The uniprotVariantId.
*/
public java.lang.String getUniprotVariantId() {
java.lang.Object ref = uniprotVariantId_;
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();
uniprotVariantId_ = s;
return s;
}
}
/**
* string uniprot_variant_id = 7;
* @return The bytes for uniprotVariantId.
*/
public com.google.protobuf.ByteString
getUniprotVariantIdBytes() {
java.lang.Object ref = uniprotVariantId_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotVariantId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int FUNCTIONAL_DESCRIPTION_FIELD_NUMBER = 8;
private volatile java.lang.Object functionalDescription_;
/**
* string functional_description = 8;
* @return The functionalDescription.
*/
public java.lang.String getFunctionalDescription() {
java.lang.Object ref = functionalDescription_;
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();
functionalDescription_ = s;
return s;
}
}
/**
* string functional_description = 8;
* @return The bytes for functionalDescription.
*/
public com.google.protobuf.ByteString
getFunctionalDescriptionBytes() {
java.lang.Object ref = functionalDescription_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
functionalDescription_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int SUBSTITUTION_SCORES_FIELD_NUMBER = 9;
private java.util.List substitutionScores_;
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public java.util.List getSubstitutionScoresList() {
return substitutionScores_;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public java.util.List
getSubstitutionScoresOrBuilderList() {
return substitutionScores_;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public int getSubstitutionScoresCount() {
return substitutionScores_.size();
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getSubstitutionScores(int index) {
return substitutionScores_.get(index);
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getSubstitutionScoresOrBuilder(
int index) {
return substitutionScores_.get(index);
}
public static final int KEYWORDS_FIELD_NUMBER = 10;
private com.google.protobuf.LazyStringList keywords_;
/**
* repeated string keywords = 10;
* @return A list containing the keywords.
*/
public com.google.protobuf.ProtocolStringList
getKeywordsList() {
return keywords_;
}
/**
* repeated string keywords = 10;
* @return The count of keywords.
*/
public int getKeywordsCount() {
return keywords_.size();
}
/**
* repeated string keywords = 10;
* @param index The index of the element to return.
* @return The keywords at the given index.
*/
public java.lang.String getKeywords(int index) {
return keywords_.get(index);
}
/**
* repeated string keywords = 10;
* @param index The index of the value to return.
* @return The bytes of the keywords at the given index.
*/
public com.google.protobuf.ByteString
getKeywordsBytes(int index) {
return keywords_.getByteString(index);
}
public static final int FEATURES_FIELD_NUMBER = 11;
private java.util.List features_;
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public java.util.List getFeaturesList() {
return features_;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public java.util.List
getFeaturesOrBuilderList() {
return features_;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public int getFeaturesCount() {
return features_.size();
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature getFeatures(int index) {
return features_.get(index);
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder getFeaturesOrBuilder(
int index) {
return features_.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 (!getUniprotAccessionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, uniprotAccession_);
}
if (!getUniprotNameBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, uniprotName_);
}
if (position_ != 0) {
output.writeInt32(3, position_);
}
if (!getReferenceBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, reference_);
}
if (!getAlternateBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, alternate_);
}
if (!getUniprotVariantIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, uniprotVariantId_);
}
if (!getFunctionalDescriptionBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 8, functionalDescription_);
}
for (int i = 0; i < substitutionScores_.size(); i++) {
output.writeMessage(9, substitutionScores_.get(i));
}
for (int i = 0; i < keywords_.size(); i++) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 10, keywords_.getRaw(i));
}
for (int i = 0; i < features_.size(); i++) {
output.writeMessage(11, features_.get(i));
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getUniprotAccessionBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, uniprotAccession_);
}
if (!getUniprotNameBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, uniprotName_);
}
if (position_ != 0) {
size += com.google.protobuf.CodedOutputStream
.computeInt32Size(3, position_);
}
if (!getReferenceBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, reference_);
}
if (!getAlternateBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, alternate_);
}
if (!getUniprotVariantIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(7, uniprotVariantId_);
}
if (!getFunctionalDescriptionBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(8, functionalDescription_);
}
for (int i = 0; i < substitutionScores_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, substitutionScores_.get(i));
}
{
int dataSize = 0;
for (int i = 0; i < keywords_.size(); i++) {
dataSize += computeStringSizeNoTag(keywords_.getRaw(i));
}
size += dataSize;
size += 1 * getKeywordsList().size();
}
for (int i = 0; i < features_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(11, features_.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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation) obj;
if (!getUniprotAccession()
.equals(other.getUniprotAccession())) return false;
if (!getUniprotName()
.equals(other.getUniprotName())) return false;
if (getPosition()
!= other.getPosition()) return false;
if (!getReference()
.equals(other.getReference())) return false;
if (!getAlternate()
.equals(other.getAlternate())) return false;
if (!getUniprotVariantId()
.equals(other.getUniprotVariantId())) return false;
if (!getFunctionalDescription()
.equals(other.getFunctionalDescription())) return false;
if (!getSubstitutionScoresList()
.equals(other.getSubstitutionScoresList())) return false;
if (!getKeywordsList()
.equals(other.getKeywordsList())) return false;
if (!getFeaturesList()
.equals(other.getFeaturesList())) 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) + UNIPROT_ACCESSION_FIELD_NUMBER;
hash = (53 * hash) + getUniprotAccession().hashCode();
hash = (37 * hash) + UNIPROT_NAME_FIELD_NUMBER;
hash = (53 * hash) + getUniprotName().hashCode();
hash = (37 * hash) + POSITION_FIELD_NUMBER;
hash = (53 * hash) + getPosition();
hash = (37 * hash) + REFERENCE_FIELD_NUMBER;
hash = (53 * hash) + getReference().hashCode();
hash = (37 * hash) + ALTERNATE_FIELD_NUMBER;
hash = (53 * hash) + getAlternate().hashCode();
hash = (37 * hash) + UNIPROT_VARIANT_ID_FIELD_NUMBER;
hash = (53 * hash) + getUniprotVariantId().hashCode();
hash = (37 * hash) + FUNCTIONAL_DESCRIPTION_FIELD_NUMBER;
hash = (53 * hash) + getFunctionalDescription().hashCode();
if (getSubstitutionScoresCount() > 0) {
hash = (37 * hash) + SUBSTITUTION_SCORES_FIELD_NUMBER;
hash = (53 * hash) + getSubstitutionScoresList().hashCode();
}
if (getKeywordsCount() > 0) {
hash = (37 * hash) + KEYWORDS_FIELD_NUMBER;
hash = (53 * hash) + getKeywordsList().hashCode();
}
if (getFeaturesCount() > 0) {
hash = (37 * hash) + FEATURES_FIELD_NUMBER;
hash = (53 * hash) + getFeaturesList().hashCode();
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation 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;
}
/**
* Protobuf type {@code protobuf.opencb.ProteinVariantAnnotation}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.ProteinVariantAnnotation)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ProteinVariantAnnotation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ProteinVariantAnnotation_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder.class);
}
// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getSubstitutionScoresFieldBuilder();
getFeaturesFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
uniprotAccession_ = "";
uniprotName_ = "";
position_ = 0;
reference_ = "";
alternate_ = "";
uniprotVariantId_ = "";
functionalDescription_ = "";
if (substitutionScoresBuilder_ == null) {
substitutionScores_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
substitutionScoresBuilder_.clear();
}
keywords_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
if (featuresBuilder_ == null) {
features_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
featuresBuilder_.clear();
}
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ProteinVariantAnnotation_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation(this);
int from_bitField0_ = bitField0_;
result.uniprotAccession_ = uniprotAccession_;
result.uniprotName_ = uniprotName_;
result.position_ = position_;
result.reference_ = reference_;
result.alternate_ = alternate_;
result.uniprotVariantId_ = uniprotVariantId_;
result.functionalDescription_ = functionalDescription_;
if (substitutionScoresBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
substitutionScores_ = java.util.Collections.unmodifiableList(substitutionScores_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.substitutionScores_ = substitutionScores_;
} else {
result.substitutionScores_ = substitutionScoresBuilder_.build();
}
if (((bitField0_ & 0x00000002) != 0)) {
keywords_ = keywords_.getUnmodifiableView();
bitField0_ = (bitField0_ & ~0x00000002);
}
result.keywords_ = keywords_;
if (featuresBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
features_ = java.util.Collections.unmodifiableList(features_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.features_ = features_;
} else {
result.features_ = featuresBuilder_.build();
}
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
}
@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
}
@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
}
@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
}
@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
}
@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.getDefaultInstance()) return this;
if (!other.getUniprotAccession().isEmpty()) {
uniprotAccession_ = other.uniprotAccession_;
onChanged();
}
if (!other.getUniprotName().isEmpty()) {
uniprotName_ = other.uniprotName_;
onChanged();
}
if (other.getPosition() != 0) {
setPosition(other.getPosition());
}
if (!other.getReference().isEmpty()) {
reference_ = other.reference_;
onChanged();
}
if (!other.getAlternate().isEmpty()) {
alternate_ = other.alternate_;
onChanged();
}
if (!other.getUniprotVariantId().isEmpty()) {
uniprotVariantId_ = other.uniprotVariantId_;
onChanged();
}
if (!other.getFunctionalDescription().isEmpty()) {
functionalDescription_ = other.functionalDescription_;
onChanged();
}
if (substitutionScoresBuilder_ == null) {
if (!other.substitutionScores_.isEmpty()) {
if (substitutionScores_.isEmpty()) {
substitutionScores_ = other.substitutionScores_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureSubstitutionScoresIsMutable();
substitutionScores_.addAll(other.substitutionScores_);
}
onChanged();
}
} else {
if (!other.substitutionScores_.isEmpty()) {
if (substitutionScoresBuilder_.isEmpty()) {
substitutionScoresBuilder_.dispose();
substitutionScoresBuilder_ = null;
substitutionScores_ = other.substitutionScores_;
bitField0_ = (bitField0_ & ~0x00000001);
substitutionScoresBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getSubstitutionScoresFieldBuilder() : null;
} else {
substitutionScoresBuilder_.addAllMessages(other.substitutionScores_);
}
}
}
if (!other.keywords_.isEmpty()) {
if (keywords_.isEmpty()) {
keywords_ = other.keywords_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureKeywordsIsMutable();
keywords_.addAll(other.keywords_);
}
onChanged();
}
if (featuresBuilder_ == null) {
if (!other.features_.isEmpty()) {
if (features_.isEmpty()) {
features_ = other.features_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureFeaturesIsMutable();
features_.addAll(other.features_);
}
onChanged();
}
} else {
if (!other.features_.isEmpty()) {
if (featuresBuilder_.isEmpty()) {
featuresBuilder_.dispose();
featuresBuilder_ = null;
features_ = other.features_;
bitField0_ = (bitField0_ & ~0x00000004);
featuresBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getFeaturesFieldBuilder() : null;
} else {
featuresBuilder_.addAllMessages(other.features_);
}
}
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object uniprotAccession_ = "";
/**
* string uniprot_accession = 1;
* @return The uniprotAccession.
*/
public java.lang.String getUniprotAccession() {
java.lang.Object ref = uniprotAccession_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
uniprotAccession_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string uniprot_accession = 1;
* @return The bytes for uniprotAccession.
*/
public com.google.protobuf.ByteString
getUniprotAccessionBytes() {
java.lang.Object ref = uniprotAccession_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotAccession_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string uniprot_accession = 1;
* @param value The uniprotAccession to set.
* @return This builder for chaining.
*/
public Builder setUniprotAccession(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
uniprotAccession_ = value;
onChanged();
return this;
}
/**
* string uniprot_accession = 1;
* @return This builder for chaining.
*/
public Builder clearUniprotAccession() {
uniprotAccession_ = getDefaultInstance().getUniprotAccession();
onChanged();
return this;
}
/**
* string uniprot_accession = 1;
* @param value The bytes for uniprotAccession to set.
* @return This builder for chaining.
*/
public Builder setUniprotAccessionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
uniprotAccession_ = value;
onChanged();
return this;
}
private java.lang.Object uniprotName_ = "";
/**
* string uniprot_name = 2;
* @return The uniprotName.
*/
public java.lang.String getUniprotName() {
java.lang.Object ref = uniprotName_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
uniprotName_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string uniprot_name = 2;
* @return The bytes for uniprotName.
*/
public com.google.protobuf.ByteString
getUniprotNameBytes() {
java.lang.Object ref = uniprotName_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string uniprot_name = 2;
* @param value The uniprotName to set.
* @return This builder for chaining.
*/
public Builder setUniprotName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
uniprotName_ = value;
onChanged();
return this;
}
/**
* string uniprot_name = 2;
* @return This builder for chaining.
*/
public Builder clearUniprotName() {
uniprotName_ = getDefaultInstance().getUniprotName();
onChanged();
return this;
}
/**
* string uniprot_name = 2;
* @param value The bytes for uniprotName to set.
* @return This builder for chaining.
*/
public Builder setUniprotNameBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
uniprotName_ = value;
onChanged();
return this;
}
private int position_ ;
/**
* int32 position = 3;
* @return The position.
*/
public int getPosition() {
return position_;
}
/**
* int32 position = 3;
* @param value The position to set.
* @return This builder for chaining.
*/
public Builder setPosition(int value) {
position_ = value;
onChanged();
return this;
}
/**
* int32 position = 3;
* @return This builder for chaining.
*/
public Builder clearPosition() {
position_ = 0;
onChanged();
return this;
}
private java.lang.Object reference_ = "";
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @return The reference.
*/
public java.lang.String getReference() {
java.lang.Object ref = reference_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
reference_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @return The bytes for reference.
*/
public com.google.protobuf.ByteString
getReferenceBytes() {
java.lang.Object ref = reference_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
reference_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @param value The reference to set.
* @return This builder for chaining.
*/
public Builder setReference(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
reference_ = value;
onChanged();
return this;
}
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @return This builder for chaining.
*/
public Builder clearReference() {
reference_ = getDefaultInstance().getReference();
onChanged();
return this;
}
/**
*
*string aaChange = 4;
*
*
* string reference = 5;
* @param value The bytes for reference to set.
* @return This builder for chaining.
*/
public Builder setReferenceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
reference_ = value;
onChanged();
return this;
}
private java.lang.Object alternate_ = "";
/**
* string alternate = 6;
* @return The alternate.
*/
public java.lang.String getAlternate() {
java.lang.Object ref = alternate_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
alternate_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string alternate = 6;
* @return The bytes for alternate.
*/
public com.google.protobuf.ByteString
getAlternateBytes() {
java.lang.Object ref = alternate_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alternate_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string alternate = 6;
* @param value The alternate to set.
* @return This builder for chaining.
*/
public Builder setAlternate(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
alternate_ = value;
onChanged();
return this;
}
/**
* string alternate = 6;
* @return This builder for chaining.
*/
public Builder clearAlternate() {
alternate_ = getDefaultInstance().getAlternate();
onChanged();
return this;
}
/**
* string alternate = 6;
* @param value The bytes for alternate to set.
* @return This builder for chaining.
*/
public Builder setAlternateBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
alternate_ = value;
onChanged();
return this;
}
private java.lang.Object uniprotVariantId_ = "";
/**
* string uniprot_variant_id = 7;
* @return The uniprotVariantId.
*/
public java.lang.String getUniprotVariantId() {
java.lang.Object ref = uniprotVariantId_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
uniprotVariantId_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string uniprot_variant_id = 7;
* @return The bytes for uniprotVariantId.
*/
public com.google.protobuf.ByteString
getUniprotVariantIdBytes() {
java.lang.Object ref = uniprotVariantId_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
uniprotVariantId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string uniprot_variant_id = 7;
* @param value The uniprotVariantId to set.
* @return This builder for chaining.
*/
public Builder setUniprotVariantId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
uniprotVariantId_ = value;
onChanged();
return this;
}
/**
* string uniprot_variant_id = 7;
* @return This builder for chaining.
*/
public Builder clearUniprotVariantId() {
uniprotVariantId_ = getDefaultInstance().getUniprotVariantId();
onChanged();
return this;
}
/**
* string uniprot_variant_id = 7;
* @param value The bytes for uniprotVariantId to set.
* @return This builder for chaining.
*/
public Builder setUniprotVariantIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
uniprotVariantId_ = value;
onChanged();
return this;
}
private java.lang.Object functionalDescription_ = "";
/**
* string functional_description = 8;
* @return The functionalDescription.
*/
public java.lang.String getFunctionalDescription() {
java.lang.Object ref = functionalDescription_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
functionalDescription_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string functional_description = 8;
* @return The bytes for functionalDescription.
*/
public com.google.protobuf.ByteString
getFunctionalDescriptionBytes() {
java.lang.Object ref = functionalDescription_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
functionalDescription_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string functional_description = 8;
* @param value The functionalDescription to set.
* @return This builder for chaining.
*/
public Builder setFunctionalDescription(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
functionalDescription_ = value;
onChanged();
return this;
}
/**
* string functional_description = 8;
* @return This builder for chaining.
*/
public Builder clearFunctionalDescription() {
functionalDescription_ = getDefaultInstance().getFunctionalDescription();
onChanged();
return this;
}
/**
* string functional_description = 8;
* @param value The bytes for functionalDescription to set.
* @return This builder for chaining.
*/
public Builder setFunctionalDescriptionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
functionalDescription_ = value;
onChanged();
return this;
}
private java.util.List substitutionScores_ =
java.util.Collections.emptyList();
private void ensureSubstitutionScoresIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
substitutionScores_ = new java.util.ArrayList(substitutionScores_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder> substitutionScoresBuilder_;
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public java.util.List getSubstitutionScoresList() {
if (substitutionScoresBuilder_ == null) {
return java.util.Collections.unmodifiableList(substitutionScores_);
} else {
return substitutionScoresBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public int getSubstitutionScoresCount() {
if (substitutionScoresBuilder_ == null) {
return substitutionScores_.size();
} else {
return substitutionScoresBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getSubstitutionScores(int index) {
if (substitutionScoresBuilder_ == null) {
return substitutionScores_.get(index);
} else {
return substitutionScoresBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder setSubstitutionScores(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (substitutionScoresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubstitutionScoresIsMutable();
substitutionScores_.set(index, value);
onChanged();
} else {
substitutionScoresBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder setSubstitutionScores(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (substitutionScoresBuilder_ == null) {
ensureSubstitutionScoresIsMutable();
substitutionScores_.set(index, builderForValue.build());
onChanged();
} else {
substitutionScoresBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder addSubstitutionScores(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (substitutionScoresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubstitutionScoresIsMutable();
substitutionScores_.add(value);
onChanged();
} else {
substitutionScoresBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder addSubstitutionScores(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (substitutionScoresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubstitutionScoresIsMutable();
substitutionScores_.add(index, value);
onChanged();
} else {
substitutionScoresBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder addSubstitutionScores(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (substitutionScoresBuilder_ == null) {
ensureSubstitutionScoresIsMutable();
substitutionScores_.add(builderForValue.build());
onChanged();
} else {
substitutionScoresBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder addSubstitutionScores(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (substitutionScoresBuilder_ == null) {
ensureSubstitutionScoresIsMutable();
substitutionScores_.add(index, builderForValue.build());
onChanged();
} else {
substitutionScoresBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder addAllSubstitutionScores(
java.lang.Iterable values) {
if (substitutionScoresBuilder_ == null) {
ensureSubstitutionScoresIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, substitutionScores_);
onChanged();
} else {
substitutionScoresBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder clearSubstitutionScores() {
if (substitutionScoresBuilder_ == null) {
substitutionScores_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
substitutionScoresBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public Builder removeSubstitutionScores(int index) {
if (substitutionScoresBuilder_ == null) {
ensureSubstitutionScoresIsMutable();
substitutionScores_.remove(index);
onChanged();
} else {
substitutionScoresBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder getSubstitutionScoresBuilder(
int index) {
return getSubstitutionScoresFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getSubstitutionScoresOrBuilder(
int index) {
if (substitutionScoresBuilder_ == null) {
return substitutionScores_.get(index); } else {
return substitutionScoresBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public java.util.List
getSubstitutionScoresOrBuilderList() {
if (substitutionScoresBuilder_ != null) {
return substitutionScoresBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(substitutionScores_);
}
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder addSubstitutionScoresBuilder() {
return getSubstitutionScoresFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder addSubstitutionScoresBuilder(
int index) {
return getSubstitutionScoresFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Score substitution_scores = 9;
*/
public java.util.List
getSubstitutionScoresBuilderList() {
return getSubstitutionScoresFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder>
getSubstitutionScoresFieldBuilder() {
if (substitutionScoresBuilder_ == null) {
substitutionScoresBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder>(
substitutionScores_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
substitutionScores_ = null;
}
return substitutionScoresBuilder_;
}
private com.google.protobuf.LazyStringList keywords_ = com.google.protobuf.LazyStringArrayList.EMPTY;
private void ensureKeywordsIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
keywords_ = new com.google.protobuf.LazyStringArrayList(keywords_);
bitField0_ |= 0x00000002;
}
}
/**
* repeated string keywords = 10;
* @return A list containing the keywords.
