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A Protobuf schema for capturing clinical phenotypes
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: base.proto
package org.phenopackets.schema.v1.core;
/**
*
* A single SPDI allele.
* The SPDI notation uses four fields and is written out as four elements delimited by colons S:P:D:I, where
* S = SequenceId
* P = Position , a 0-based coordinate for where the Deleted Sequence starts
* D = DeletedSequence , sequence for the deletion, can be empty
* I = InsertedSequence , sequence for the insertion, can be empty
* The SPDI notation represents variation as deletion of a sequence (D) at a given position (P) in reference sequence (S)
* followed by insertion of a replacement sequence (I) at that same position. Position 0 indicates a deletion that
* starts immediately before the first nucleotide, and position 1 represents a deletion interval that starts between the
* first and second residues, and so on. Either the deleted or the inserted interval can be empty, resulting a pure
* insertion or deletion.
* The deleted and inserted sequences in SPDI are all written on the positive strand for two-stranded molecules.
* See https://www.ncbi.nlm.nih.gov/variation/notation/
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.SpdiAllele}
*/
public final class SpdiAllele extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:org.phenopackets.schema.v1.core.SpdiAllele)
SpdiAlleleOrBuilder {
private static final long serialVersionUID = 0L;
// Use SpdiAllele.newBuilder() to construct.
private SpdiAllele(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private SpdiAllele() {
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seqId_ = "";
deletedSequence_ = "";
insertedSequence_ = "";
}
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protected java.lang.Object newInstance(
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return new SpdiAllele();
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private SpdiAllele(
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@java.lang.Override
public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.phenopackets.schema.v1.core.SpdiAllele)) {
return super.equals(obj);
}
org.phenopackets.schema.v1.core.SpdiAllele other = (org.phenopackets.schema.v1.core.SpdiAllele) obj;
if (!getId()
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if (!getSeqId()
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if (getPosition()
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if (!getDeletedSequence()
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if (!getInsertedSequence()
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hash = (19 * hash) + getDescriptor().hashCode();
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public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
public static org.phenopackets.schema.v1.core.SpdiAllele parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.core.SpdiAllele parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.phenopackets.schema.v1.core.SpdiAllele 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 static Builder newBuilder() {
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public static Builder newBuilder(org.phenopackets.schema.v1.core.SpdiAllele prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
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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;
}
/**
*
* A single SPDI allele.
* The SPDI notation uses four fields and is written out as four elements delimited by colons S:P:D:I, where
* S = SequenceId
* P = Position , a 0-based coordinate for where the Deleted Sequence starts
* D = DeletedSequence , sequence for the deletion, can be empty
* I = InsertedSequence , sequence for the insertion, can be empty
* The SPDI notation represents variation as deletion of a sequence (D) at a given position (P) in reference sequence (S)
* followed by insertion of a replacement sequence (I) at that same position. Position 0 indicates a deletion that
* starts immediately before the first nucleotide, and position 1 represents a deletion interval that starts between the
* first and second residues, and so on. Either the deleted or the inserted interval can be empty, resulting a pure
* insertion or deletion.
* The deleted and inserted sequences in SPDI are all written on the positive strand for two-stranded molecules.
* See https://www.ncbi.nlm.nih.gov/variation/notation/
*
*
* Protobuf type {@code org.phenopackets.schema.v1.core.SpdiAllele}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:org.phenopackets.schema.v1.core.SpdiAllele)
org.phenopackets.schema.v1.core.SpdiAlleleOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_SpdiAllele_descriptor;
}
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return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_SpdiAllele_fieldAccessorTable
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org.phenopackets.schema.v1.core.SpdiAllele.class, org.phenopackets.schema.v1.core.SpdiAllele.Builder.class);
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// Construct using org.phenopackets.schema.v1.core.SpdiAllele.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
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private Builder(
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maybeForceBuilderInitialization();
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id_ = "";
seqId_ = "";
position_ = 0;
deletedSequence_ = "";
insertedSequence_ = "";
return this;
}
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getDescriptorForType() {
return org.phenopackets.schema.v1.core.Base.internal_static_org_phenopackets_schema_v1_core_SpdiAllele_descriptor;
}
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throw newUninitializedMessageException(result);
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return result;
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@java.lang.Override
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result.id_ = id_;
result.seqId_ = seqId_;
result.position_ = position_;
result.deletedSequence_ = deletedSequence_;
result.insertedSequence_ = insertedSequence_;
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onChanged();
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onChanged();
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onChanged();
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onChanged();
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if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
deletedSequence_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string deleted_sequence = 4;
*/
public Builder setDeletedSequence(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
deletedSequence_ = value;
onChanged();
return this;
}
/**
* string deleted_sequence = 4;
*/
public Builder clearDeletedSequence() {
deletedSequence_ = getDefaultInstance().getDeletedSequence();
onChanged();
return this;
}
/**
* string deleted_sequence = 4;
*/
public Builder setDeletedSequenceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
deletedSequence_ = value;
onChanged();
return this;
}
private java.lang.Object insertedSequence_ = "";
/**
* string inserted_sequence = 5;
*/
public java.lang.String getInsertedSequence() {
java.lang.Object ref = insertedSequence_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
insertedSequence_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* string inserted_sequence = 5;
*/
public com.google.protobuf.ByteString
getInsertedSequenceBytes() {
java.lang.Object ref = insertedSequence_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
insertedSequence_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* string inserted_sequence = 5;
*/
public Builder setInsertedSequence(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
insertedSequence_ = value;
onChanged();
return this;
}
/**
* string inserted_sequence = 5;
*/
public Builder clearInsertedSequence() {
insertedSequence_ = getDefaultInstance().getInsertedSequence();
onChanged();
return this;
}
/**
* string inserted_sequence = 5;
*/
public Builder setInsertedSequenceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
insertedSequence_ = value;
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:org.phenopackets.schema.v1.core.SpdiAllele)
}
// @@protoc_insertion_point(class_scope:org.phenopackets.schema.v1.core.SpdiAllele)
private static final org.phenopackets.schema.v1.core.SpdiAllele DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.phenopackets.schema.v1.core.SpdiAllele();
}
public static org.phenopackets.schema.v1.core.SpdiAllele getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public SpdiAllele parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new SpdiAllele(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.phenopackets.schema.v1.core.SpdiAllele getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}