*/
public com.google.protobuf.ProtocolStringList
getKeywordsList() {
return keywords_.getUnmodifiableView();
}
/**
* repeated string keywords = 10;
* @return The count of keywords.
*/
public int getKeywordsCount() {
return keywords_.size();
}
/**
* repeated string keywords = 10;
* @param index The index of the element to return.
* @return The keywords at the given index.
*/
public java.lang.String getKeywords(int index) {
return keywords_.get(index);
}
/**
* repeated string keywords = 10;
* @param index The index of the value to return.
* @return The bytes of the keywords at the given index.
*/
public com.google.protobuf.ByteString
getKeywordsBytes(int index) {
return keywords_.getByteString(index);
}
/**
* repeated string keywords = 10;
* @param index The index to set the value at.
* @param value The keywords to set.
* @return This builder for chaining.
*/
public Builder setKeywords(
int index, java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureKeywordsIsMutable();
keywords_.set(index, value);
onChanged();
return this;
}
/**
* repeated string keywords = 10;
* @param value The keywords to add.
* @return This builder for chaining.
*/
public Builder addKeywords(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureKeywordsIsMutable();
keywords_.add(value);
onChanged();
return this;
}
/**
* repeated string keywords = 10;
* @param values The keywords to add.
* @return This builder for chaining.
*/
public Builder addAllKeywords(
java.lang.Iterable values) {
ensureKeywordsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, keywords_);
onChanged();
return this;
}
/**
* repeated string keywords = 10;
* @return This builder for chaining.
*/
public Builder clearKeywords() {
keywords_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
return this;
}
/**
* repeated string keywords = 10;
* @param value The bytes of the keywords to add.
* @return This builder for chaining.
*/
public Builder addKeywordsBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensureKeywordsIsMutable();
keywords_.add(value);
onChanged();
return this;
}
private java.util.List features_ =
java.util.Collections.emptyList();
private void ensureFeaturesIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
features_ = new java.util.ArrayList(features_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder> featuresBuilder_;
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public java.util.List getFeaturesList() {
if (featuresBuilder_ == null) {
return java.util.Collections.unmodifiableList(features_);
} else {
return featuresBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public int getFeaturesCount() {
if (featuresBuilder_ == null) {
return features_.size();
} else {
return featuresBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature getFeatures(int index) {
if (featuresBuilder_ == null) {
return features_.get(index);
} else {
return featuresBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder setFeatures(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature value) {
if (featuresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureFeaturesIsMutable();
features_.set(index, value);
onChanged();
} else {
featuresBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder setFeatures(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder builderForValue) {
if (featuresBuilder_ == null) {
ensureFeaturesIsMutable();
features_.set(index, builderForValue.build());
onChanged();
} else {
featuresBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder addFeatures(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature value) {
if (featuresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureFeaturesIsMutable();
features_.add(value);
onChanged();
} else {
featuresBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder addFeatures(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature value) {
if (featuresBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureFeaturesIsMutable();
features_.add(index, value);
onChanged();
} else {
featuresBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder addFeatures(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder builderForValue) {
if (featuresBuilder_ == null) {
ensureFeaturesIsMutable();
features_.add(builderForValue.build());
onChanged();
} else {
featuresBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder addFeatures(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder builderForValue) {
if (featuresBuilder_ == null) {
ensureFeaturesIsMutable();
features_.add(index, builderForValue.build());
onChanged();
} else {
featuresBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder addAllFeatures(
java.lang.Iterable values) {
if (featuresBuilder_ == null) {
ensureFeaturesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, features_);
onChanged();
} else {
featuresBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder clearFeatures() {
if (featuresBuilder_ == null) {
features_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
featuresBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public Builder removeFeatures(int index) {
if (featuresBuilder_ == null) {
ensureFeaturesIsMutable();
features_.remove(index);
onChanged();
} else {
featuresBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder getFeaturesBuilder(
int index) {
return getFeaturesFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder getFeaturesOrBuilder(
int index) {
if (featuresBuilder_ == null) {
return features_.get(index); } else {
return featuresBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public java.util.List
getFeaturesOrBuilderList() {
if (featuresBuilder_ != null) {
return featuresBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(features_);
}
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder addFeaturesBuilder() {
return getFeaturesFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder addFeaturesBuilder(
int index) {
return getFeaturesFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ProteinFeature features = 11;
*/
public java.util.List
getFeaturesBuilderList() {
return getFeaturesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder>
getFeaturesFieldBuilder() {
if (featuresBuilder_ == null) {
featuresBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeature.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinFeatureOrBuilder>(
features_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
features_ = null;
}
return featuresBuilder_;
}
@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:protobuf.opencb.ProteinVariantAnnotation)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.ProteinVariantAnnotation)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public ProteinVariantAnnotation parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new ProteinVariantAnnotation(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface ExonOverlapOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.ExonOverlap)
com.google.protobuf.MessageOrBuilder {
/**
* string number = 1;
* @return The number.
*/
java.lang.String getNumber();
/**
* string number = 1;
* @return The bytes for number.
*/
com.google.protobuf.ByteString
getNumberBytes();
/**
* float percentage = 2;
* @return The percentage.
*/
float getPercentage();
}
/**
* Protobuf type {@code protobuf.opencb.ExonOverlap}
*/
public static final class ExonOverlap extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.ExonOverlap)
ExonOverlapOrBuilder {
private static final long serialVersionUID = 0L;
// Use ExonOverlap.newBuilder() to construct.
private ExonOverlap(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
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protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new ExonOverlap();
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getUnknownFields() {
return this.unknownFields;
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private ExonOverlap(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
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com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
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java.lang.String s = input.readStringRequireUtf8();
number_ = s;
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case 21: {
percentage_ = input.readFloat();
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if (!parseUnknownField(
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} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
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throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
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public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ExonOverlap_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ExonOverlap_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder.class);
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public static final int NUMBER_FIELD_NUMBER = 1;
private volatile java.lang.Object number_;
/**
* string number = 1;
* @return The number.
*/
public java.lang.String getNumber() {
java.lang.Object ref = number_;
if (ref instanceof java.lang.String) {
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
number_ = s;
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com.google.protobuf.ByteString b =
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number_ = b;
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public static final int PERCENTAGE_FIELD_NUMBER = 2;
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byte isInitialized = memoizedIsInitialized;
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memoizedIsInitialized = 1;
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throws java.io.IOException {
if (!getNumberBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, number_);
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if (percentage_ != 0F) {
output.writeFloat(2, percentage_);
}
unknownFields.writeTo(output);
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@java.lang.Override
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int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getNumberBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, number_);
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if (percentage_ != 0F) {
size += com.google.protobuf.CodedOutputStream
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size += unknownFields.getSerializedSize();
memoizedSize = size;
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@java.lang.Override
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if (obj == this) {
return true;
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if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap)) {
return super.equals(obj);
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap) obj;
if (!getNumber()
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if (java.lang.Float.floatToIntBits(getPercentage())
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int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + NUMBER_FIELD_NUMBER;
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
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@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
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/**
* Protobuf type {@code protobuf.opencb.ExonOverlap}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.ExonOverlap)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ExonOverlap_descriptor;
}
@java.lang.Override
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// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
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private Builder(
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@java.lang.Override
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percentage_ = 0F;
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if (!result.isInitialized()) {
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result.percentage_ = percentage_;
onBuilt();
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@java.lang.Override
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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.ExtensionRegistryLite extensionRegistry)
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
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parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
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private java.lang.Object number_ = "";
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number_ = s;
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java.lang.Object ref = number_;
if (ref instanceof String) {
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* string number = 1;
* @param value The number to set.
* @return This builder for chaining.
*/
public Builder setNumber(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
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number_ = value;
onChanged();
return this;
}
/**
* string number = 1;
* @return This builder for chaining.
*/
public Builder clearNumber() {
number_ = getDefaultInstance().getNumber();
onChanged();
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* string number = 1;
* @param value The bytes for number to set.
* @return This builder for chaining.
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com.google.protobuf.ByteString value) {
if (value == null) {
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checkByteStringIsUtf8(value);
number_ = value;
onChanged();
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private float percentage_ ;
/**
* float percentage = 2;
* @return The percentage.
*/
public float getPercentage() {
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}
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* float percentage = 2;
* @param value The percentage to set.
* @return This builder for chaining.
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onChanged();
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* float percentage = 2;
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onChanged();
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@java.lang.Override
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@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.ExonOverlap)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.ExonOverlap)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public ExonOverlap parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new ExonOverlap(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface ConsequenceTypeOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.ConsequenceType)
com.google.protobuf.MessageOrBuilder {
/**
* string gene_name = 1;
* @return The geneName.
*/
java.lang.String getGeneName();
/**
* string gene_name = 1;
* @return The bytes for geneName.
*/
com.google.protobuf.ByteString
getGeneNameBytes();
/**
* string ensembl_gene_id = 2;
* @return The ensemblGeneId.
*/
java.lang.String getEnsemblGeneId();
/**
* string ensembl_gene_id = 2;
* @return The bytes for ensemblGeneId.
*/
com.google.protobuf.ByteString
getEnsemblGeneIdBytes();
/**
* string ensembl_transcript_id = 3;
* @return The ensemblTranscriptId.
*/
java.lang.String getEnsemblTranscriptId();
/**
* string ensembl_transcript_id = 3;
* @return The bytes for ensemblTranscriptId.
*/
com.google.protobuf.ByteString
getEnsemblTranscriptIdBytes();
/**
* string strand = 4;
* @return The strand.
*/
java.lang.String getStrand();
/**
* string strand = 4;
* @return The bytes for strand.
*/
com.google.protobuf.ByteString
getStrandBytes();
/**
* string biotype = 5;
* @return The biotype.
*/
java.lang.String getBiotype();
/**
* string biotype = 5;
* @return The bytes for biotype.
*/
com.google.protobuf.ByteString
getBiotypeBytes();
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
java.util.List
getExonOverlapList();
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap getExonOverlap(int index);
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
int getExonOverlapCount();
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
java.util.List
getExonOverlapOrBuilderList();
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder getExonOverlapOrBuilder(
int index);
/**
* repeated string transcript_annotation_flags = 7;
* @return A list containing the transcriptAnnotationFlags.
*/
java.util.List
getTranscriptAnnotationFlagsList();
/**
* repeated string transcript_annotation_flags = 7;
* @return The count of transcriptAnnotationFlags.
*/
int getTranscriptAnnotationFlagsCount();
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the element to return.
* @return The transcriptAnnotationFlags at the given index.
*/
java.lang.String getTranscriptAnnotationFlags(int index);
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the value to return.
* @return The bytes of the transcriptAnnotationFlags at the given index.
*/
com.google.protobuf.ByteString
getTranscriptAnnotationFlagsBytes(int index);
/**
* int32 c_dna_position = 8;
* @return The cDnaPosition.
*/
int getCDnaPosition();
/**
* int32 cds_position = 9;
* @return The cdsPosition.
*/
int getCdsPosition();
/**
* string codon = 10;
* @return The codon.
*/
java.lang.String getCodon();
/**
* string codon = 10;
* @return The bytes for codon.
*/
com.google.protobuf.ByteString
getCodonBytes();
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return Whether the proteinVariantAnnotation field is set.
*/
boolean hasProteinVariantAnnotation();
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return The proteinVariantAnnotation.
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getProteinVariantAnnotation();
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder getProteinVariantAnnotationOrBuilder();
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
java.util.List
getSequenceOntologyTermsList();
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm getSequenceOntologyTerms(int index);
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
int getSequenceOntologyTermsCount();
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
java.util.List
getSequenceOntologyTermsOrBuilderList();
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder getSequenceOntologyTermsOrBuilder(
int index);
}
/**
* Protobuf type {@code protobuf.opencb.ConsequenceType}
*/
public static final class ConsequenceType extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.ConsequenceType)
ConsequenceTypeOrBuilder {
private static final long serialVersionUID = 0L;
// Use ConsequenceType.newBuilder() to construct.
private ConsequenceType(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private ConsequenceType() {
geneName_ = "";
ensemblGeneId_ = "";
ensemblTranscriptId_ = "";
strand_ = "";
biotype_ = "";
exonOverlap_ = java.util.Collections.emptyList();
transcriptAnnotationFlags_ = com.google.protobuf.LazyStringArrayList.EMPTY;
codon_ = "";
sequenceOntologyTerms_ = java.util.Collections.emptyList();
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new ConsequenceType();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private ConsequenceType(
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();
geneName_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
ensemblGeneId_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
ensemblTranscriptId_ = s;
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
strand_ = s;
break;
}
case 42: {
java.lang.String s = input.readStringRequireUtf8();
biotype_ = s;
break;
}
case 50: {
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
exonOverlap_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
}
exonOverlap_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.parser(), extensionRegistry));
break;
}
case 58: {
java.lang.String s = input.readStringRequireUtf8();
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
transcriptAnnotationFlags_ = new com.google.protobuf.LazyStringArrayList();
mutable_bitField0_ |= 0x00000002;
}
transcriptAnnotationFlags_.add(s);
break;
}
case 64: {
cDnaPosition_ = input.readInt32();
break;
}
case 72: {
cdsPosition_ = input.readInt32();
break;
}
case 82: {
java.lang.String s = input.readStringRequireUtf8();
codon_ = s;
break;
}
case 90: {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder subBuilder = null;
if (proteinVariantAnnotation_ != null) {
subBuilder = proteinVariantAnnotation_.toBuilder();
}
proteinVariantAnnotation_ = input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(proteinVariantAnnotation_);
proteinVariantAnnotation_ = subBuilder.buildPartial();
}
break;
}
case 98: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
sequenceOntologyTerms_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
sequenceOntologyTerms_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.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)) {
exonOverlap_ = java.util.Collections.unmodifiableList(exonOverlap_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
transcriptAnnotationFlags_ = transcriptAnnotationFlags_.getUnmodifiableView();
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
sequenceOntologyTerms_ = java.util.Collections.unmodifiableList(sequenceOntologyTerms_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ConsequenceType_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ConsequenceType_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder.class);
}
public static final int GENE_NAME_FIELD_NUMBER = 1;
private volatile java.lang.Object geneName_;
/**
* string gene_name = 1;
* @return The geneName.
*/
public java.lang.String getGeneName() {
java.lang.Object ref = geneName_;
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();
geneName_ = s;
return s;
}
}
/**
* string gene_name = 1;
* @return The bytes for geneName.
*/
public com.google.protobuf.ByteString
getGeneNameBytes() {
java.lang.Object ref = geneName_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
geneName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ENSEMBL_GENE_ID_FIELD_NUMBER = 2;
private volatile java.lang.Object ensemblGeneId_;
/**
* string ensembl_gene_id = 2;
* @return The ensemblGeneId.
*/
public java.lang.String getEnsemblGeneId() {
java.lang.Object ref = ensemblGeneId_;
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();
ensemblGeneId_ = s;
return s;
}
}
/**
* string ensembl_gene_id = 2;
* @return The bytes for ensemblGeneId.
*/
public com.google.protobuf.ByteString
getEnsemblGeneIdBytes() {
java.lang.Object ref = ensemblGeneId_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ensemblGeneId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ENSEMBL_TRANSCRIPT_ID_FIELD_NUMBER = 3;
private volatile java.lang.Object ensemblTranscriptId_;
/**
* string ensembl_transcript_id = 3;
* @return The ensemblTranscriptId.
*/
public java.lang.String getEnsemblTranscriptId() {
java.lang.Object ref = ensemblTranscriptId_;
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();
ensemblTranscriptId_ = s;
return s;
}
}
/**
* string ensembl_transcript_id = 3;
* @return The bytes for ensemblTranscriptId.
*/
public com.google.protobuf.ByteString
getEnsemblTranscriptIdBytes() {
java.lang.Object ref = ensemblTranscriptId_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ensemblTranscriptId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int STRAND_FIELD_NUMBER = 4;
private volatile java.lang.Object strand_;
/**
* string strand = 4;
* @return The strand.
*/
public java.lang.String getStrand() {
java.lang.Object ref = strand_;
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();
strand_ = s;
return s;
}
}
/**
* string strand = 4;
* @return The bytes for strand.
*/
public com.google.protobuf.ByteString
getStrandBytes() {
java.lang.Object ref = strand_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
strand_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int BIOTYPE_FIELD_NUMBER = 5;
private volatile java.lang.Object biotype_;
/**
* string biotype = 5;
* @return The biotype.
*/
public java.lang.String getBiotype() {
java.lang.Object ref = biotype_;
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();
biotype_ = s;
return s;
}
}
/**
* string biotype = 5;
* @return The bytes for biotype.
*/
public com.google.protobuf.ByteString
getBiotypeBytes() {
java.lang.Object ref = biotype_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
biotype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int EXON_OVERLAP_FIELD_NUMBER = 6;
private java.util.List exonOverlap_;
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public java.util.List getExonOverlapList() {
return exonOverlap_;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public java.util.List
getExonOverlapOrBuilderList() {
return exonOverlap_;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public int getExonOverlapCount() {
return exonOverlap_.size();
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap getExonOverlap(int index) {
return exonOverlap_.get(index);
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder getExonOverlapOrBuilder(
int index) {
return exonOverlap_.get(index);
}
public static final int TRANSCRIPT_ANNOTATION_FLAGS_FIELD_NUMBER = 7;
private com.google.protobuf.LazyStringList transcriptAnnotationFlags_;
/**
* repeated string transcript_annotation_flags = 7;
* @return A list containing the transcriptAnnotationFlags.
*/
public com.google.protobuf.ProtocolStringList
getTranscriptAnnotationFlagsList() {
return transcriptAnnotationFlags_;
}
/**
* repeated string transcript_annotation_flags = 7;
* @return The count of transcriptAnnotationFlags.
*/
public int getTranscriptAnnotationFlagsCount() {
return transcriptAnnotationFlags_.size();
}
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the element to return.
* @return The transcriptAnnotationFlags at the given index.
*/
public java.lang.String getTranscriptAnnotationFlags(int index) {
return transcriptAnnotationFlags_.get(index);
}
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the value to return.
* @return The bytes of the transcriptAnnotationFlags at the given index.
*/
public com.google.protobuf.ByteString
getTranscriptAnnotationFlagsBytes(int index) {
return transcriptAnnotationFlags_.getByteString(index);
}
public static final int C_DNA_POSITION_FIELD_NUMBER = 8;
private int cDnaPosition_;
/**
* int32 c_dna_position = 8;
* @return The cDnaPosition.
*/
public int getCDnaPosition() {
return cDnaPosition_;
}
public static final int CDS_POSITION_FIELD_NUMBER = 9;
private int cdsPosition_;
/**
* int32 cds_position = 9;
* @return The cdsPosition.
*/
public int getCdsPosition() {
return cdsPosition_;
}
public static final int CODON_FIELD_NUMBER = 10;
private volatile java.lang.Object codon_;
/**
* string codon = 10;
* @return The codon.
*/
public java.lang.String getCodon() {
java.lang.Object ref = codon_;
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();
codon_ = s;
return s;
}
}
/**
* string codon = 10;
* @return The bytes for codon.
*/
public com.google.protobuf.ByteString
getCodonBytes() {
java.lang.Object ref = codon_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
codon_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int PROTEIN_VARIANT_ANNOTATION_FIELD_NUMBER = 11;
private org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation proteinVariantAnnotation_;
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return Whether the proteinVariantAnnotation field is set.
*/
public boolean hasProteinVariantAnnotation() {
return proteinVariantAnnotation_ != null;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return The proteinVariantAnnotation.
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getProteinVariantAnnotation() {
return proteinVariantAnnotation_ == null ? org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.getDefaultInstance() : proteinVariantAnnotation_;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder getProteinVariantAnnotationOrBuilder() {
return getProteinVariantAnnotation();
}
public static final int SEQUENCE_ONTOLOGY_TERMS_FIELD_NUMBER = 12;
private java.util.List sequenceOntologyTerms_;
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public java.util.List getSequenceOntologyTermsList() {
return sequenceOntologyTerms_;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public java.util.List
getSequenceOntologyTermsOrBuilderList() {
return sequenceOntologyTerms_;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public int getSequenceOntologyTermsCount() {
return sequenceOntologyTerms_.size();
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm getSequenceOntologyTerms(int index) {
return sequenceOntologyTerms_.get(index);
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder getSequenceOntologyTermsOrBuilder(
int index) {
return sequenceOntologyTerms_.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 (!getGeneNameBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, geneName_);
}
if (!getEnsemblGeneIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, ensemblGeneId_);
}
if (!getEnsemblTranscriptIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, ensemblTranscriptId_);
}
if (!getStrandBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, strand_);
}
if (!getBiotypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, biotype_);
}
for (int i = 0; i < exonOverlap_.size(); i++) {
output.writeMessage(6, exonOverlap_.get(i));
}
for (int i = 0; i < transcriptAnnotationFlags_.size(); i++) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, transcriptAnnotationFlags_.getRaw(i));
}
if (cDnaPosition_ != 0) {
output.writeInt32(8, cDnaPosition_);
}
if (cdsPosition_ != 0) {
output.writeInt32(9, cdsPosition_);
}
if (!getCodonBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 10, codon_);
}
if (proteinVariantAnnotation_ != null) {
output.writeMessage(11, getProteinVariantAnnotation());
}
for (int i = 0; i < sequenceOntologyTerms_.size(); i++) {
output.writeMessage(12, sequenceOntologyTerms_.get(i));
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getGeneNameBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, geneName_);
}
if (!getEnsemblGeneIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, ensemblGeneId_);
}
if (!getEnsemblTranscriptIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(3, ensemblTranscriptId_);
}
if (!getStrandBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(4, strand_);
}
if (!getBiotypeBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, biotype_);
}
for (int i = 0; i < exonOverlap_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(6, exonOverlap_.get(i));
}
{
int dataSize = 0;
for (int i = 0; i < transcriptAnnotationFlags_.size(); i++) {
dataSize += computeStringSizeNoTag(transcriptAnnotationFlags_.getRaw(i));
}
size += dataSize;
size += 1 * getTranscriptAnnotationFlagsList().size();
}
if (cDnaPosition_ != 0) {
size += com.google.protobuf.CodedOutputStream
.computeInt32Size(8, cDnaPosition_);
}
if (cdsPosition_ != 0) {
size += com.google.protobuf.CodedOutputStream
.computeInt32Size(9, cdsPosition_);
}
if (!getCodonBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(10, codon_);
}
if (proteinVariantAnnotation_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(11, getProteinVariantAnnotation());
}
for (int i = 0; i < sequenceOntologyTerms_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(12, sequenceOntologyTerms_.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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType) obj;
if (!getGeneName()
.equals(other.getGeneName())) return false;
if (!getEnsemblGeneId()
.equals(other.getEnsemblGeneId())) return false;
if (!getEnsemblTranscriptId()
.equals(other.getEnsemblTranscriptId())) return false;
if (!getStrand()
.equals(other.getStrand())) return false;
if (!getBiotype()
.equals(other.getBiotype())) return false;
if (!getExonOverlapList()
.equals(other.getExonOverlapList())) return false;
if (!getTranscriptAnnotationFlagsList()
.equals(other.getTranscriptAnnotationFlagsList())) return false;
if (getCDnaPosition()
!= other.getCDnaPosition()) return false;
if (getCdsPosition()
!= other.getCdsPosition()) return false;
if (!getCodon()
.equals(other.getCodon())) return false;
if (hasProteinVariantAnnotation() != other.hasProteinVariantAnnotation()) return false;
if (hasProteinVariantAnnotation()) {
if (!getProteinVariantAnnotation()
.equals(other.getProteinVariantAnnotation())) return false;
}
if (!getSequenceOntologyTermsList()
.equals(other.getSequenceOntologyTermsList())) 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) + GENE_NAME_FIELD_NUMBER;
hash = (53 * hash) + getGeneName().hashCode();
hash = (37 * hash) + ENSEMBL_GENE_ID_FIELD_NUMBER;
hash = (53 * hash) + getEnsemblGeneId().hashCode();
hash = (37 * hash) + ENSEMBL_TRANSCRIPT_ID_FIELD_NUMBER;
hash = (53 * hash) + getEnsemblTranscriptId().hashCode();
hash = (37 * hash) + STRAND_FIELD_NUMBER;
hash = (53 * hash) + getStrand().hashCode();
hash = (37 * hash) + BIOTYPE_FIELD_NUMBER;
hash = (53 * hash) + getBiotype().hashCode();
if (getExonOverlapCount() > 0) {
hash = (37 * hash) + EXON_OVERLAP_FIELD_NUMBER;
hash = (53 * hash) + getExonOverlapList().hashCode();
}
if (getTranscriptAnnotationFlagsCount() > 0) {
hash = (37 * hash) + TRANSCRIPT_ANNOTATION_FLAGS_FIELD_NUMBER;
hash = (53 * hash) + getTranscriptAnnotationFlagsList().hashCode();
}
hash = (37 * hash) + C_DNA_POSITION_FIELD_NUMBER;
hash = (53 * hash) + getCDnaPosition();
hash = (37 * hash) + CDS_POSITION_FIELD_NUMBER;
hash = (53 * hash) + getCdsPosition();
hash = (37 * hash) + CODON_FIELD_NUMBER;
hash = (53 * hash) + getCodon().hashCode();
if (hasProteinVariantAnnotation()) {
hash = (37 * hash) + PROTEIN_VARIANT_ANNOTATION_FIELD_NUMBER;
hash = (53 * hash) + getProteinVariantAnnotation().hashCode();
}
if (getSequenceOntologyTermsCount() > 0) {
hash = (37 * hash) + SEQUENCE_ONTOLOGY_TERMS_FIELD_NUMBER;
hash = (53 * hash) + getSequenceOntologyTermsList().hashCode();
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input, extensionRegistry);
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType 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;
}
/**
* Protobuf type {@code protobuf.opencb.ConsequenceType}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.ConsequenceType)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ConsequenceType_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ConsequenceType_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder.class);
}
// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
getExonOverlapFieldBuilder();
getSequenceOntologyTermsFieldBuilder();
}
}
@java.lang.Override
public Builder clear() {
super.clear();
geneName_ = "";
ensemblGeneId_ = "";
ensemblTranscriptId_ = "";
strand_ = "";
biotype_ = "";
if (exonOverlapBuilder_ == null) {
exonOverlap_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
exonOverlapBuilder_.clear();
}
transcriptAnnotationFlags_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
cDnaPosition_ = 0;
cdsPosition_ = 0;
codon_ = "";
if (proteinVariantAnnotationBuilder_ == null) {
proteinVariantAnnotation_ = null;
} else {
proteinVariantAnnotation_ = null;
proteinVariantAnnotationBuilder_ = null;
}
if (sequenceOntologyTermsBuilder_ == null) {
sequenceOntologyTerms_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
sequenceOntologyTermsBuilder_.clear();
}
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_ConsequenceType_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType(this);
int from_bitField0_ = bitField0_;
result.geneName_ = geneName_;
result.ensemblGeneId_ = ensemblGeneId_;
result.ensemblTranscriptId_ = ensemblTranscriptId_;
result.strand_ = strand_;
result.biotype_ = biotype_;
if (exonOverlapBuilder_ == null) {
if (((bitField0_ & 0x00000001) != 0)) {
exonOverlap_ = java.util.Collections.unmodifiableList(exonOverlap_);
bitField0_ = (bitField0_ & ~0x00000001);
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result.exonOverlap_ = exonOverlap_;
} else {
result.exonOverlap_ = exonOverlapBuilder_.build();
}
if (((bitField0_ & 0x00000002) != 0)) {
transcriptAnnotationFlags_ = transcriptAnnotationFlags_.getUnmodifiableView();
bitField0_ = (bitField0_ & ~0x00000002);
}
result.transcriptAnnotationFlags_ = transcriptAnnotationFlags_;
result.cDnaPosition_ = cDnaPosition_;
result.cdsPosition_ = cdsPosition_;
result.codon_ = codon_;
if (proteinVariantAnnotationBuilder_ == null) {
result.proteinVariantAnnotation_ = proteinVariantAnnotation_;
} else {
result.proteinVariantAnnotation_ = proteinVariantAnnotationBuilder_.build();
}
if (sequenceOntologyTermsBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
sequenceOntologyTerms_ = java.util.Collections.unmodifiableList(sequenceOntologyTerms_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.sequenceOntologyTerms_ = sequenceOntologyTerms_;
} else {
result.sequenceOntologyTerms_ = sequenceOntologyTermsBuilder_.build();
}
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
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@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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.getDefaultInstance()) return this;
if (!other.getGeneName().isEmpty()) {
geneName_ = other.geneName_;
onChanged();
}
if (!other.getEnsemblGeneId().isEmpty()) {
ensemblGeneId_ = other.ensemblGeneId_;
onChanged();
}
if (!other.getEnsemblTranscriptId().isEmpty()) {
ensemblTranscriptId_ = other.ensemblTranscriptId_;
onChanged();
}
if (!other.getStrand().isEmpty()) {
strand_ = other.strand_;
onChanged();
}
if (!other.getBiotype().isEmpty()) {
biotype_ = other.biotype_;
onChanged();
}
if (exonOverlapBuilder_ == null) {
if (!other.exonOverlap_.isEmpty()) {
if (exonOverlap_.isEmpty()) {
exonOverlap_ = other.exonOverlap_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureExonOverlapIsMutable();
exonOverlap_.addAll(other.exonOverlap_);
}
onChanged();
}
} else {
if (!other.exonOverlap_.isEmpty()) {
if (exonOverlapBuilder_.isEmpty()) {
exonOverlapBuilder_.dispose();
exonOverlapBuilder_ = null;
exonOverlap_ = other.exonOverlap_;
bitField0_ = (bitField0_ & ~0x00000001);
exonOverlapBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
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} else {
exonOverlapBuilder_.addAllMessages(other.exonOverlap_);
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}
}
if (!other.transcriptAnnotationFlags_.isEmpty()) {
if (transcriptAnnotationFlags_.isEmpty()) {
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bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureTranscriptAnnotationFlagsIsMutable();
transcriptAnnotationFlags_.addAll(other.transcriptAnnotationFlags_);
}
onChanged();
}
if (other.getCDnaPosition() != 0) {
setCDnaPosition(other.getCDnaPosition());
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if (other.getCdsPosition() != 0) {
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if (!other.getCodon().isEmpty()) {
codon_ = other.codon_;
onChanged();
}
if (other.hasProteinVariantAnnotation()) {
mergeProteinVariantAnnotation(other.getProteinVariantAnnotation());
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if (sequenceOntologyTermsBuilder_ == null) {
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sequenceOntologyTerms_ = other.sequenceOntologyTerms_;
bitField0_ = (bitField0_ & ~0x00000004);
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sequenceOntologyTerms_.addAll(other.sequenceOntologyTerms_);
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onChanged();
}
} else {
if (!other.sequenceOntologyTerms_.isEmpty()) {
if (sequenceOntologyTermsBuilder_.isEmpty()) {
sequenceOntologyTermsBuilder_.dispose();
sequenceOntologyTermsBuilder_ = null;
sequenceOntologyTerms_ = other.sequenceOntologyTerms_;
bitField0_ = (bitField0_ & ~0x00000004);
sequenceOntologyTermsBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getSequenceOntologyTermsFieldBuilder() : null;
} else {
sequenceOntologyTermsBuilder_.addAllMessages(other.sequenceOntologyTerms_);
}
}
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object geneName_ = "";
/**
* string gene_name = 1;
* @return The geneName.
*/
public java.lang.String getGeneName() {
java.lang.Object ref = geneName_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
geneName_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string gene_name = 1;
* @return The bytes for geneName.
*/
public com.google.protobuf.ByteString
getGeneNameBytes() {
java.lang.Object ref = geneName_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
geneName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string gene_name = 1;
* @param value The geneName to set.
* @return This builder for chaining.
*/
public Builder setGeneName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
geneName_ = value;
onChanged();
return this;
}
/**
* string gene_name = 1;
* @return This builder for chaining.
*/
public Builder clearGeneName() {
geneName_ = getDefaultInstance().getGeneName();
onChanged();
return this;
}
/**
* string gene_name = 1;
* @param value The bytes for geneName to set.
* @return This builder for chaining.
*/
public Builder setGeneNameBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
geneName_ = value;
onChanged();
return this;
}
private java.lang.Object ensemblGeneId_ = "";
/**
* string ensembl_gene_id = 2;
* @return The ensemblGeneId.
*/
public java.lang.String getEnsemblGeneId() {
java.lang.Object ref = ensemblGeneId_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
ensemblGeneId_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string ensembl_gene_id = 2;
* @return The bytes for ensemblGeneId.
*/
public com.google.protobuf.ByteString
getEnsemblGeneIdBytes() {
java.lang.Object ref = ensemblGeneId_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ensemblGeneId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string ensembl_gene_id = 2;
* @param value The ensemblGeneId to set.
* @return This builder for chaining.
*/
public Builder setEnsemblGeneId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensemblGeneId_ = value;
onChanged();
return this;
}
/**
* string ensembl_gene_id = 2;
* @return This builder for chaining.
*/
public Builder clearEnsemblGeneId() {
ensemblGeneId_ = getDefaultInstance().getEnsemblGeneId();
onChanged();
return this;
}
/**
* string ensembl_gene_id = 2;
* @param value The bytes for ensemblGeneId to set.
* @return This builder for chaining.
*/
public Builder setEnsemblGeneIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensemblGeneId_ = value;
onChanged();
return this;
}
private java.lang.Object ensemblTranscriptId_ = "";
/**
* string ensembl_transcript_id = 3;
* @return The ensemblTranscriptId.
*/
public java.lang.String getEnsemblTranscriptId() {
java.lang.Object ref = ensemblTranscriptId_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
ensemblTranscriptId_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string ensembl_transcript_id = 3;
* @return The bytes for ensemblTranscriptId.
*/
public com.google.protobuf.ByteString
getEnsemblTranscriptIdBytes() {
java.lang.Object ref = ensemblTranscriptId_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ensemblTranscriptId_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string ensembl_transcript_id = 3;
* @param value The ensemblTranscriptId to set.
* @return This builder for chaining.
*/
public Builder setEnsemblTranscriptId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensemblTranscriptId_ = value;
onChanged();
return this;
}
/**
* string ensembl_transcript_id = 3;
* @return This builder for chaining.
*/
public Builder clearEnsemblTranscriptId() {
ensemblTranscriptId_ = getDefaultInstance().getEnsemblTranscriptId();
onChanged();
return this;
}
/**
* string ensembl_transcript_id = 3;
* @param value The bytes for ensemblTranscriptId to set.
* @return This builder for chaining.
*/
public Builder setEnsemblTranscriptIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensemblTranscriptId_ = value;
onChanged();
return this;
}
private java.lang.Object strand_ = "";
/**
* string strand = 4;
* @return The strand.
*/
public java.lang.String getStrand() {
java.lang.Object ref = strand_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
strand_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string strand = 4;
* @return The bytes for strand.
*/
public com.google.protobuf.ByteString
getStrandBytes() {
java.lang.Object ref = strand_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
strand_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string strand = 4;
* @param value The strand to set.
* @return This builder for chaining.
*/
public Builder setStrand(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
strand_ = value;
onChanged();
return this;
}
/**
* string strand = 4;
* @return This builder for chaining.
*/
public Builder clearStrand() {
strand_ = getDefaultInstance().getStrand();
onChanged();
return this;
}
/**
* string strand = 4;
* @param value The bytes for strand to set.
* @return This builder for chaining.
*/
public Builder setStrandBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
strand_ = value;
onChanged();
return this;
}
private java.lang.Object biotype_ = "";
/**
* string biotype = 5;
* @return The biotype.
*/
public java.lang.String getBiotype() {
java.lang.Object ref = biotype_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
biotype_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string biotype = 5;
* @return The bytes for biotype.
*/
public com.google.protobuf.ByteString
getBiotypeBytes() {
java.lang.Object ref = biotype_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
biotype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string biotype = 5;
* @param value The biotype to set.
* @return This builder for chaining.
*/
public Builder setBiotype(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
biotype_ = value;
onChanged();
return this;
}
/**
* string biotype = 5;
* @return This builder for chaining.
*/
public Builder clearBiotype() {
biotype_ = getDefaultInstance().getBiotype();
onChanged();
return this;
}
/**
* string biotype = 5;
* @param value The bytes for biotype to set.
* @return This builder for chaining.
*/
public Builder setBiotypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
biotype_ = value;
onChanged();
return this;
}
private java.util.List exonOverlap_ =
java.util.Collections.emptyList();
private void ensureExonOverlapIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
exonOverlap_ = new java.util.ArrayList(exonOverlap_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder> exonOverlapBuilder_;
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public java.util.List getExonOverlapList() {
if (exonOverlapBuilder_ == null) {
return java.util.Collections.unmodifiableList(exonOverlap_);
} else {
return exonOverlapBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public int getExonOverlapCount() {
if (exonOverlapBuilder_ == null) {
return exonOverlap_.size();
} else {
return exonOverlapBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap getExonOverlap(int index) {
if (exonOverlapBuilder_ == null) {
return exonOverlap_.get(index);
} else {
return exonOverlapBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder setExonOverlap(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap value) {
if (exonOverlapBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureExonOverlapIsMutable();
exonOverlap_.set(index, value);
onChanged();
} else {
exonOverlapBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder setExonOverlap(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder builderForValue) {
if (exonOverlapBuilder_ == null) {
ensureExonOverlapIsMutable();
exonOverlap_.set(index, builderForValue.build());
onChanged();
} else {
exonOverlapBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder addExonOverlap(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap value) {
if (exonOverlapBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureExonOverlapIsMutable();
exonOverlap_.add(value);
onChanged();
} else {
exonOverlapBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder addExonOverlap(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap value) {
if (exonOverlapBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureExonOverlapIsMutable();
exonOverlap_.add(index, value);
onChanged();
} else {
exonOverlapBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder addExonOverlap(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder builderForValue) {
if (exonOverlapBuilder_ == null) {
ensureExonOverlapIsMutable();
exonOverlap_.add(builderForValue.build());
onChanged();
} else {
exonOverlapBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder addExonOverlap(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder builderForValue) {
if (exonOverlapBuilder_ == null) {
ensureExonOverlapIsMutable();
exonOverlap_.add(index, builderForValue.build());
onChanged();
} else {
exonOverlapBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder addAllExonOverlap(
java.lang.Iterable values) {
if (exonOverlapBuilder_ == null) {
ensureExonOverlapIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, exonOverlap_);
onChanged();
} else {
exonOverlapBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder clearExonOverlap() {
if (exonOverlapBuilder_ == null) {
exonOverlap_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
exonOverlapBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public Builder removeExonOverlap(int index) {
if (exonOverlapBuilder_ == null) {
ensureExonOverlapIsMutable();
exonOverlap_.remove(index);
onChanged();
} else {
exonOverlapBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder getExonOverlapBuilder(
int index) {
return getExonOverlapFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder getExonOverlapOrBuilder(
int index) {
if (exonOverlapBuilder_ == null) {
return exonOverlap_.get(index); } else {
return exonOverlapBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public java.util.List
getExonOverlapOrBuilderList() {
if (exonOverlapBuilder_ != null) {
return exonOverlapBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(exonOverlap_);
}
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder addExonOverlapBuilder() {
return getExonOverlapFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder addExonOverlapBuilder(
int index) {
return getExonOverlapFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ExonOverlap exon_overlap = 6;
*/
public java.util.List
getExonOverlapBuilderList() {
return getExonOverlapFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder>
getExonOverlapFieldBuilder() {
if (exonOverlapBuilder_ == null) {
exonOverlapBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlap.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ExonOverlapOrBuilder>(
exonOverlap_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
exonOverlap_ = null;
}
return exonOverlapBuilder_;
}
private com.google.protobuf.LazyStringList transcriptAnnotationFlags_ = com.google.protobuf.LazyStringArrayList.EMPTY;
private void ensureTranscriptAnnotationFlagsIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
transcriptAnnotationFlags_ = new com.google.protobuf.LazyStringArrayList(transcriptAnnotationFlags_);
bitField0_ |= 0x00000002;
}
}
/**
* repeated string transcript_annotation_flags = 7;
* @return A list containing the transcriptAnnotationFlags.
*/
public com.google.protobuf.ProtocolStringList
getTranscriptAnnotationFlagsList() {
return transcriptAnnotationFlags_.getUnmodifiableView();
}
/**
* repeated string transcript_annotation_flags = 7;
* @return The count of transcriptAnnotationFlags.
*/
public int getTranscriptAnnotationFlagsCount() {
return transcriptAnnotationFlags_.size();
}
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the element to return.
* @return The transcriptAnnotationFlags at the given index.
*/
public java.lang.String getTranscriptAnnotationFlags(int index) {
return transcriptAnnotationFlags_.get(index);
}
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index of the value to return.
* @return The bytes of the transcriptAnnotationFlags at the given index.
*/
public com.google.protobuf.ByteString
getTranscriptAnnotationFlagsBytes(int index) {
return transcriptAnnotationFlags_.getByteString(index);
}
/**
* repeated string transcript_annotation_flags = 7;
* @param index The index to set the value at.
* @param value The transcriptAnnotationFlags to set.
* @return This builder for chaining.
*/
public Builder setTranscriptAnnotationFlags(
int index, java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureTranscriptAnnotationFlagsIsMutable();
transcriptAnnotationFlags_.set(index, value);
onChanged();
return this;
}
/**
* repeated string transcript_annotation_flags = 7;
* @param value The transcriptAnnotationFlags to add.
* @return This builder for chaining.
*/
public Builder addTranscriptAnnotationFlags(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureTranscriptAnnotationFlagsIsMutable();
transcriptAnnotationFlags_.add(value);
onChanged();
return this;
}
/**
* repeated string transcript_annotation_flags = 7;
* @param values The transcriptAnnotationFlags to add.
* @return This builder for chaining.
*/
public Builder addAllTranscriptAnnotationFlags(
java.lang.Iterable values) {
ensureTranscriptAnnotationFlagsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, transcriptAnnotationFlags_);
onChanged();
return this;
}
/**
* repeated string transcript_annotation_flags = 7;
* @return This builder for chaining.
*/
public Builder clearTranscriptAnnotationFlags() {
transcriptAnnotationFlags_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
return this;
}
/**
* repeated string transcript_annotation_flags = 7;
* @param value The bytes of the transcriptAnnotationFlags to add.
* @return This builder for chaining.
*/
public Builder addTranscriptAnnotationFlagsBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensureTranscriptAnnotationFlagsIsMutable();
transcriptAnnotationFlags_.add(value);
onChanged();
return this;
}
private int cDnaPosition_ ;
/**
* int32 c_dna_position = 8;
* @return The cDnaPosition.
*/
public int getCDnaPosition() {
return cDnaPosition_;
}
/**
* int32 c_dna_position = 8;
* @param value The cDnaPosition to set.
* @return This builder for chaining.
*/
public Builder setCDnaPosition(int value) {
cDnaPosition_ = value;
onChanged();
return this;
}
/**
* int32 c_dna_position = 8;
* @return This builder for chaining.
*/
public Builder clearCDnaPosition() {
cDnaPosition_ = 0;
onChanged();
return this;
}
private int cdsPosition_ ;
/**
* int32 cds_position = 9;
* @return The cdsPosition.
*/
public int getCdsPosition() {
return cdsPosition_;
}
/**
* int32 cds_position = 9;
* @param value The cdsPosition to set.
* @return This builder for chaining.
*/
public Builder setCdsPosition(int value) {
cdsPosition_ = value;
onChanged();
return this;
}
/**
* int32 cds_position = 9;
* @return This builder for chaining.
*/
public Builder clearCdsPosition() {
cdsPosition_ = 0;
onChanged();
return this;
}
private java.lang.Object codon_ = "";
/**
* string codon = 10;
* @return The codon.
*/
public java.lang.String getCodon() {
java.lang.Object ref = codon_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
codon_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string codon = 10;
* @return The bytes for codon.
*/
public com.google.protobuf.ByteString
getCodonBytes() {
java.lang.Object ref = codon_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
codon_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string codon = 10;
* @param value The codon to set.
* @return This builder for chaining.
*/
public Builder setCodon(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
codon_ = value;
onChanged();
return this;
}
/**
* string codon = 10;
* @return This builder for chaining.
*/
public Builder clearCodon() {
codon_ = getDefaultInstance().getCodon();
onChanged();
return this;
}
/**
* string codon = 10;
* @param value The bytes for codon to set.
* @return This builder for chaining.
*/
public Builder setCodonBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
codon_ = value;
onChanged();
return this;
}
private org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation proteinVariantAnnotation_;
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder> proteinVariantAnnotationBuilder_;
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return Whether the proteinVariantAnnotation field is set.
*/
public boolean hasProteinVariantAnnotation() {
return proteinVariantAnnotationBuilder_ != null || proteinVariantAnnotation_ != null;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
* @return The proteinVariantAnnotation.
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation getProteinVariantAnnotation() {
if (proteinVariantAnnotationBuilder_ == null) {
return proteinVariantAnnotation_ == null ? org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.getDefaultInstance() : proteinVariantAnnotation_;
} else {
return proteinVariantAnnotationBuilder_.getMessage();
}
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public Builder setProteinVariantAnnotation(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation value) {
if (proteinVariantAnnotationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
proteinVariantAnnotation_ = value;
onChanged();
} else {
proteinVariantAnnotationBuilder_.setMessage(value);
}
return this;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public Builder setProteinVariantAnnotation(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder builderForValue) {
if (proteinVariantAnnotationBuilder_ == null) {
proteinVariantAnnotation_ = builderForValue.build();
onChanged();
} else {
proteinVariantAnnotationBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public Builder mergeProteinVariantAnnotation(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation value) {
if (proteinVariantAnnotationBuilder_ == null) {
if (proteinVariantAnnotation_ != null) {
proteinVariantAnnotation_ =
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.newBuilder(proteinVariantAnnotation_).mergeFrom(value).buildPartial();
} else {
proteinVariantAnnotation_ = value;
}
onChanged();
} else {
proteinVariantAnnotationBuilder_.mergeFrom(value);
}
return this;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public Builder clearProteinVariantAnnotation() {
if (proteinVariantAnnotationBuilder_ == null) {
proteinVariantAnnotation_ = null;
onChanged();
} else {
proteinVariantAnnotation_ = null;
proteinVariantAnnotationBuilder_ = null;
}
return this;
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder getProteinVariantAnnotationBuilder() {
onChanged();
return getProteinVariantAnnotationFieldBuilder().getBuilder();
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder getProteinVariantAnnotationOrBuilder() {
if (proteinVariantAnnotationBuilder_ != null) {
return proteinVariantAnnotationBuilder_.getMessageOrBuilder();
} else {
return proteinVariantAnnotation_ == null ?
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.getDefaultInstance() : proteinVariantAnnotation_;
}
}
/**
* .protobuf.opencb.ProteinVariantAnnotation protein_variant_annotation = 11;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder>
getProteinVariantAnnotationFieldBuilder() {
if (proteinVariantAnnotationBuilder_ == null) {
proteinVariantAnnotationBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotation.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ProteinVariantAnnotationOrBuilder>(
getProteinVariantAnnotation(),
getParentForChildren(),
isClean());
proteinVariantAnnotation_ = null;
}
return proteinVariantAnnotationBuilder_;
}
private java.util.List sequenceOntologyTerms_ =
java.util.Collections.emptyList();
private void ensureSequenceOntologyTermsIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
sequenceOntologyTerms_ = new java.util.ArrayList(sequenceOntologyTerms_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder> sequenceOntologyTermsBuilder_;
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public java.util.List getSequenceOntologyTermsList() {
if (sequenceOntologyTermsBuilder_ == null) {
return java.util.Collections.unmodifiableList(sequenceOntologyTerms_);
} else {
return sequenceOntologyTermsBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public int getSequenceOntologyTermsCount() {
if (sequenceOntologyTermsBuilder_ == null) {
return sequenceOntologyTerms_.size();
} else {
return sequenceOntologyTermsBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm getSequenceOntologyTerms(int index) {
if (sequenceOntologyTermsBuilder_ == null) {
return sequenceOntologyTerms_.get(index);
} else {
return sequenceOntologyTermsBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder setSequenceOntologyTerms(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm value) {
if (sequenceOntologyTermsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.set(index, value);
onChanged();
} else {
sequenceOntologyTermsBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder setSequenceOntologyTerms(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder builderForValue) {
if (sequenceOntologyTermsBuilder_ == null) {
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.set(index, builderForValue.build());
onChanged();
} else {
sequenceOntologyTermsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder addSequenceOntologyTerms(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm value) {
if (sequenceOntologyTermsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.add(value);
onChanged();
} else {
sequenceOntologyTermsBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder addSequenceOntologyTerms(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm value) {
if (sequenceOntologyTermsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.add(index, value);
onChanged();
} else {
sequenceOntologyTermsBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder addSequenceOntologyTerms(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder builderForValue) {
if (sequenceOntologyTermsBuilder_ == null) {
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.add(builderForValue.build());
onChanged();
} else {
sequenceOntologyTermsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder addSequenceOntologyTerms(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder builderForValue) {
if (sequenceOntologyTermsBuilder_ == null) {
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.add(index, builderForValue.build());
onChanged();
} else {
sequenceOntologyTermsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder addAllSequenceOntologyTerms(
java.lang.Iterable values) {
if (sequenceOntologyTermsBuilder_ == null) {
ensureSequenceOntologyTermsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, sequenceOntologyTerms_);
onChanged();
} else {
sequenceOntologyTermsBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder clearSequenceOntologyTerms() {
if (sequenceOntologyTermsBuilder_ == null) {
sequenceOntologyTerms_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
sequenceOntologyTermsBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public Builder removeSequenceOntologyTerms(int index) {
if (sequenceOntologyTermsBuilder_ == null) {
ensureSequenceOntologyTermsIsMutable();
sequenceOntologyTerms_.remove(index);
onChanged();
} else {
sequenceOntologyTermsBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder getSequenceOntologyTermsBuilder(
int index) {
return getSequenceOntologyTermsFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder getSequenceOntologyTermsOrBuilder(
int index) {
if (sequenceOntologyTermsBuilder_ == null) {
return sequenceOntologyTerms_.get(index); } else {
return sequenceOntologyTermsBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public java.util.List
getSequenceOntologyTermsOrBuilderList() {
if (sequenceOntologyTermsBuilder_ != null) {
return sequenceOntologyTermsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(sequenceOntologyTerms_);
}
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder addSequenceOntologyTermsBuilder() {
return getSequenceOntologyTermsFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder addSequenceOntologyTermsBuilder(
int index) {
return getSequenceOntologyTermsFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.SequenceOntologyTerm sequence_ontology_terms = 12;
*/
public java.util.List
getSequenceOntologyTermsBuilderList() {
return getSequenceOntologyTermsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder>
getSequenceOntologyTermsFieldBuilder() {
if (sequenceOntologyTermsBuilder_ == null) {
sequenceOntologyTermsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTerm.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.SequenceOntologyTermOrBuilder>(
sequenceOntologyTerms_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
sequenceOntologyTerms_ = null;
}
return sequenceOntologyTermsBuilder_;
}
@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:protobuf.opencb.ConsequenceType)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.ConsequenceType)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public ConsequenceType parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new ConsequenceType(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface RepeatOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.Repeat)
com.google.protobuf.MessageOrBuilder {
/**
* string id = 1;
* @return The id.
*/
java.lang.String getId();
/**
* string id = 1;
* @return The bytes for id.
*/
com.google.protobuf.ByteString
getIdBytes();
/**
* string chromosome = 2;
* @return The chromosome.
*/
java.lang.String getChromosome();
/**
* string chromosome = 2;
* @return The bytes for chromosome.
*/
com.google.protobuf.ByteString
getChromosomeBytes();
/**
* int32 start = 3;
* @return The start.
*/
int getStart();
/**
* int32 end = 4;
* @return The end.
*/
int getEnd();
/**
* int32 period = 5;
* @return The period.
*/
int getPeriod();
/**
* int32 consensusSize = 6;
* @return The consensusSize.
*/
int getConsensusSize();
/**
* float copy_number = 7;
* @return The copyNumber.
*/
float getCopyNumber();
/**
* float percentage_match = 8;
* @return The percentageMatch.
*/
float getPercentageMatch();
/**
* float score = 9;
* @return The score.
*/
float getScore();
/**
* string sequence = 10;
* @return The sequence.
*/
java.lang.String getSequence();
/**
* string sequence = 10;
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*/
com.google.protobuf.ByteString
getSequenceBytes();
/**
* string source = 11;
* @return The source.
*/
java.lang.String getSource();
/**
* string source = 11;
* @return The bytes for source.
*/
com.google.protobuf.ByteString
getSourceBytes();
}
/**
* Protobuf type {@code protobuf.opencb.Repeat}
*/
public static final class Repeat extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.Repeat)
RepeatOrBuilder {
private static final long serialVersionUID = 0L;
// Use Repeat.newBuilder() to construct.
private Repeat(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private Repeat() {
id_ = "";
chromosome_ = "";
sequence_ = "";
source_ = "";
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new Repeat();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Repeat(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
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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();
id_ = s;
break;
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case 18: {
java.lang.String s = input.readStringRequireUtf8();
chromosome_ = s;
break;
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case 24: {
start_ = input.readInt32();
break;
}
case 32: {
end_ = input.readInt32();
break;
}
case 40: {
period_ = input.readInt32();
break;
}
case 48: {
consensusSize_ = input.readInt32();
break;
}
case 61: {
copyNumber_ = input.readFloat();
break;
}
case 69: {
percentageMatch_ = input.readFloat();
break;
}
case 77: {
score_ = input.readFloat();
break;
}
case 82: {
java.lang.String s = input.readStringRequireUtf8();
sequence_ = s;
break;
}
case 90: {
java.lang.String s = input.readStringRequireUtf8();
source_ = s;
break;
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default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
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} 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 {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Repeat_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Repeat_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Repeat.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Repeat.Builder.class);
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public static final int ID_FIELD_NUMBER = 1;
private volatile java.lang.Object id_;
/**
* string id = 1;
* @return The id.
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public java.lang.String getId() {
java.lang.Object ref = id_;
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();
id_ = s;
return s;
}
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/**
* string id = 1;
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getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int CHROMOSOME_FIELD_NUMBER = 2;
private volatile java.lang.Object chromosome_;
/**
* string chromosome = 2;
* @return The chromosome.
*/
public java.lang.String getChromosome() {
java.lang.Object ref = chromosome_;
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();
chromosome_ = s;
return s;
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/**
* string chromosome = 2;
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public com.google.protobuf.ByteString
getChromosomeBytes() {
java.lang.Object ref = chromosome_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chromosome_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int START_FIELD_NUMBER = 3;
private int start_;
/**
* int32 start = 3;
* @return The start.
*/
public int getStart() {
return start_;
}
public static final int END_FIELD_NUMBER = 4;
private int end_;
/**
* int32 end = 4;
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*/
public int getEnd() {
return end_;
}
public static final int PERIOD_FIELD_NUMBER = 5;
private int period_;
/**
* int32 period = 5;
* @return The period.
*/
public int getPeriod() {
return period_;
}
public static final int CONSENSUSSIZE_FIELD_NUMBER = 6;
private int consensusSize_;
/**
* int32 consensusSize = 6;
* @return The consensusSize.
*/
public int getConsensusSize() {
return consensusSize_;
}
public static final int COPY_NUMBER_FIELD_NUMBER = 7;
private float copyNumber_;
/**
* float copy_number = 7;
* @return The copyNumber.
*/
public float getCopyNumber() {
return copyNumber_;
}
public static final int PERCENTAGE_MATCH_FIELD_NUMBER = 8;
private float percentageMatch_;
/**
* float percentage_match = 8;
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*/
public float getPercentageMatch() {
return percentageMatch_;
}
public static final int SCORE_FIELD_NUMBER = 9;
private float score_;
/**
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return score_;
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private volatile java.lang.Object sequence_;
/**
* string sequence = 10;
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java.lang.Object ref = sequence_;
if (ref instanceof java.lang.String) {
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
sequence_ = s;
return s;
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/**
* string sequence = 10;
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getSequenceBytes() {
java.lang.Object ref = sequence_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
sequence_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int SOURCE_FIELD_NUMBER = 11;
private volatile java.lang.Object source_;
/**
* string source = 11;
* @return The source.
*/
public java.lang.String getSource() {
java.lang.Object ref = source_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
source_ = s;
return s;
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java.lang.Object ref = source_;
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com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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source_ = b;
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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java.lang.String value) {
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stain_ = value;
onChanged();
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stain_ = getDefaultInstance().getStain();
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com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
stain_ = value;
onChanged();
return this;
}
private java.lang.Object name_ = "";
/**
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*/
public java.lang.String getName() {
java.lang.Object ref = name_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
name_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string name = 3;
* @return The bytes for name.
*/
public com.google.protobuf.ByteString
getNameBytes() {
java.lang.Object ref = name_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
name_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string name = 3;
* @param value The name to set.
* @return This builder for chaining.
*/
public Builder setName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
name_ = value;
onChanged();
return this;
}
/**
* string name = 3;
* @return This builder for chaining.
*/
public Builder clearName() {
name_ = getDefaultInstance().getName();
onChanged();
return this;
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/**
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com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
name_ = value;
onChanged();
return this;
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/**
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*/
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return start_;
}
/**
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* @return This builder for chaining.
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start_ = value;
onChanged();
return this;
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* int32 start = 4;
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start_ = 0;
onChanged();
return this;
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onChanged();
return this;
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onChanged();
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@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.Cytoband)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.Cytoband)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Cytoband parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Cytoband(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface DrugOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.Drug)
com.google.protobuf.MessageOrBuilder {
/**
* string therapeuticContext = 1;
* @return The therapeuticContext.
*/
java.lang.String getTherapeuticContext();
/**
* string therapeuticContext = 1;
* @return The bytes for therapeuticContext.
*/
com.google.protobuf.ByteString
getTherapeuticContextBytes();
/**
* string pathway = 2;
* @return The pathway.
*/
java.lang.String getPathway();
/**
* string pathway = 2;
* @return The bytes for pathway.
*/
com.google.protobuf.ByteString
getPathwayBytes();
/**
* string effect = 3;
* @return The effect.
*/
java.lang.String getEffect();
/**
* string effect = 3;
* @return The bytes for effect.
*/
com.google.protobuf.ByteString
getEffectBytes();
/**
* string association = 4;
* @return The association.
*/
java.lang.String getAssociation();
/**
* string association = 4;
* @return The bytes for association.
*/
com.google.protobuf.ByteString
getAssociationBytes();
/**
* string status = 5;
* @return The status.
*/
java.lang.String getStatus();
/**
* string status = 5;
* @return The bytes for status.
*/
com.google.protobuf.ByteString
getStatusBytes();
/**
* string evidence = 6;
* @return The evidence.
*/
java.lang.String getEvidence();
/**
* string evidence = 6;
* @return The bytes for evidence.
*/
com.google.protobuf.ByteString
getEvidenceBytes();
/**
* repeated string bibliography = 7;
* @return A list containing the bibliography.
*/
java.util.List
getBibliographyList();
/**
* repeated string bibliography = 7;
* @return The count of bibliography.
*/
int getBibliographyCount();
/**
* repeated string bibliography = 7;
* @param index The index of the element to return.
* @return The bibliography at the given index.
*/
java.lang.String getBibliography(int index);
/**
* repeated string bibliography = 7;
* @param index The index of the value to return.
* @return The bytes of the bibliography at the given index.
*/
com.google.protobuf.ByteString
getBibliographyBytes(int index);
}
/**
* Protobuf type {@code protobuf.opencb.Drug}
*/
public static final class Drug extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.Drug)
DrugOrBuilder {
private static final long serialVersionUID = 0L;
// Use Drug.newBuilder() to construct.
private Drug(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private Drug() {
therapeuticContext_ = "";
pathway_ = "";
effect_ = "";
association_ = "";
status_ = "";
evidence_ = "";
bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new Drug();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Drug(
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();
therapeuticContext_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
pathway_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
effect_ = s;
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
association_ = s;
break;
}
case 42: {
java.lang.String s = input.readStringRequireUtf8();
status_ = s;
break;
}
case 50: {
java.lang.String s = input.readStringRequireUtf8();
evidence_ = s;
break;
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java.lang.String s = input.readStringRequireUtf8();
if (!((mutable_bitField0_ & 0x00000001) != 0)) {
bibliography_ = new com.google.protobuf.LazyStringArrayList();
mutable_bitField0_ |= 0x00000001;
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bibliography_.add(s);
break;
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default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
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} 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)) {
bibliography_ = bibliography_.getUnmodifiableView();
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this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Drug_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Drug_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.Builder.class);
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public static final int THERAPEUTICCONTEXT_FIELD_NUMBER = 1;
private volatile java.lang.Object therapeuticContext_;
/**
* string therapeuticContext = 1;
* @return The therapeuticContext.
*/
public java.lang.String getTherapeuticContext() {
java.lang.Object ref = therapeuticContext_;
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();
therapeuticContext_ = s;
return s;
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}
/**
* string therapeuticContext = 1;
* @return The bytes for therapeuticContext.
*/
public com.google.protobuf.ByteString
getTherapeuticContextBytes() {
java.lang.Object ref = therapeuticContext_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
therapeuticContext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int PATHWAY_FIELD_NUMBER = 2;
private volatile java.lang.Object pathway_;
/**
* string pathway = 2;
* @return The pathway.
*/
public java.lang.String getPathway() {
java.lang.Object ref = pathway_;
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();
pathway_ = s;
return s;
}
}
/**
* string pathway = 2;
* @return The bytes for pathway.
*/
public com.google.protobuf.ByteString
getPathwayBytes() {
java.lang.Object ref = pathway_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
pathway_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int EFFECT_FIELD_NUMBER = 3;
private volatile java.lang.Object effect_;
/**
* string effect = 3;
* @return The effect.
*/
public java.lang.String getEffect() {
java.lang.Object ref = effect_;
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();
effect_ = s;
return s;
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/**
* string effect = 3;
* @return The bytes for effect.
*/
public com.google.protobuf.ByteString
getEffectBytes() {
java.lang.Object ref = effect_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
effect_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int ASSOCIATION_FIELD_NUMBER = 4;
private volatile java.lang.Object association_;
/**
* string association = 4;
* @return The association.
*/
public java.lang.String getAssociation() {
java.lang.Object ref = association_;
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();
association_ = s;
return s;
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* string association = 4;
* @return The bytes for association.
*/
public com.google.protobuf.ByteString
getAssociationBytes() {
java.lang.Object ref = association_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
association_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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public static final int STATUS_FIELD_NUMBER = 5;
private volatile java.lang.Object status_;
/**
* string status = 5;
* @return The status.
*/
public java.lang.String getStatus() {
java.lang.Object ref = status_;
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();
status_ = s;
return s;
}
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/**
* string status = 5;
* @return The bytes for status.
*/
public com.google.protobuf.ByteString
getStatusBytes() {
java.lang.Object ref = status_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
status_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int EVIDENCE_FIELD_NUMBER = 6;
private volatile java.lang.Object evidence_;
/**
* string evidence = 6;
* @return The evidence.
*/
public java.lang.String getEvidence() {
java.lang.Object ref = evidence_;
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();
evidence_ = s;
return s;
}
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/**
* string evidence = 6;
* @return The bytes for evidence.
*/
public com.google.protobuf.ByteString
getEvidenceBytes() {
java.lang.Object ref = evidence_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
evidence_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int BIBLIOGRAPHY_FIELD_NUMBER = 7;
private com.google.protobuf.LazyStringList bibliography_;
/**
* repeated string bibliography = 7;
* @return A list containing the bibliography.
*/
public com.google.protobuf.ProtocolStringList
getBibliographyList() {
return bibliography_;
}
/**
* repeated string bibliography = 7;
* @return The count of bibliography.
*/
public int getBibliographyCount() {
return bibliography_.size();
}
/**
* repeated string bibliography = 7;
* @param index The index of the element to return.
* @return The bibliography at the given index.
*/
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return bibliography_.get(index);
}
/**
* repeated string bibliography = 7;
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return bibliography_.getByteString(index);
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@java.lang.Override
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byte isInitialized = memoizedIsInitialized;
if (isInitialized == 1) return true;
if (isInitialized == 0) return false;
memoizedIsInitialized = 1;
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public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
if (!getTherapeuticContextBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, therapeuticContext_);
}
if (!getPathwayBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, pathway_);
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if (!getEffectBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, effect_);
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if (!getAssociationBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, association_);
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if (!getStatusBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, status_);
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if (!getEvidenceBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, evidence_);
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for (int i = 0; i < bibliography_.size(); i++) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, bibliography_.getRaw(i));
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unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getTherapeuticContextBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, therapeuticContext_);
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if (!getPathwayBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, pathway_);
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if (!getEffectBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(3, effect_);
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if (!getAssociationBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(4, association_);
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if (!getStatusBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, status_);
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if (!getEvidenceBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, evidence_);
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size += dataSize;
size += 1 * getBibliographyList().size();
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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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug) obj;
if (!getTherapeuticContext()
.equals(other.getTherapeuticContext())) return false;
if (!getPathway()
.equals(other.getPathway())) return false;
if (!getEffect()
.equals(other.getEffect())) return false;
if (!getAssociation()
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if (!getStatus()
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if (!getEvidence()
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if (!getBibliographyList()
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if (!unknownFields.equals(other.unknownFields)) return false;
return true;
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if (memoizedHashCode != 0) {
return memoizedHashCode;
}
int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + THERAPEUTICCONTEXT_FIELD_NUMBER;
hash = (53 * hash) + getTherapeuticContext().hashCode();
hash = (37 * hash) + PATHWAY_FIELD_NUMBER;
hash = (53 * hash) + getPathway().hashCode();
hash = (37 * hash) + EFFECT_FIELD_NUMBER;
hash = (53 * hash) + getEffect().hashCode();
hash = (37 * hash) + ASSOCIATION_FIELD_NUMBER;
hash = (53 * hash) + getAssociation().hashCode();
hash = (37 * hash) + STATUS_FIELD_NUMBER;
hash = (53 * hash) + getStatus().hashCode();
hash = (37 * hash) + EVIDENCE_FIELD_NUMBER;
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if (getBibliographyCount() > 0) {
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hash = (53 * hash) + getBibliographyList().hashCode();
}
hash = (29 * hash) + unknownFields.hashCode();
memoizedHashCode = hash;
return hash;
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug 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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug 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;
}
/**
* Protobuf type {@code protobuf.opencb.Drug}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.Drug)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.DrugOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Drug_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Drug_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.class, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.Builder.class);
}
// Construct using org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
.alwaysUseFieldBuilders) {
}
}
@java.lang.Override
public Builder clear() {
super.clear();
therapeuticContext_ = "";
pathway_ = "";
effect_ = "";
association_ = "";
status_ = "";
evidence_ = "";
bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000001);
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_Drug_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug build() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug buildPartial() {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug result = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug(this);
int from_bitField0_ = bitField0_;
result.therapeuticContext_ = therapeuticContext_;
result.pathway_ = pathway_;
result.effect_ = effect_;
result.association_ = association_;
result.status_ = status_;
result.evidence_ = evidence_;
if (((bitField0_ & 0x00000001) != 0)) {
bibliography_ = bibliography_.getUnmodifiableView();
bitField0_ = (bitField0_ & ~0x00000001);
}
result.bibliography_ = bibliography_;
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug other) {
if (other == org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.getDefaultInstance()) return this;
if (!other.getTherapeuticContext().isEmpty()) {
therapeuticContext_ = other.therapeuticContext_;
onChanged();
}
if (!other.getPathway().isEmpty()) {
pathway_ = other.pathway_;
onChanged();
}
if (!other.getEffect().isEmpty()) {
effect_ = other.effect_;
onChanged();
}
if (!other.getAssociation().isEmpty()) {
association_ = other.association_;
onChanged();
}
if (!other.getStatus().isEmpty()) {
status_ = other.status_;
onChanged();
}
if (!other.getEvidence().isEmpty()) {
evidence_ = other.evidence_;
onChanged();
}
if (!other.bibliography_.isEmpty()) {
if (bibliography_.isEmpty()) {
bibliography_ = other.bibliography_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureBibliographyIsMutable();
bibliography_.addAll(other.bibliography_);
}
onChanged();
}
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object therapeuticContext_ = "";
/**
* string therapeuticContext = 1;
* @return The therapeuticContext.
*/
public java.lang.String getTherapeuticContext() {
java.lang.Object ref = therapeuticContext_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
therapeuticContext_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string therapeuticContext = 1;
* @return The bytes for therapeuticContext.
*/
public com.google.protobuf.ByteString
getTherapeuticContextBytes() {
java.lang.Object ref = therapeuticContext_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
therapeuticContext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string therapeuticContext = 1;
* @param value The therapeuticContext to set.
* @return This builder for chaining.
*/
public Builder setTherapeuticContext(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
therapeuticContext_ = value;
onChanged();
return this;
}
/**
* string therapeuticContext = 1;
* @return This builder for chaining.
*/
public Builder clearTherapeuticContext() {
therapeuticContext_ = getDefaultInstance().getTherapeuticContext();
onChanged();
return this;
}
/**
* string therapeuticContext = 1;
* @param value The bytes for therapeuticContext to set.
* @return This builder for chaining.
*/
public Builder setTherapeuticContextBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
therapeuticContext_ = value;
onChanged();
return this;
}
private java.lang.Object pathway_ = "";
/**
* string pathway = 2;
* @return The pathway.
*/
public java.lang.String getPathway() {
java.lang.Object ref = pathway_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
pathway_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string pathway = 2;
* @return The bytes for pathway.
*/
public com.google.protobuf.ByteString
getPathwayBytes() {
java.lang.Object ref = pathway_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
pathway_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string pathway = 2;
* @param value The pathway to set.
* @return This builder for chaining.
*/
public Builder setPathway(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
pathway_ = value;
onChanged();
return this;
}
/**
* string pathway = 2;
* @return This builder for chaining.
*/
public Builder clearPathway() {
pathway_ = getDefaultInstance().getPathway();
onChanged();
return this;
}
/**
* string pathway = 2;
* @param value The bytes for pathway to set.
* @return This builder for chaining.
*/
public Builder setPathwayBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
pathway_ = value;
onChanged();
return this;
}
private java.lang.Object effect_ = "";
/**
* string effect = 3;
* @return The effect.
*/
public java.lang.String getEffect() {
java.lang.Object ref = effect_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
effect_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string effect = 3;
* @return The bytes for effect.
*/
public com.google.protobuf.ByteString
getEffectBytes() {
java.lang.Object ref = effect_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
effect_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string effect = 3;
* @param value The effect to set.
* @return This builder for chaining.
*/
public Builder setEffect(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
effect_ = value;
onChanged();
return this;
}
/**
* string effect = 3;
* @return This builder for chaining.
*/
public Builder clearEffect() {
effect_ = getDefaultInstance().getEffect();
onChanged();
return this;
}
/**
* string effect = 3;
* @param value The bytes for effect to set.
* @return This builder for chaining.
*/
public Builder setEffectBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
effect_ = value;
onChanged();
return this;
}
private java.lang.Object association_ = "";
/**
* string association = 4;
* @return The association.
*/
public java.lang.String getAssociation() {
java.lang.Object ref = association_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
association_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string association = 4;
* @return The bytes for association.
*/
public com.google.protobuf.ByteString
getAssociationBytes() {
java.lang.Object ref = association_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
association_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string association = 4;
* @param value The association to set.
* @return This builder for chaining.
*/
public Builder setAssociation(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
association_ = value;
onChanged();
return this;
}
/**
* string association = 4;
* @return This builder for chaining.
*/
public Builder clearAssociation() {
association_ = getDefaultInstance().getAssociation();
onChanged();
return this;
}
/**
* string association = 4;
* @param value The bytes for association to set.
* @return This builder for chaining.
*/
public Builder setAssociationBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
association_ = value;
onChanged();
return this;
}
private java.lang.Object status_ = "";
/**
* string status = 5;
* @return The status.
*/
public java.lang.String getStatus() {
java.lang.Object ref = status_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
status_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string status = 5;
* @return The bytes for status.
*/
public com.google.protobuf.ByteString
getStatusBytes() {
java.lang.Object ref = status_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
status_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string status = 5;
* @param value The status to set.
* @return This builder for chaining.
*/
public Builder setStatus(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
status_ = value;
onChanged();
return this;
}
/**
* string status = 5;
* @return This builder for chaining.
*/
public Builder clearStatus() {
status_ = getDefaultInstance().getStatus();
onChanged();
return this;
}
/**
* string status = 5;
* @param value The bytes for status to set.
* @return This builder for chaining.
*/
public Builder setStatusBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
status_ = value;
onChanged();
return this;
}
private java.lang.Object evidence_ = "";
/**
* string evidence = 6;
* @return The evidence.
*/
public java.lang.String getEvidence() {
java.lang.Object ref = evidence_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
evidence_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string evidence = 6;
* @return The bytes for evidence.
*/
public com.google.protobuf.ByteString
getEvidenceBytes() {
java.lang.Object ref = evidence_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
evidence_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string evidence = 6;
* @param value The evidence to set.
* @return This builder for chaining.
*/
public Builder setEvidence(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
evidence_ = value;
onChanged();
return this;
}
/**
* string evidence = 6;
* @return This builder for chaining.
*/
public Builder clearEvidence() {
evidence_ = getDefaultInstance().getEvidence();
onChanged();
return this;
}
/**
* string evidence = 6;
* @param value The bytes for evidence to set.
* @return This builder for chaining.
*/
public Builder setEvidenceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
evidence_ = value;
onChanged();
return this;
}
private com.google.protobuf.LazyStringList bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
private void ensureBibliographyIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
bibliography_ = new com.google.protobuf.LazyStringArrayList(bibliography_);
bitField0_ |= 0x00000001;
}
}
/**
* repeated string bibliography = 7;
* @return A list containing the bibliography.
*/
public com.google.protobuf.ProtocolStringList
getBibliographyList() {
return bibliography_.getUnmodifiableView();
}
/**
* repeated string bibliography = 7;
* @return The count of bibliography.
*/
public int getBibliographyCount() {
return bibliography_.size();
}
/**
* repeated string bibliography = 7;
* @param index The index of the element to return.
* @return The bibliography at the given index.
*/
public java.lang.String getBibliography(int index) {
return bibliography_.get(index);
}
/**
* repeated string bibliography = 7;
* @param index The index of the value to return.
* @return The bytes of the bibliography at the given index.
*/
public com.google.protobuf.ByteString
getBibliographyBytes(int index) {
return bibliography_.getByteString(index);
}
/**
* repeated string bibliography = 7;
* @param index The index to set the value at.
* @param value The bibliography to set.
* @return This builder for chaining.
*/
public Builder setBibliography(
int index, java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureBibliographyIsMutable();
bibliography_.set(index, value);
onChanged();
return this;
}
/**
* repeated string bibliography = 7;
* @param value The bibliography to add.
* @return This builder for chaining.
*/
public Builder addBibliography(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureBibliographyIsMutable();
bibliography_.add(value);
onChanged();
return this;
}
/**
* repeated string bibliography = 7;
* @param values The bibliography to add.
* @return This builder for chaining.
*/
public Builder addAllBibliography(
java.lang.Iterable values) {
ensureBibliographyIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, bibliography_);
onChanged();
return this;
}
/**
* repeated string bibliography = 7;
* @return This builder for chaining.
*/
public Builder clearBibliography() {
bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
return this;
}
/**
* repeated string bibliography = 7;
* @param value The bytes of the bibliography to add.
* @return This builder for chaining.
*/
public Builder addBibliographyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensureBibliographyIsMutable();
bibliography_.add(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:protobuf.opencb.Drug)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.Drug)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug();
}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Drug parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Drug(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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface VariantAnnotationOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.VariantAnnotation)
com.google.protobuf.MessageOrBuilder {
/**
* string chromosome = 1;
* @return The chromosome.
*/
java.lang.String getChromosome();
/**
* string chromosome = 1;
* @return The bytes for chromosome.
*/
com.google.protobuf.ByteString
getChromosomeBytes();
/**
* int32 start = 2;
* @return The start.
*/
int getStart();
/**
* int32 end = 3;
* @return The end.
*/
int getEnd();
/**
* string reference = 4;
* @return The reference.
*/
java.lang.String getReference();
/**
* string reference = 4;
* @return The bytes for reference.
*/
com.google.protobuf.ByteString
getReferenceBytes();
/**
* string alternate = 5;
* @return The alternate.
*/
java.lang.String getAlternate();
/**
* string alternate = 5;
* @return The bytes for alternate.
*/
com.google.protobuf.ByteString
getAlternateBytes();
/**
* string ancestral_allele = 6;
* @return The ancestralAllele.
*/
java.lang.String getAncestralAllele();
/**
* string ancestral_allele = 6;
* @return The bytes for ancestralAllele.
*/
com.google.protobuf.ByteString
getAncestralAlleleBytes();
/**
* string id = 7;
* @return The id.
*/
java.lang.String getId();
/**
* string id = 7;
* @return The bytes for id.
*/
com.google.protobuf.ByteString
getIdBytes();
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
java.util.List
getXrefsList();
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref getXrefs(int index);
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
int getXrefsCount();
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
java.util.List
getXrefsOrBuilderList();
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder getXrefsOrBuilder(
int index);
/**
* repeated string hgvs = 9;
* @return A list containing the hgvs.
*/
java.util.List
getHgvsList();
/**
* repeated string hgvs = 9;
* @return The count of hgvs.
*/
int getHgvsCount();
/**
* repeated string hgvs = 9;
* @param index The index of the element to return.
* @return The hgvs at the given index.
*/
java.lang.String getHgvs(int index);
/**
* repeated string hgvs = 9;
* @param index The index of the value to return.
* @return The bytes of the hgvs at the given index.
*/
com.google.protobuf.ByteString
getHgvsBytes(int index);
/**
* string display_consequence_type = 10;
* @return The displayConsequenceType.
*/
java.lang.String getDisplayConsequenceType();
/**
* string display_consequence_type = 10;
* @return The bytes for displayConsequenceType.
*/
com.google.protobuf.ByteString
getDisplayConsequenceTypeBytes();
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
java.util.List
getConsequenceTypesList();
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getConsequenceTypes(int index);
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
int getConsequenceTypesCount();
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
java.util.List
getConsequenceTypesOrBuilderList();
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder getConsequenceTypesOrBuilder(
int index);
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
java.util.List
getPopulationFrequenciesList();
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency getPopulationFrequencies(int index);
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
int getPopulationFrequenciesCount();
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
java.util.List
getPopulationFrequenciesOrBuilderList();
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder getPopulationFrequenciesOrBuilder(
int index);
/**
* string minorAllele = 13;
* @return The minorAllele.
*/
java.lang.String getMinorAllele();
/**
* string minorAllele = 13;
* @return The bytes for minorAllele.
*/
com.google.protobuf.ByteString
getMinorAlleleBytes();
/**
* float minorAlleleFreq = 14;
* @return The minorAlleleFreq.
*/
float getMinorAlleleFreq();
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
java.util.List
getConservationList();
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getConservation(int index);
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
int getConservationCount();
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
java.util.List
getConservationOrBuilderList();
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getConservationOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
java.util.List
getGeneExpressionList();
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
org.opencb.biodata.models.core.protobuf.CommonModel.Expression getGeneExpression(int index);
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
int getGeneExpressionCount();
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
java.util.List
getGeneExpressionOrBuilderList();
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder getGeneExpressionOrBuilder(
int index);
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
java.util.List
getGeneTraitAssociationList();
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
org.opencb.biodata.models.core.protobuf.GeneModel.GeneTraitAssociation getGeneTraitAssociation(int index);
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
int getGeneTraitAssociationCount();
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
java.util.List
getGeneTraitAssociationOrBuilderList();
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
org.opencb.biodata.models.core.protobuf.GeneModel.GeneTraitAssociationOrBuilder getGeneTraitAssociationOrBuilder(
int index);
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
java.util.List
getGeneDrugInteractionList();
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
org.opencb.biodata.models.core.protobuf.CommonModel.GeneDrugInteraction getGeneDrugInteraction(int index);
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
int getGeneDrugInteractionCount();
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
java.util.List
getGeneDrugInteractionOrBuilderList();
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
org.opencb.biodata.models.core.protobuf.CommonModel.GeneDrugInteractionOrBuilder getGeneDrugInteractionOrBuilder(
int index);
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
* @return Whether the variantTraitAssociation field is set.
*/
boolean hasVariantTraitAssociation();
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
* @return The variantTraitAssociation.
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation getVariantTraitAssociation();
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociationOrBuilder getVariantTraitAssociationOrBuilder();
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
java.util.List
getTraitAssociationList();
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry getTraitAssociation(int index);
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
int getTraitAssociationCount();
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
java.util.List
getTraitAssociationOrBuilderList();
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntryOrBuilder getTraitAssociationOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
java.util.List
getFunctionalScoreList();
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getFunctionalScore(int index);
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
int getFunctionalScoreCount();
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
java.util.List
getFunctionalScoreOrBuilderList();
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getFunctionalScoreOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
java.util.List
getRepeatList();
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Repeat getRepeat(int index);
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
int getRepeatCount();
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
java.util.List
getRepeatOrBuilderList();
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.RepeatOrBuilder getRepeatOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
java.util.List
getCytobandList();
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband getCytoband(int index);
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
int getCytobandCount();
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
java.util.List
getCytobandOrBuilderList();
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CytobandOrBuilder getCytobandOrBuilder(
int index);
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
java.util.List
getDrugsList();
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug getDrugs(int index);
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
int getDrugsCount();
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
java.util.List
getDrugsOrBuilderList();
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.DrugOrBuilder getDrugsOrBuilder(
int index);
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
int getAdditionalAttributesCount();
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
boolean containsAdditionalAttributes(
java.lang.String key);
/**
* Use {@link #getAdditionalAttributesMap()} instead.
*/
@java.lang.Deprecated
java.util.Map
getAdditionalAttributes();
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
java.util.Map
getAdditionalAttributesMap();
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getAdditionalAttributesOrDefault(
java.lang.String key,
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute defaultValue);
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getAdditionalAttributesOrThrow(
java.lang.String key);
}
/**
* Protobuf type {@code protobuf.opencb.VariantAnnotation}
*/
public static final class VariantAnnotation extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.VariantAnnotation)
VariantAnnotationOrBuilder {
private static final long serialVersionUID = 0L;
// Use VariantAnnotation.newBuilder() to construct.
private VariantAnnotation(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
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reference_ = "";
alternate_ = "";
ancestralAllele_ = "";
id_ = "";
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consequenceTypes_ = java.util.Collections.emptyList();
populationFrequencies_ = java.util.Collections.emptyList();
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conservation_ = java.util.Collections.emptyList();
geneExpression_ = java.util.Collections.emptyList();
geneTraitAssociation_ = java.util.Collections.emptyList();
geneDrugInteraction_ = java.util.Collections.emptyList();
traitAssociation_ = java.util.Collections.emptyList();
functionalScore_ = java.util.Collections.emptyList();
repeat_ = java.util.Collections.emptyList();
cytoband_ = java.util.Collections.emptyList();
drugs_ = java.util.Collections.emptyList();
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@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
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return new VariantAnnotation();
}
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public final com.google.protobuf.UnknownFieldSet
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return this.unknownFields;
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private VariantAnnotation(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
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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) {
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java.lang.String s = input.readStringRequireUtf8();
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break;
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start_ = input.readInt32();
break;
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case 24: {
end_ = input.readInt32();
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case 34: {
java.lang.String s = input.readStringRequireUtf8();
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case 42: {
java.lang.String s = input.readStringRequireUtf8();
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case 50: {
java.lang.String s = input.readStringRequireUtf8();
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case 58: {
java.lang.String s = input.readStringRequireUtf8();
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case 66: {
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input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.parser(), extensionRegistry));
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case 74: {
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if (!((mutable_bitField0_ & 0x00000002) != 0)) {
hgvs_ = new com.google.protobuf.LazyStringArrayList();
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hgvs_.add(s);
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case 82: {
java.lang.String s = input.readStringRequireUtf8();
displayConsequenceType_ = s;
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case 90: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
consequenceTypes_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
consequenceTypes_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.parser(), extensionRegistry));
break;
}
case 98: {
if (!((mutable_bitField0_ & 0x00000008) != 0)) {
populationFrequencies_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000008;
}
populationFrequencies_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.parser(), extensionRegistry));
break;
}
case 106: {
java.lang.String s = input.readStringRequireUtf8();
minorAllele_ = s;
break;
}
case 117: {
minorAlleleFreq_ = input.readFloat();
break;
}
case 122: {
if (!((mutable_bitField0_ & 0x00000010) != 0)) {
conservation_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000010;
}
conservation_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.parser(), extensionRegistry));
break;
}
case 130: {
if (!((mutable_bitField0_ & 0x00000020) != 0)) {
geneExpression_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000020;
}
geneExpression_.add(
input.readMessage(org.opencb.biodata.models.core.protobuf.CommonModel.Expression.parser(), extensionRegistry));
break;
}
case 138: {
if (!((mutable_bitField0_ & 0x00000040) != 0)) {
geneTraitAssociation_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000040;
}
geneTraitAssociation_.add(
input.readMessage(org.opencb.biodata.models.core.protobuf.GeneModel.GeneTraitAssociation.parser(), extensionRegistry));
break;
}
case 146: {
if (!((mutable_bitField0_ & 0x00000080) != 0)) {
geneDrugInteraction_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000080;
}
geneDrugInteraction_.add(
input.readMessage(org.opencb.biodata.models.core.protobuf.CommonModel.GeneDrugInteraction.parser(), extensionRegistry));
break;
}
case 154: {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.Builder subBuilder = null;
if (variantTraitAssociation_ != null) {
subBuilder = variantTraitAssociation_.toBuilder();
}
variantTraitAssociation_ = input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(variantTraitAssociation_);
variantTraitAssociation_ = subBuilder.buildPartial();
}
break;
}
case 162: {
if (!((mutable_bitField0_ & 0x00000200) != 0)) {
functionalScore_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000200;
}
functionalScore_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.parser(), extensionRegistry));
break;
}
case 170: {
if (!((mutable_bitField0_ & 0x00000400) != 0)) {
repeat_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000400;
}
repeat_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Repeat.parser(), extensionRegistry));
break;
}
case 178: {
if (!((mutable_bitField0_ & 0x00000800) != 0)) {
cytoband_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000800;
}
cytoband_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband.parser(), extensionRegistry));
break;
}
case 186: {
if (!((mutable_bitField0_ & 0x00002000) != 0)) {
additionalAttributes_ = com.google.protobuf.MapField.newMapField(
AdditionalAttributesDefaultEntryHolder.defaultEntry);
mutable_bitField0_ |= 0x00002000;
}
com.google.protobuf.MapEntry
additionalAttributes__ = input.readMessage(
AdditionalAttributesDefaultEntryHolder.defaultEntry.getParserForType(), extensionRegistry);
additionalAttributes_.getMutableMap().put(
additionalAttributes__.getKey(), additionalAttributes__.getValue());
break;
}
case 194: {
if (!((mutable_bitField0_ & 0x00000100) != 0)) {
traitAssociation_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000100;
}
traitAssociation_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry.parser(), extensionRegistry));
break;
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case 202: {
if (!((mutable_bitField0_ & 0x00001000) != 0)) {
drugs_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00001000;
}
drugs_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug.parser(), extensionRegistry));
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
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}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
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if (((mutable_bitField0_ & 0x00000001) != 0)) {
xrefs_ = java.util.Collections.unmodifiableList(xrefs_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
hgvs_ = hgvs_.getUnmodifiableView();
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
consequenceTypes_ = java.util.Collections.unmodifiableList(consequenceTypes_);
}
if (((mutable_bitField0_ & 0x00000008) != 0)) {
populationFrequencies_ = java.util.Collections.unmodifiableList(populationFrequencies_);
}
if (((mutable_bitField0_ & 0x00000010) != 0)) {
conservation_ = java.util.Collections.unmodifiableList(conservation_);
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if (((mutable_bitField0_ & 0x00000020) != 0)) {
geneExpression_ = java.util.Collections.unmodifiableList(geneExpression_);
}
if (((mutable_bitField0_ & 0x00000040) != 0)) {
geneTraitAssociation_ = java.util.Collections.unmodifiableList(geneTraitAssociation_);
}
if (((mutable_bitField0_ & 0x00000080) != 0)) {
geneDrugInteraction_ = java.util.Collections.unmodifiableList(geneDrugInteraction_);
}
if (((mutable_bitField0_ & 0x00000200) != 0)) {
functionalScore_ = java.util.Collections.unmodifiableList(functionalScore_);
}
if (((mutable_bitField0_ & 0x00000400) != 0)) {
repeat_ = java.util.Collections.unmodifiableList(repeat_);
}
if (((mutable_bitField0_ & 0x00000800) != 0)) {
cytoband_ = java.util.Collections.unmodifiableList(cytoband_);
}
if (((mutable_bitField0_ & 0x00000100) != 0)) {
traitAssociation_ = java.util.Collections.unmodifiableList(traitAssociation_);
}
if (((mutable_bitField0_ & 0x00001000) != 0)) {
drugs_ = java.util.Collections.unmodifiableList(drugs_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
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}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantAnnotation_descriptor;
}
@SuppressWarnings({"rawtypes"})
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default:
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@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
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// @@protoc_insertion_point(interface_extends:protobuf.opencb.VariantAnnotation.Xref)
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java.lang.String getSource();
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com.google.protobuf.ByteString
getSourceBytes();
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/**
* Protobuf type {@code protobuf.opencb.VariantAnnotation.Xref}
*/
public static final class Xref extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.VariantAnnotation.Xref)
XrefOrBuilder {
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private Xref(com.google.protobuf.GeneratedMessageV3.Builder builder) {
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public static final com.google.protobuf.Descriptors.Descriptor
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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com.google.protobuf.CodedInputStream input)
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return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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/**
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// @@protoc_insertion_point(builder_implements:protobuf.opencb.VariantAnnotation.AdditionalAttribute)
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttributeOrBuilder {
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result.attribute_.makeImmutable();
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@java.lang.Override
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@java.lang.Override
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com.google.protobuf.Descriptors.FieldDescriptor field) {
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@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
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@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
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@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
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internalGetMutableAttribute().mergeFrom(
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this.mergeUnknownFields(other.unknownFields);
onChanged();
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@java.lang.Override
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@java.lang.Override
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com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute parsedMessage = null;
try {
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parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute) e.getUnfinishedMessage();
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private int bitField0_;
private com.google.protobuf.MapField<
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private com.google.protobuf.MapField
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if (attribute_ == null) {
return com.google.protobuf.MapField.emptyMapField(
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return attribute_;
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private com.google.protobuf.MapField
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onChanged();;
if (attribute_ == null) {
attribute_ = com.google.protobuf.MapField.newMapField(
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/**
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*/
public boolean containsAttribute(
java.lang.String key) {
if (key == null) { throw new java.lang.NullPointerException(); }
return internalGetAttribute().getMap().containsKey(key);
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/**
* Use {@link #getAttributeMap()} instead.
*/
@java.lang.Deprecated
public java.util.Map getAttribute() {
return getAttributeMap();
}
/**
* map<string, string> attribute = 1;
*/
public java.util.Map getAttributeMap() {
return internalGetAttribute().getMap();
}
/**
* map<string, string> attribute = 1;
*/
public java.lang.String getAttributeOrDefault(
java.lang.String key,
java.lang.String defaultValue) {
if (key == null) { throw new java.lang.NullPointerException(); }
java.util.Map map =
internalGetAttribute().getMap();
return map.containsKey(key) ? map.get(key) : defaultValue;
}
/**
* map<string, string> attribute = 1;
*/
public java.lang.String getAttributeOrThrow(
java.lang.String key) {
if (key == null) { throw new java.lang.NullPointerException(); }
java.util.Map map =
internalGetAttribute().getMap();
if (!map.containsKey(key)) {
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}
return map.get(key);
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/**
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*/
public Builder removeAttribute(
java.lang.String key) {
if (key == null) { throw new java.lang.NullPointerException(); }
internalGetMutableAttribute().getMutableMap()
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return this;
}
/**
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*/
@java.lang.Deprecated
public java.util.Map
getMutableAttribute() {
return internalGetMutableAttribute().getMutableMap();
}
/**
* map<string, string> attribute = 1;
*/
public Builder putAttribute(
java.lang.String key,
java.lang.String value) {
if (key == null) { throw new java.lang.NullPointerException(); }
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internalGetMutableAttribute().getMutableMap()
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return this;
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/**
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java.util.Map values) {
internalGetMutableAttribute().getMutableMap()
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return this;
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@java.lang.Override
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@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
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// @@protoc_insertion_point(builder_scope:protobuf.opencb.VariantAnnotation.AdditionalAttribute)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.VariantAnnotation.AdditionalAttribute)
private static final org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute DEFAULT_INSTANCE;
static {
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}
public static org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
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public AdditionalAttribute parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new AdditionalAttribute(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
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public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getDefaultInstanceForType() {
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}
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public static final int CHROMOSOME_FIELD_NUMBER = 1;
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/**
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
chromosome_ = s;
return s;
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/**
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java.lang.Object ref = chromosome_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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chromosome_ = b;
return b;
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public static final int START_FIELD_NUMBER = 2;
private int start_;
/**
* int32 start = 2;
* @return The start.
*/
public int getStart() {
return start_;
}
public static final int END_FIELD_NUMBER = 3;
private int end_;
/**
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*/
public int getEnd() {
return end_;
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public static final int REFERENCE_FIELD_NUMBER = 4;
private volatile java.lang.Object reference_;
/**
* string reference = 4;
* @return The reference.
*/
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java.lang.Object ref = reference_;
if (ref instanceof java.lang.String) {
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
reference_ = s;
return s;
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getReferenceBytes() {
java.lang.Object ref = reference_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
reference_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
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public static final int ALTERNATE_FIELD_NUMBER = 5;
private volatile java.lang.Object alternate_;
/**
* string alternate = 5;
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*/
public java.lang.String getAlternate() {
java.lang.Object ref = alternate_;
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();
alternate_ = s;
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getAlternateBytes() {
java.lang.Object ref = alternate_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alternate_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int ANCESTRAL_ALLELE_FIELD_NUMBER = 6;
private volatile java.lang.Object ancestralAllele_;
/**
* string ancestral_allele = 6;
* @return The ancestralAllele.
*/
public java.lang.String getAncestralAllele() {
java.lang.Object ref = ancestralAllele_;
if (ref instanceof java.lang.String) {
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com.google.protobuf.ByteString bs =
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java.lang.String s = bs.toStringUtf8();
ancestralAllele_ = s;
return s;
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getAncestralAlleleBytes() {
java.lang.Object ref = ancestralAllele_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ancestralAllele_ = b;
return b;
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return (com.google.protobuf.ByteString) ref;
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public static final int ID_FIELD_NUMBER = 7;
private volatile java.lang.Object id_;
/**
* string id = 7;
* @return The id.
*/
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 =
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java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
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/**
* string id = 7;
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getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int XREFS_FIELD_NUMBER = 8;
private java.util.List xrefs_;
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public java.util.List getXrefsList() {
return xrefs_;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public java.util.List
getXrefsOrBuilderList() {
return xrefs_;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public int getXrefsCount() {
return xrefs_.size();
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref getXrefs(int index) {
return xrefs_.get(index);
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder getXrefsOrBuilder(
int index) {
return xrefs_.get(index);
}
public static final int HGVS_FIELD_NUMBER = 9;
private com.google.protobuf.LazyStringList hgvs_;
/**
* repeated string hgvs = 9;
* @return A list containing the hgvs.
*/
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return hgvs_;
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/**
* repeated string hgvs = 9;
* @return The count of hgvs.
*/
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return hgvs_.size();
}
/**
* repeated string hgvs = 9;
* @param index The index of the element to return.
* @return The hgvs at the given index.
*/
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return hgvs_.get(index);
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* repeated string hgvs = 9;
* @param index The index of the value to return.
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public static final int DISPLAY_CONSEQUENCE_TYPE_FIELD_NUMBER = 10;
private volatile java.lang.Object displayConsequenceType_;
/**
* string display_consequence_type = 10;
* @return The displayConsequenceType.
*/
public java.lang.String getDisplayConsequenceType() {
java.lang.Object ref = displayConsequenceType_;
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();
displayConsequenceType_ = s;
return s;
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/**
* string display_consequence_type = 10;
* @return The bytes for displayConsequenceType.
*/
public com.google.protobuf.ByteString
getDisplayConsequenceTypeBytes() {
java.lang.Object ref = displayConsequenceType_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
displayConsequenceType_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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public static final int CONSEQUENCE_TYPES_FIELD_NUMBER = 11;
private java.util.List consequenceTypes_;
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
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/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
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getConsequenceTypesOrBuilderList() {
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/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public int getConsequenceTypesCount() {
return consequenceTypes_.size();
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getConsequenceTypes(int index) {
return consequenceTypes_.get(index);
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder getConsequenceTypesOrBuilder(
int index) {
return consequenceTypes_.get(index);
}
public static final int POPULATION_FREQUENCIES_FIELD_NUMBER = 12;
private java.util.List populationFrequencies_;
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public java.util.List getPopulationFrequenciesList() {
return populationFrequencies_;
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/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public java.util.List
getPopulationFrequenciesOrBuilderList() {
return populationFrequencies_;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public int getPopulationFrequenciesCount() {
return populationFrequencies_.size();
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency getPopulationFrequencies(int index) {
return populationFrequencies_.get(index);
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder getPopulationFrequenciesOrBuilder(
int index) {
return populationFrequencies_.get(index);
}
public static final int MINORALLELE_FIELD_NUMBER = 13;
private volatile java.lang.Object minorAllele_;
/**
* string minorAllele = 13;
* @return The minorAllele.
*/
public java.lang.String getMinorAllele() {
java.lang.Object ref = minorAllele_;
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();
minorAllele_ = s;
return s;
}
}
/**
* string minorAllele = 13;
* @return The bytes for minorAllele.
*/
public com.google.protobuf.ByteString
getMinorAlleleBytes() {
java.lang.Object ref = minorAllele_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
minorAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int MINORALLELEFREQ_FIELD_NUMBER = 14;
private float minorAlleleFreq_;
/**
* float minorAlleleFreq = 14;
* @return The minorAlleleFreq.
*/
public float getMinorAlleleFreq() {
return minorAlleleFreq_;
}
public static final int CONSERVATION_FIELD_NUMBER = 15;
private java.util.List conservation_;
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public java.util.List getConservationList() {
return conservation_;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public java.util.List
getConservationOrBuilderList() {
return conservation_;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public int getConservationCount() {
return conservation_.size();
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getConservation(int index) {
return conservation_.get(index);
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getConservationOrBuilder(
int index) {
return conservation_.get(index);
}
public static final int GENE_EXPRESSION_FIELD_NUMBER = 16;
private java.util.List geneExpression_;
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public java.util.List getGeneExpressionList() {
return geneExpression_;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public java.util.List
getGeneExpressionOrBuilderList() {
return geneExpression_;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public int getGeneExpressionCount() {
return geneExpression_.size();
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.Expression getGeneExpression(int index) {
return geneExpression_.get(index);
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder getGeneExpressionOrBuilder(
int index) {
return geneExpression_.get(index);
}
public static final int GENE_TRAIT_ASSOCIATION_FIELD_NUMBER = 17;
private java.util.List geneTraitAssociation_;
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
public java.util.List getGeneTraitAssociationList() {
return geneTraitAssociation_;
}
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
public java.util.List
getGeneTraitAssociationOrBuilderList() {
return geneTraitAssociation_;
}
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
public int getGeneTraitAssociationCount() {
return geneTraitAssociation_.size();
}
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
public org.opencb.biodata.models.core.protobuf.GeneModel.GeneTraitAssociation getGeneTraitAssociation(int index) {
return geneTraitAssociation_.get(index);
}
/**
* repeated .protobuf.opencb.GeneTraitAssociation gene_trait_association = 17;
*/
public org.opencb.biodata.models.core.protobuf.GeneModel.GeneTraitAssociationOrBuilder getGeneTraitAssociationOrBuilder(
int index) {
return geneTraitAssociation_.get(index);
}
public static final int GENE_DRUG_INTERACTION_FIELD_NUMBER = 18;
private java.util.List geneDrugInteraction_;
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
public java.util.List getGeneDrugInteractionList() {
return geneDrugInteraction_;
}
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
public java.util.List
getGeneDrugInteractionOrBuilderList() {
return geneDrugInteraction_;
}
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
public int getGeneDrugInteractionCount() {
return geneDrugInteraction_.size();
}
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.GeneDrugInteraction getGeneDrugInteraction(int index) {
return geneDrugInteraction_.get(index);
}
/**
* repeated .protobuf.opencb.GeneDrugInteraction gene_drug_interaction = 18;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.GeneDrugInteractionOrBuilder getGeneDrugInteractionOrBuilder(
int index) {
return geneDrugInteraction_.get(index);
}
public static final int VARIANT_TRAIT_ASSOCIATION_FIELD_NUMBER = 19;
private org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation variantTraitAssociation_;
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
* @return Whether the variantTraitAssociation field is set.
*/
public boolean hasVariantTraitAssociation() {
return variantTraitAssociation_ != null;
}
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
* @return The variantTraitAssociation.
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation getVariantTraitAssociation() {
return variantTraitAssociation_ == null ? org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociation.getDefaultInstance() : variantTraitAssociation_;
}
/**
* .protobuf.opencb.VariantTraitAssociation variant_trait_association = 19;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantTraitAssociationOrBuilder getVariantTraitAssociationOrBuilder() {
return getVariantTraitAssociation();
}
public static final int TRAIT_ASSOCIATION_FIELD_NUMBER = 24;
private java.util.List traitAssociation_;
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
public java.util.List getTraitAssociationList() {
return traitAssociation_;
}
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
public java.util.List
getTraitAssociationOrBuilderList() {
return traitAssociation_;
}
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
public int getTraitAssociationCount() {
return traitAssociation_.size();
}
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry getTraitAssociation(int index) {
return traitAssociation_.get(index);
}
/**
* repeated .protobuf.opencb.EvidenceEntry trait_association = 24;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntryOrBuilder getTraitAssociationOrBuilder(
int index) {
return traitAssociation_.get(index);
}
public static final int FUNCTIONAL_SCORE_FIELD_NUMBER = 20;
private java.util.List functionalScore_;
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
public java.util.List getFunctionalScoreList() {
return functionalScore_;
}
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
public java.util.List
getFunctionalScoreOrBuilderList() {
return functionalScore_;
}
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
public int getFunctionalScoreCount() {
return functionalScore_.size();
}
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getFunctionalScore(int index) {
return functionalScore_.get(index);
}
/**
* repeated .protobuf.opencb.Score functional_score = 20;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getFunctionalScoreOrBuilder(
int index) {
return functionalScore_.get(index);
}
public static final int REPEAT_FIELD_NUMBER = 21;
private java.util.List repeat_;
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
public java.util.List getRepeatList() {
return repeat_;
}
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
public java.util.List
getRepeatOrBuilderList() {
return repeat_;
}
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
public int getRepeatCount() {
return repeat_.size();
}
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Repeat getRepeat(int index) {
return repeat_.get(index);
}
/**
* repeated .protobuf.opencb.Repeat repeat = 21;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.RepeatOrBuilder getRepeatOrBuilder(
int index) {
return repeat_.get(index);
}
public static final int CYTOBAND_FIELD_NUMBER = 22;
private java.util.List cytoband_;
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
public java.util.List getCytobandList() {
return cytoband_;
}
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
public java.util.List
getCytobandOrBuilderList() {
return cytoband_;
}
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
public int getCytobandCount() {
return cytoband_.size();
}
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Cytoband getCytoband(int index) {
return cytoband_.get(index);
}
/**
* repeated .protobuf.opencb.Cytoband cytoband = 22;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.CytobandOrBuilder getCytobandOrBuilder(
int index) {
return cytoband_.get(index);
}
public static final int DRUGS_FIELD_NUMBER = 25;
private java.util.List drugs_;
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
public java.util.List getDrugsList() {
return drugs_;
}
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
public java.util.List
getDrugsOrBuilderList() {
return drugs_;
}
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
public int getDrugsCount() {
return drugs_.size();
}
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Drug getDrugs(int index) {
return drugs_.get(index);
}
/**
* repeated .protobuf.opencb.Drug drugs = 25;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.DrugOrBuilder getDrugsOrBuilder(
int index) {
return drugs_.get(index);
}
public static final int ADDITIONAL_ATTRIBUTES_FIELD_NUMBER = 23;
private static final class AdditionalAttributesDefaultEntryHolder {
static final com.google.protobuf.MapEntry<
java.lang.String, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute> defaultEntry =
com.google.protobuf.MapEntry
.newDefaultInstance(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.internal_static_protobuf_opencb_VariantAnnotation_AdditionalAttributesEntry_descriptor,
com.google.protobuf.WireFormat.FieldType.STRING,
"",
com.google.protobuf.WireFormat.FieldType.MESSAGE,
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute.getDefaultInstance());
}
private com.google.protobuf.MapField<
java.lang.String, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute> additionalAttributes_;
private com.google.protobuf.MapField
internalGetAdditionalAttributes() {
if (additionalAttributes_ == null) {
return com.google.protobuf.MapField.emptyMapField(
AdditionalAttributesDefaultEntryHolder.defaultEntry);
}
return additionalAttributes_;
}
public int getAdditionalAttributesCount() {
return internalGetAdditionalAttributes().getMap().size();
}
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
public boolean containsAdditionalAttributes(
java.lang.String key) {
if (key == null) { throw new java.lang.NullPointerException(); }
return internalGetAdditionalAttributes().getMap().containsKey(key);
}
/**
* Use {@link #getAdditionalAttributesMap()} instead.
*/
@java.lang.Deprecated
public java.util.Map getAdditionalAttributes() {
return getAdditionalAttributesMap();
}
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
public java.util.Map getAdditionalAttributesMap() {
return internalGetAdditionalAttributes().getMap();
}
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getAdditionalAttributesOrDefault(
java.lang.String key,
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute defaultValue) {
if (key == null) { throw new java.lang.NullPointerException(); }
java.util.Map map =
internalGetAdditionalAttributes().getMap();
return map.containsKey(key) ? map.get(key) : defaultValue;
}
/**
* map<string, .protobuf.opencb.VariantAnnotation.AdditionalAttribute> additional_attributes = 23;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.AdditionalAttribute getAdditionalAttributesOrThrow(
java.lang.String key) {
if (key == null) { throw new java.lang.NullPointerException(); }
java.util.Map map =
internalGetAdditionalAttributes().getMap();
if (!map.containsKey(key)) {
throw new java.lang.IllegalArgumentException();
}
return map.get(key);
}
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 (!getChromosomeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, chromosome_);
}
if (start_ != 0) {
output.writeInt32(2, start_);
}
if (end_ != 0) {
output.writeInt32(3, end_);
}
if (!getReferenceBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, reference_);
}
if (!getAlternateBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, alternate_);
}
if (!getAncestralAlleleBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, ancestralAllele_);
}
if (!getIdBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 7, id_);
}
for (int i = 0; i < xrefs_.size(); i++) {
output.writeMessage(8, xrefs_.get(i));
}
for (int i = 0; i < hgvs_.size(); i++) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 9, hgvs_.getRaw(i));
}
if (!getDisplayConsequenceTypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 10, displayConsequenceType_);
}
for (int i = 0; i < consequenceTypes_.size(); i++) {
output.writeMessage(11, consequenceTypes_.get(i));
}
for (int i = 0; i < populationFrequencies_.size(); i++) {
output.writeMessage(12, populationFrequencies_.get(i));
}
if (!getMinorAlleleBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 13, minorAllele_);
}
if (minorAlleleFreq_ != 0F) {
output.writeFloat(14, minorAlleleFreq_);
}
for (int i = 0; i < conservation_.size(); i++) {
output.writeMessage(15, conservation_.get(i));
}
for (int i = 0; i < geneExpression_.size(); i++) {
output.writeMessage(16, geneExpression_.get(i));
}
for (int i = 0; i < geneTraitAssociation_.size(); i++) {
output.writeMessage(17, geneTraitAssociation_.get(i));
}
for (int i = 0; i < geneDrugInteraction_.size(); i++) {
output.writeMessage(18, geneDrugInteraction_.get(i));
}
if (variantTraitAssociation_ != null) {
output.writeMessage(19, getVariantTraitAssociation());
}
for (int i = 0; i < functionalScore_.size(); i++) {
output.writeMessage(20, functionalScore_.get(i));
}
for (int i = 0; i < repeat_.size(); i++) {
output.writeMessage(21, repeat_.get(i));
}
for (int i = 0; i < cytoband_.size(); i++) {
output.writeMessage(22, cytoband_.get(i));
}
com.google.protobuf.GeneratedMessageV3
.serializeStringMapTo(
output,
internalGetAdditionalAttributes(),
AdditionalAttributesDefaultEntryHolder.defaultEntry,
23);
for (int i = 0; i < traitAssociation_.size(); i++) {
output.writeMessage(24, traitAssociation_.get(i));
}
for (int i = 0; i < drugs_.size(); i++) {
output.writeMessage(25, drugs_.get(i));
}
unknownFields.writeTo(output);
}
@java.lang.Override
public int getSerializedSize() {
int size = memoizedSize;
if (size != -1) return size;
size = 0;
if (!getChromosomeBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, chromosome_);
}
if (start_ != 0) {
size += com.google.protobuf.CodedOutputStream
.computeInt32Size(2, start_);
}
if (end_ != 0) {
size += com.google.protobuf.CodedOutputStream
.computeInt32Size(3, end_);
}
if (!getReferenceBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(4, reference_);
}
if (!getAlternateBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, alternate_);
}
if (!getAncestralAlleleBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, ancestralAllele_);
}
if (!getIdBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(7, id_);
}
for (int i = 0; i < xrefs_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(8, xrefs_.get(i));
}
{
int dataSize = 0;
for (int i = 0; i < hgvs_.size(); i++) {
dataSize += computeStringSizeNoTag(hgvs_.getRaw(i));
}
size += dataSize;
size += 1 * getHgvsList().size();
}
if (!getDisplayConsequenceTypeBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(10, displayConsequenceType_);
}
for (int i = 0; i < consequenceTypes_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(11, consequenceTypes_.get(i));
}
for (int i = 0; i < populationFrequencies_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(12, populationFrequencies_.get(i));
}
if (!getMinorAlleleBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(13, minorAllele_);
}
if (minorAlleleFreq_ != 0F) {
size += com.google.protobuf.CodedOutputStream
.computeFloatSize(14, minorAlleleFreq_);
}
for (int i = 0; i < conservation_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(15, conservation_.get(i));
}
for (int i = 0; i < geneExpression_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(16, geneExpression_.get(i));
}
for (int i = 0; i < geneTraitAssociation_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(17, geneTraitAssociation_.get(i));
}
for (int i = 0; i < geneDrugInteraction_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(18, geneDrugInteraction_.get(i));
}
if (variantTraitAssociation_ != null) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(19, getVariantTraitAssociation());
}
for (int i = 0; i < functionalScore_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(20, functionalScore_.get(i));
}
for (int i = 0; i < repeat_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(21, repeat_.get(i));
}
for (int i = 0; i < cytoband_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(22, cytoband_.get(i));
}
for (java.util.Map.Entry entry
: internalGetAdditionalAttributes().getMap().entrySet()) {
com.google.protobuf.MapEntry
additionalAttributes__ = AdditionalAttributesDefaultEntryHolder.defaultEntry.newBuilderForType()
.setKey(entry.getKey())
.setValue(entry.getValue())
.build();
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(23, additionalAttributes__);
}
for (int i = 0; i < traitAssociation_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
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}
for (int i = 0; i < drugs_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(25, drugs_.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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation other = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation) obj;
if (!getChromosome()
.equals(other.getChromosome())) return false;
if (getStart()
!= other.getStart()) return false;
if (getEnd()
!= other.getEnd()) return false;
if (!getReference()
.equals(other.getReference())) return false;
if (!getAlternate()
.equals(other.getAlternate())) return false;
if (!getAncestralAllele()
.equals(other.getAncestralAllele())) return false;
if (!getId()
.equals(other.getId())) return false;
if (!getXrefsList()
.equals(other.getXrefsList())) return false;
if (!getHgvsList()
.equals(other.getHgvsList())) return false;
if (!getDisplayConsequenceType()
.equals(other.getDisplayConsequenceType())) return false;
if (!getConsequenceTypesList()
.equals(other.getConsequenceTypesList())) return false;
if (!getPopulationFrequenciesList()
.equals(other.getPopulationFrequenciesList())) return false;
if (!getMinorAllele()
.equals(other.getMinorAllele())) return false;
if (java.lang.Float.floatToIntBits(getMinorAlleleFreq())
!= java.lang.Float.floatToIntBits(
other.getMinorAlleleFreq())) return false;
if (!getConservationList()
.equals(other.getConservationList())) return false;
if (!getGeneExpressionList()
.equals(other.getGeneExpressionList())) return false;
if (!getGeneTraitAssociationList()
.equals(other.getGeneTraitAssociationList())) return false;
if (!getGeneDrugInteractionList()
.equals(other.getGeneDrugInteractionList())) return false;
if (hasVariantTraitAssociation() != other.hasVariantTraitAssociation()) return false;
if (hasVariantTraitAssociation()) {
if (!getVariantTraitAssociation()
.equals(other.getVariantTraitAssociation())) return false;
}
if (!getTraitAssociationList()
.equals(other.getTraitAssociationList())) return false;
if (!getFunctionalScoreList()
.equals(other.getFunctionalScoreList())) return false;
if (!getRepeatList()
.equals(other.getRepeatList())) return false;
if (!getCytobandList()
.equals(other.getCytobandList())) return false;
if (!getDrugsList()
.equals(other.getDrugsList())) return false;
if (!internalGetAdditionalAttributes().equals(
other.internalGetAdditionalAttributes())) 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) + CHROMOSOME_FIELD_NUMBER;
hash = (53 * hash) + getChromosome().hashCode();
hash = (37 * hash) + START_FIELD_NUMBER;
hash = (53 * hash) + getStart();
hash = (37 * hash) + END_FIELD_NUMBER;
hash = (53 * hash) + getEnd();
hash = (37 * hash) + REFERENCE_FIELD_NUMBER;
hash = (53 * hash) + getReference().hashCode();
hash = (37 * hash) + ALTERNATE_FIELD_NUMBER;
hash = (53 * hash) + getAlternate().hashCode();
hash = (37 * hash) + ANCESTRAL_ALLELE_FIELD_NUMBER;
hash = (53 * hash) + getAncestralAllele().hashCode();
hash = (37 * hash) + ID_FIELD_NUMBER;
hash = (53 * hash) + getId().hashCode();
if (getXrefsCount() > 0) {
hash = (37 * hash) + XREFS_FIELD_NUMBER;
hash = (53 * hash) + getXrefsList().hashCode();
}
if (getHgvsCount() > 0) {
hash = (37 * hash) + HGVS_FIELD_NUMBER;
hash = (53 * hash) + getHgvsList().hashCode();
}
hash = (37 * hash) + DISPLAY_CONSEQUENCE_TYPE_FIELD_NUMBER;
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traitAssociation_.addAll(other.traitAssociation_);
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if (!other.traitAssociation_.isEmpty()) {
if (traitAssociationBuilder_.isEmpty()) {
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traitAssociationBuilder_.addAllMessages(other.traitAssociation_);
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if (functionalScoreBuilder_ == null) {
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if (functionalScore_.isEmpty()) {
functionalScore_ = other.functionalScore_;
bitField0_ = (bitField0_ & ~0x00000200);
} else {
ensureFunctionalScoreIsMutable();
functionalScore_.addAll(other.functionalScore_);
}
onChanged();
}
} else {
if (!other.functionalScore_.isEmpty()) {
if (functionalScoreBuilder_.isEmpty()) {
functionalScoreBuilder_.dispose();
functionalScoreBuilder_ = null;
functionalScore_ = other.functionalScore_;
bitField0_ = (bitField0_ & ~0x00000200);
functionalScoreBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getFunctionalScoreFieldBuilder() : null;
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functionalScoreBuilder_.addAllMessages(other.functionalScore_);
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}
if (repeatBuilder_ == null) {
if (!other.repeat_.isEmpty()) {
if (repeat_.isEmpty()) {
repeat_ = other.repeat_;
bitField0_ = (bitField0_ & ~0x00000400);
} else {
ensureRepeatIsMutable();
repeat_.addAll(other.repeat_);
}
onChanged();
}
} else {
if (!other.repeat_.isEmpty()) {
if (repeatBuilder_.isEmpty()) {
repeatBuilder_.dispose();
repeatBuilder_ = null;
repeat_ = other.repeat_;
bitField0_ = (bitField0_ & ~0x00000400);
repeatBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getRepeatFieldBuilder() : null;
} else {
repeatBuilder_.addAllMessages(other.repeat_);
}
}
}
if (cytobandBuilder_ == null) {
if (!other.cytoband_.isEmpty()) {
if (cytoband_.isEmpty()) {
cytoband_ = other.cytoband_;
bitField0_ = (bitField0_ & ~0x00000800);
} else {
ensureCytobandIsMutable();
cytoband_.addAll(other.cytoband_);
}
onChanged();
}
} else {
if (!other.cytoband_.isEmpty()) {
if (cytobandBuilder_.isEmpty()) {
cytobandBuilder_.dispose();
cytobandBuilder_ = null;
cytoband_ = other.cytoband_;
bitField0_ = (bitField0_ & ~0x00000800);
cytobandBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
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cytobandBuilder_.addAllMessages(other.cytoband_);
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if (drugsBuilder_ == null) {
if (!other.drugs_.isEmpty()) {
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drugs_ = other.drugs_;
bitField0_ = (bitField0_ & ~0x00001000);
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onChanged();
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if (!other.drugs_.isEmpty()) {
if (drugsBuilder_.isEmpty()) {
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bitField0_ = (bitField0_ & ~0x00001000);
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com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getDrugsFieldBuilder() : null;
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drugsBuilder_.addAllMessages(other.drugs_);
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}
}
internalGetMutableAdditionalAttributes().mergeFrom(
other.internalGetAdditionalAttributes());
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.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private java.lang.Object chromosome_ = "";
/**
* string chromosome = 1;
* @return The chromosome.
*/
public java.lang.String getChromosome() {
java.lang.Object ref = chromosome_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
chromosome_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string chromosome = 1;
* @return The bytes for chromosome.
*/
public com.google.protobuf.ByteString
getChromosomeBytes() {
java.lang.Object ref = chromosome_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chromosome_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string chromosome = 1;
* @param value The chromosome to set.
* @return This builder for chaining.
*/
public Builder setChromosome(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
chromosome_ = value;
onChanged();
return this;
}
/**
* string chromosome = 1;
* @return This builder for chaining.
*/
public Builder clearChromosome() {
chromosome_ = getDefaultInstance().getChromosome();
onChanged();
return this;
}
/**
* string chromosome = 1;
* @param value The bytes for chromosome to set.
* @return This builder for chaining.
*/
public Builder setChromosomeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
chromosome_ = value;
onChanged();
return this;
}
private int start_ ;
/**
* int32 start = 2;
* @return The start.
*/
public int getStart() {
return start_;
}
/**
* int32 start = 2;
* @param value The start to set.
* @return This builder for chaining.
*/
public Builder setStart(int value) {
start_ = value;
onChanged();
return this;
}
/**
* int32 start = 2;
* @return This builder for chaining.
*/
public Builder clearStart() {
start_ = 0;
onChanged();
return this;
}
private int end_ ;
/**
* int32 end = 3;
* @return The end.
*/
public int getEnd() {
return end_;
}
/**
* int32 end = 3;
* @param value The end to set.
* @return This builder for chaining.
*/
public Builder setEnd(int value) {
end_ = value;
onChanged();
return this;
}
/**
* int32 end = 3;
* @return This builder for chaining.
*/
public Builder clearEnd() {
end_ = 0;
onChanged();
return this;
}
private java.lang.Object reference_ = "";
/**
* string reference = 4;
* @return The reference.
*/
public java.lang.String getReference() {
java.lang.Object ref = reference_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
reference_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string reference = 4;
* @return The bytes for reference.
*/
public com.google.protobuf.ByteString
getReferenceBytes() {
java.lang.Object ref = reference_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
reference_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string reference = 4;
* @param value The reference to set.
* @return This builder for chaining.
*/
public Builder setReference(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
reference_ = value;
onChanged();
return this;
}
/**
* string reference = 4;
* @return This builder for chaining.
*/
public Builder clearReference() {
reference_ = getDefaultInstance().getReference();
onChanged();
return this;
}
/**
* string reference = 4;
* @param value The bytes for reference to set.
* @return This builder for chaining.
*/
public Builder setReferenceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
reference_ = value;
onChanged();
return this;
}
private java.lang.Object alternate_ = "";
/**
* string alternate = 5;
* @return The alternate.
*/
public java.lang.String getAlternate() {
java.lang.Object ref = alternate_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
alternate_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string alternate = 5;
* @return The bytes for alternate.
*/
public com.google.protobuf.ByteString
getAlternateBytes() {
java.lang.Object ref = alternate_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
alternate_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string alternate = 5;
* @param value The alternate to set.
* @return This builder for chaining.
*/
public Builder setAlternate(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
alternate_ = value;
onChanged();
return this;
}
/**
* string alternate = 5;
* @return This builder for chaining.
*/
public Builder clearAlternate() {
alternate_ = getDefaultInstance().getAlternate();
onChanged();
return this;
}
/**
* string alternate = 5;
* @param value The bytes for alternate to set.
* @return This builder for chaining.
*/
public Builder setAlternateBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
alternate_ = value;
onChanged();
return this;
}
private java.lang.Object ancestralAllele_ = "";
/**
* string ancestral_allele = 6;
* @return The ancestralAllele.
*/
public java.lang.String getAncestralAllele() {
java.lang.Object ref = ancestralAllele_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
ancestralAllele_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string ancestral_allele = 6;
* @return The bytes for ancestralAllele.
*/
public com.google.protobuf.ByteString
getAncestralAlleleBytes() {
java.lang.Object ref = ancestralAllele_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
ancestralAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string ancestral_allele = 6;
* @param value The ancestralAllele to set.
* @return This builder for chaining.
*/
public Builder setAncestralAllele(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ancestralAllele_ = value;
onChanged();
return this;
}
/**
* string ancestral_allele = 6;
* @return This builder for chaining.
*/
public Builder clearAncestralAllele() {
ancestralAllele_ = getDefaultInstance().getAncestralAllele();
onChanged();
return this;
}
/**
* string ancestral_allele = 6;
* @param value The bytes for ancestralAllele to set.
* @return This builder for chaining.
*/
public Builder setAncestralAlleleBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ancestralAllele_ = value;
onChanged();
return this;
}
private java.lang.Object id_ = "";
/**
* string id = 7;
* @return The id.
*/
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 = 7;
* @return The bytes for id.
*/
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 = 7;
* @param value The id to set.
* @return This builder for chaining.
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
* string id = 7;
* @return This builder for chaining.
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
* string id = 7;
* @param value The bytes for id to set.
* @return This builder for chaining.
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
private java.util.List xrefs_ =
java.util.Collections.emptyList();
private void ensureXrefsIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
xrefs_ = new java.util.ArrayList(xrefs_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder> xrefsBuilder_;
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public java.util.List getXrefsList() {
if (xrefsBuilder_ == null) {
return java.util.Collections.unmodifiableList(xrefs_);
} else {
return xrefsBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public int getXrefsCount() {
if (xrefsBuilder_ == null) {
return xrefs_.size();
} else {
return xrefsBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref getXrefs(int index) {
if (xrefsBuilder_ == null) {
return xrefs_.get(index);
} else {
return xrefsBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder setXrefs(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref value) {
if (xrefsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureXrefsIsMutable();
xrefs_.set(index, value);
onChanged();
} else {
xrefsBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder setXrefs(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder builderForValue) {
if (xrefsBuilder_ == null) {
ensureXrefsIsMutable();
xrefs_.set(index, builderForValue.build());
onChanged();
} else {
xrefsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder addXrefs(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref value) {
if (xrefsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureXrefsIsMutable();
xrefs_.add(value);
onChanged();
} else {
xrefsBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder addXrefs(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref value) {
if (xrefsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureXrefsIsMutable();
xrefs_.add(index, value);
onChanged();
} else {
xrefsBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder addXrefs(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder builderForValue) {
if (xrefsBuilder_ == null) {
ensureXrefsIsMutable();
xrefs_.add(builderForValue.build());
onChanged();
} else {
xrefsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder addXrefs(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder builderForValue) {
if (xrefsBuilder_ == null) {
ensureXrefsIsMutable();
xrefs_.add(index, builderForValue.build());
onChanged();
} else {
xrefsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder addAllXrefs(
java.lang.Iterable values) {
if (xrefsBuilder_ == null) {
ensureXrefsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, xrefs_);
onChanged();
} else {
xrefsBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder clearXrefs() {
if (xrefsBuilder_ == null) {
xrefs_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
xrefsBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public Builder removeXrefs(int index) {
if (xrefsBuilder_ == null) {
ensureXrefsIsMutable();
xrefs_.remove(index);
onChanged();
} else {
xrefsBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder getXrefsBuilder(
int index) {
return getXrefsFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder getXrefsOrBuilder(
int index) {
if (xrefsBuilder_ == null) {
return xrefs_.get(index); } else {
return xrefsBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public java.util.List
getXrefsOrBuilderList() {
if (xrefsBuilder_ != null) {
return xrefsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(xrefs_);
}
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder addXrefsBuilder() {
return getXrefsFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder addXrefsBuilder(
int index) {
return getXrefsFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.VariantAnnotation.Xref xrefs = 8;
*/
public java.util.List
getXrefsBuilderList() {
return getXrefsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder>
getXrefsFieldBuilder() {
if (xrefsBuilder_ == null) {
xrefsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.Xref.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.VariantAnnotation.XrefOrBuilder>(
xrefs_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
xrefs_ = null;
}
return xrefsBuilder_;
}
private com.google.protobuf.LazyStringList hgvs_ = com.google.protobuf.LazyStringArrayList.EMPTY;
private void ensureHgvsIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
hgvs_ = new com.google.protobuf.LazyStringArrayList(hgvs_);
bitField0_ |= 0x00000002;
}
}
/**
* repeated string hgvs = 9;
* @return A list containing the hgvs.
*/
public com.google.protobuf.ProtocolStringList
getHgvsList() {
return hgvs_.getUnmodifiableView();
}
/**
* repeated string hgvs = 9;
* @return The count of hgvs.
*/
public int getHgvsCount() {
return hgvs_.size();
}
/**
* repeated string hgvs = 9;
* @param index The index of the element to return.
* @return The hgvs at the given index.
*/
public java.lang.String getHgvs(int index) {
return hgvs_.get(index);
}
/**
* repeated string hgvs = 9;
* @param index The index of the value to return.
* @return The bytes of the hgvs at the given index.
*/
public com.google.protobuf.ByteString
getHgvsBytes(int index) {
return hgvs_.getByteString(index);
}
/**
* repeated string hgvs = 9;
* @param index The index to set the value at.
* @param value The hgvs to set.
* @return This builder for chaining.
*/
public Builder setHgvs(
int index, java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureHgvsIsMutable();
hgvs_.set(index, value);
onChanged();
return this;
}
/**
* repeated string hgvs = 9;
* @param value The hgvs to add.
* @return This builder for chaining.
*/
public Builder addHgvs(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureHgvsIsMutable();
hgvs_.add(value);
onChanged();
return this;
}
/**
* repeated string hgvs = 9;
* @param values The hgvs to add.
* @return This builder for chaining.
*/
public Builder addAllHgvs(
java.lang.Iterable values) {
ensureHgvsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, hgvs_);
onChanged();
return this;
}
/**
* repeated string hgvs = 9;
* @return This builder for chaining.
*/
public Builder clearHgvs() {
hgvs_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
return this;
}
/**
* repeated string hgvs = 9;
* @param value The bytes of the hgvs to add.
* @return This builder for chaining.
*/
public Builder addHgvsBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensureHgvsIsMutable();
hgvs_.add(value);
onChanged();
return this;
}
private java.lang.Object displayConsequenceType_ = "";
/**
* string display_consequence_type = 10;
* @return The displayConsequenceType.
*/
public java.lang.String getDisplayConsequenceType() {
java.lang.Object ref = displayConsequenceType_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
displayConsequenceType_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string display_consequence_type = 10;
* @return The bytes for displayConsequenceType.
*/
public com.google.protobuf.ByteString
getDisplayConsequenceTypeBytes() {
java.lang.Object ref = displayConsequenceType_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
displayConsequenceType_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string display_consequence_type = 10;
* @param value The displayConsequenceType to set.
* @return This builder for chaining.
*/
public Builder setDisplayConsequenceType(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
displayConsequenceType_ = value;
onChanged();
return this;
}
/**
* string display_consequence_type = 10;
* @return This builder for chaining.
*/
public Builder clearDisplayConsequenceType() {
displayConsequenceType_ = getDefaultInstance().getDisplayConsequenceType();
onChanged();
return this;
}
/**
* string display_consequence_type = 10;
* @param value The bytes for displayConsequenceType to set.
* @return This builder for chaining.
*/
public Builder setDisplayConsequenceTypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
displayConsequenceType_ = value;
onChanged();
return this;
}
private java.util.List consequenceTypes_ =
java.util.Collections.emptyList();
private void ensureConsequenceTypesIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
consequenceTypes_ = new java.util.ArrayList(consequenceTypes_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder> consequenceTypesBuilder_;
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public java.util.List getConsequenceTypesList() {
if (consequenceTypesBuilder_ == null) {
return java.util.Collections.unmodifiableList(consequenceTypes_);
} else {
return consequenceTypesBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public int getConsequenceTypesCount() {
if (consequenceTypesBuilder_ == null) {
return consequenceTypes_.size();
} else {
return consequenceTypesBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType getConsequenceTypes(int index) {
if (consequenceTypesBuilder_ == null) {
return consequenceTypes_.get(index);
} else {
return consequenceTypesBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder setConsequenceTypes(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType value) {
if (consequenceTypesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConsequenceTypesIsMutable();
consequenceTypes_.set(index, value);
onChanged();
} else {
consequenceTypesBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder setConsequenceTypes(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder builderForValue) {
if (consequenceTypesBuilder_ == null) {
ensureConsequenceTypesIsMutable();
consequenceTypes_.set(index, builderForValue.build());
onChanged();
} else {
consequenceTypesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder addConsequenceTypes(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType value) {
if (consequenceTypesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConsequenceTypesIsMutable();
consequenceTypes_.add(value);
onChanged();
} else {
consequenceTypesBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder addConsequenceTypes(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType value) {
if (consequenceTypesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConsequenceTypesIsMutable();
consequenceTypes_.add(index, value);
onChanged();
} else {
consequenceTypesBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder addConsequenceTypes(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder builderForValue) {
if (consequenceTypesBuilder_ == null) {
ensureConsequenceTypesIsMutable();
consequenceTypes_.add(builderForValue.build());
onChanged();
} else {
consequenceTypesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder addConsequenceTypes(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder builderForValue) {
if (consequenceTypesBuilder_ == null) {
ensureConsequenceTypesIsMutable();
consequenceTypes_.add(index, builderForValue.build());
onChanged();
} else {
consequenceTypesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder addAllConsequenceTypes(
java.lang.Iterable values) {
if (consequenceTypesBuilder_ == null) {
ensureConsequenceTypesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, consequenceTypes_);
onChanged();
} else {
consequenceTypesBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder clearConsequenceTypes() {
if (consequenceTypesBuilder_ == null) {
consequenceTypes_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
consequenceTypesBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public Builder removeConsequenceTypes(int index) {
if (consequenceTypesBuilder_ == null) {
ensureConsequenceTypesIsMutable();
consequenceTypes_.remove(index);
onChanged();
} else {
consequenceTypesBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder getConsequenceTypesBuilder(
int index) {
return getConsequenceTypesFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder getConsequenceTypesOrBuilder(
int index) {
if (consequenceTypesBuilder_ == null) {
return consequenceTypes_.get(index); } else {
return consequenceTypesBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public java.util.List
getConsequenceTypesOrBuilderList() {
if (consequenceTypesBuilder_ != null) {
return consequenceTypesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(consequenceTypes_);
}
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder addConsequenceTypesBuilder() {
return getConsequenceTypesFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder addConsequenceTypesBuilder(
int index) {
return getConsequenceTypesFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.ConsequenceType consequence_types = 11;
*/
public java.util.List
getConsequenceTypesBuilderList() {
return getConsequenceTypesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder>
getConsequenceTypesFieldBuilder() {
if (consequenceTypesBuilder_ == null) {
consequenceTypesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceType.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ConsequenceTypeOrBuilder>(
consequenceTypes_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
consequenceTypes_ = null;
}
return consequenceTypesBuilder_;
}
private java.util.List populationFrequencies_ =
java.util.Collections.emptyList();
private void ensurePopulationFrequenciesIsMutable() {
if (!((bitField0_ & 0x00000008) != 0)) {
populationFrequencies_ = new java.util.ArrayList(populationFrequencies_);
bitField0_ |= 0x00000008;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder> populationFrequenciesBuilder_;
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public java.util.List getPopulationFrequenciesList() {
if (populationFrequenciesBuilder_ == null) {
return java.util.Collections.unmodifiableList(populationFrequencies_);
} else {
return populationFrequenciesBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public int getPopulationFrequenciesCount() {
if (populationFrequenciesBuilder_ == null) {
return populationFrequencies_.size();
} else {
return populationFrequenciesBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency getPopulationFrequencies(int index) {
if (populationFrequenciesBuilder_ == null) {
return populationFrequencies_.get(index);
} else {
return populationFrequenciesBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder setPopulationFrequencies(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency value) {
if (populationFrequenciesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.set(index, value);
onChanged();
} else {
populationFrequenciesBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder setPopulationFrequencies(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder builderForValue) {
if (populationFrequenciesBuilder_ == null) {
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.set(index, builderForValue.build());
onChanged();
} else {
populationFrequenciesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder addPopulationFrequencies(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency value) {
if (populationFrequenciesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.add(value);
onChanged();
} else {
populationFrequenciesBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder addPopulationFrequencies(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency value) {
if (populationFrequenciesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.add(index, value);
onChanged();
} else {
populationFrequenciesBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder addPopulationFrequencies(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder builderForValue) {
if (populationFrequenciesBuilder_ == null) {
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.add(builderForValue.build());
onChanged();
} else {
populationFrequenciesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder addPopulationFrequencies(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder builderForValue) {
if (populationFrequenciesBuilder_ == null) {
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.add(index, builderForValue.build());
onChanged();
} else {
populationFrequenciesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder addAllPopulationFrequencies(
java.lang.Iterable values) {
if (populationFrequenciesBuilder_ == null) {
ensurePopulationFrequenciesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, populationFrequencies_);
onChanged();
} else {
populationFrequenciesBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder clearPopulationFrequencies() {
if (populationFrequenciesBuilder_ == null) {
populationFrequencies_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
onChanged();
} else {
populationFrequenciesBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public Builder removePopulationFrequencies(int index) {
if (populationFrequenciesBuilder_ == null) {
ensurePopulationFrequenciesIsMutable();
populationFrequencies_.remove(index);
onChanged();
} else {
populationFrequenciesBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder getPopulationFrequenciesBuilder(
int index) {
return getPopulationFrequenciesFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder getPopulationFrequenciesOrBuilder(
int index) {
if (populationFrequenciesBuilder_ == null) {
return populationFrequencies_.get(index); } else {
return populationFrequenciesBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public java.util.List
getPopulationFrequenciesOrBuilderList() {
if (populationFrequenciesBuilder_ != null) {
return populationFrequenciesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(populationFrequencies_);
}
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder addPopulationFrequenciesBuilder() {
return getPopulationFrequenciesFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder addPopulationFrequenciesBuilder(
int index) {
return getPopulationFrequenciesFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.PopulationFrequency population_frequencies = 12;
*/
public java.util.List
getPopulationFrequenciesBuilderList() {
return getPopulationFrequenciesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder>
getPopulationFrequenciesFieldBuilder() {
if (populationFrequenciesBuilder_ == null) {
populationFrequenciesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequency.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.PopulationFrequencyOrBuilder>(
populationFrequencies_,
((bitField0_ & 0x00000008) != 0),
getParentForChildren(),
isClean());
populationFrequencies_ = null;
}
return populationFrequenciesBuilder_;
}
private java.lang.Object minorAllele_ = "";
/**
* string minorAllele = 13;
* @return The minorAllele.
*/
public java.lang.String getMinorAllele() {
java.lang.Object ref = minorAllele_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
minorAllele_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string minorAllele = 13;
* @return The bytes for minorAllele.
*/
public com.google.protobuf.ByteString
getMinorAlleleBytes() {
java.lang.Object ref = minorAllele_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
minorAllele_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string minorAllele = 13;
* @param value The minorAllele to set.
* @return This builder for chaining.
*/
public Builder setMinorAllele(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
minorAllele_ = value;
onChanged();
return this;
}
/**
* string minorAllele = 13;
* @return This builder for chaining.
*/
public Builder clearMinorAllele() {
minorAllele_ = getDefaultInstance().getMinorAllele();
onChanged();
return this;
}
/**
* string minorAllele = 13;
* @param value The bytes for minorAllele to set.
* @return This builder for chaining.
*/
public Builder setMinorAlleleBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
minorAllele_ = value;
onChanged();
return this;
}
private float minorAlleleFreq_ ;
/**
* float minorAlleleFreq = 14;
* @return The minorAlleleFreq.
*/
public float getMinorAlleleFreq() {
return minorAlleleFreq_;
}
/**
* float minorAlleleFreq = 14;
* @param value The minorAlleleFreq to set.
* @return This builder for chaining.
*/
public Builder setMinorAlleleFreq(float value) {
minorAlleleFreq_ = value;
onChanged();
return this;
}
/**
* float minorAlleleFreq = 14;
* @return This builder for chaining.
*/
public Builder clearMinorAlleleFreq() {
minorAlleleFreq_ = 0F;
onChanged();
return this;
}
private java.util.List conservation_ =
java.util.Collections.emptyList();
private void ensureConservationIsMutable() {
if (!((bitField0_ & 0x00000010) != 0)) {
conservation_ = new java.util.ArrayList(conservation_);
bitField0_ |= 0x00000010;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder> conservationBuilder_;
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public java.util.List getConservationList() {
if (conservationBuilder_ == null) {
return java.util.Collections.unmodifiableList(conservation_);
} else {
return conservationBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public int getConservationCount() {
if (conservationBuilder_ == null) {
return conservation_.size();
} else {
return conservationBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score getConservation(int index) {
if (conservationBuilder_ == null) {
return conservation_.get(index);
} else {
return conservationBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder setConservation(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (conservationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConservationIsMutable();
conservation_.set(index, value);
onChanged();
} else {
conservationBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder setConservation(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (conservationBuilder_ == null) {
ensureConservationIsMutable();
conservation_.set(index, builderForValue.build());
onChanged();
} else {
conservationBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder addConservation(org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (conservationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConservationIsMutable();
conservation_.add(value);
onChanged();
} else {
conservationBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder addConservation(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score value) {
if (conservationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureConservationIsMutable();
conservation_.add(index, value);
onChanged();
} else {
conservationBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder addConservation(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (conservationBuilder_ == null) {
ensureConservationIsMutable();
conservation_.add(builderForValue.build());
onChanged();
} else {
conservationBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder addConservation(
int index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder builderForValue) {
if (conservationBuilder_ == null) {
ensureConservationIsMutable();
conservation_.add(index, builderForValue.build());
onChanged();
} else {
conservationBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder addAllConservation(
java.lang.Iterable values) {
if (conservationBuilder_ == null) {
ensureConservationIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, conservation_);
onChanged();
} else {
conservationBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder clearConservation() {
if (conservationBuilder_ == null) {
conservation_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
onChanged();
} else {
conservationBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public Builder removeConservation(int index) {
if (conservationBuilder_ == null) {
ensureConservationIsMutable();
conservation_.remove(index);
onChanged();
} else {
conservationBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder getConservationBuilder(
int index) {
return getConservationFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder getConservationOrBuilder(
int index) {
if (conservationBuilder_ == null) {
return conservation_.get(index); } else {
return conservationBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public java.util.List
getConservationOrBuilderList() {
if (conservationBuilder_ != null) {
return conservationBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(conservation_);
}
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder addConservationBuilder() {
return getConservationFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder addConservationBuilder(
int index) {
return getConservationFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Score conservation = 15;
*/
public java.util.List
getConservationBuilderList() {
return getConservationFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder>
getConservationFieldBuilder() {
if (conservationBuilder_ == null) {
conservationBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.Score.Builder, org.opencb.biodata.models.variant.protobuf.VariantAnnotationProto.ScoreOrBuilder>(
conservation_,
((bitField0_ & 0x00000010) != 0),
getParentForChildren(),
isClean());
conservation_ = null;
}
return conservationBuilder_;
}
private java.util.List geneExpression_ =
java.util.Collections.emptyList();
private void ensureGeneExpressionIsMutable() {
if (!((bitField0_ & 0x00000020) != 0)) {
geneExpression_ = new java.util.ArrayList(geneExpression_);
bitField0_ |= 0x00000020;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.core.protobuf.CommonModel.Expression, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder, org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder> geneExpressionBuilder_;
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public java.util.List getGeneExpressionList() {
if (geneExpressionBuilder_ == null) {
return java.util.Collections.unmodifiableList(geneExpression_);
} else {
return geneExpressionBuilder_.getMessageList();
}
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public int getGeneExpressionCount() {
if (geneExpressionBuilder_ == null) {
return geneExpression_.size();
} else {
return geneExpressionBuilder_.getCount();
}
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.Expression getGeneExpression(int index) {
if (geneExpressionBuilder_ == null) {
return geneExpression_.get(index);
} else {
return geneExpressionBuilder_.getMessage(index);
}
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder setGeneExpression(
int index, org.opencb.biodata.models.core.protobuf.CommonModel.Expression value) {
if (geneExpressionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGeneExpressionIsMutable();
geneExpression_.set(index, value);
onChanged();
} else {
geneExpressionBuilder_.setMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder setGeneExpression(
int index, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder builderForValue) {
if (geneExpressionBuilder_ == null) {
ensureGeneExpressionIsMutable();
geneExpression_.set(index, builderForValue.build());
onChanged();
} else {
geneExpressionBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder addGeneExpression(org.opencb.biodata.models.core.protobuf.CommonModel.Expression value) {
if (geneExpressionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGeneExpressionIsMutable();
geneExpression_.add(value);
onChanged();
} else {
geneExpressionBuilder_.addMessage(value);
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder addGeneExpression(
int index, org.opencb.biodata.models.core.protobuf.CommonModel.Expression value) {
if (geneExpressionBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGeneExpressionIsMutable();
geneExpression_.add(index, value);
onChanged();
} else {
geneExpressionBuilder_.addMessage(index, value);
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder addGeneExpression(
org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder builderForValue) {
if (geneExpressionBuilder_ == null) {
ensureGeneExpressionIsMutable();
geneExpression_.add(builderForValue.build());
onChanged();
} else {
geneExpressionBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder addGeneExpression(
int index, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder builderForValue) {
if (geneExpressionBuilder_ == null) {
ensureGeneExpressionIsMutable();
geneExpression_.add(index, builderForValue.build());
onChanged();
} else {
geneExpressionBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder addAllGeneExpression(
java.lang.Iterable values) {
if (geneExpressionBuilder_ == null) {
ensureGeneExpressionIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, geneExpression_);
onChanged();
} else {
geneExpressionBuilder_.addAllMessages(values);
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder clearGeneExpression() {
if (geneExpressionBuilder_ == null) {
geneExpression_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000020);
onChanged();
} else {
geneExpressionBuilder_.clear();
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public Builder removeGeneExpression(int index) {
if (geneExpressionBuilder_ == null) {
ensureGeneExpressionIsMutable();
geneExpression_.remove(index);
onChanged();
} else {
geneExpressionBuilder_.remove(index);
}
return this;
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder getGeneExpressionBuilder(
int index) {
return getGeneExpressionFieldBuilder().getBuilder(index);
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder getGeneExpressionOrBuilder(
int index) {
if (geneExpressionBuilder_ == null) {
return geneExpression_.get(index); } else {
return geneExpressionBuilder_.getMessageOrBuilder(index);
}
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public java.util.List
getGeneExpressionOrBuilderList() {
if (geneExpressionBuilder_ != null) {
return geneExpressionBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(geneExpression_);
}
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder addGeneExpressionBuilder() {
return getGeneExpressionFieldBuilder().addBuilder(
org.opencb.biodata.models.core.protobuf.CommonModel.Expression.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder addGeneExpressionBuilder(
int index) {
return getGeneExpressionFieldBuilder().addBuilder(
index, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.getDefaultInstance());
}
/**
* repeated .protobuf.opencb.Expression gene_expression = 16;
*/
public java.util.List
getGeneExpressionBuilderList() {
return getGeneExpressionFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.core.protobuf.CommonModel.Expression, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder, org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder>
getGeneExpressionFieldBuilder() {
if (geneExpressionBuilder_ == null) {
geneExpressionBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.core.protobuf.CommonModel.Expression, org.opencb.biodata.models.core.protobuf.CommonModel.Expression.Builder, org.opencb.biodata.models.core.protobuf.CommonModel.ExpressionOrBuilder>(
geneExpression_,
((bitField0_ & 0x00000020) != 0),
getParentForChildren(),
isClean());
geneExpression_ = null;
}
return geneExpressionBuilder_;
}
private java.util.List