/*
* Copyright 2015-2016 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: Alignment.proto
package org.opencb.opencga.storage.alignment.proto;
public final class AlignmentProto {
private AlignmentProto() {}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistry registry) {
}
public interface DifferenceOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
boolean hasOperator();
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator getOperator();
// optional uint32 pos = 2;
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
boolean hasPos();
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
int getPos();
// optional uint32 length = 3;
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
boolean hasLength();
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
int getLength();
// optional bytes sequence = 4;
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
boolean hasSequence();
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
com.google.protobuf.ByteString getSequence();
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Difference}
*/
public static final class Difference extends
com.google.protobuf.GeneratedMessage
implements DifferenceOrBuilder {
// Use Difference.newBuilder() to construct.
private Difference(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Difference(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Difference defaultInstance;
public static Difference getDefaultInstance() {
return defaultInstance;
}
public Difference getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Difference(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 8: {
int rawValue = input.readEnum();
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator value = org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator.valueOf(rawValue);
if (value == null) {
unknownFields.mergeVarintField(1, rawValue);
} else {
bitField0_ |= 0x00000001;
operator_ = value;
}
break;
}
case 16: {
bitField0_ |= 0x00000002;
pos_ = input.readUInt32();
break;
}
case 24: {
bitField0_ |= 0x00000004;
length_ = input.readUInt32();
break;
}
case 34: {
bitField0_ |= 0x00000008;
sequence_ = input.readBytes();
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Difference_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder.class);
}
public static com.google.protobuf.Parser<Difference> PARSER =
new com.google.protobuf.AbstractParser<Difference>() {
public Difference parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Difference(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Difference> getParserForType() {
return PARSER;
}
/**
* Protobuf enum {@code org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator}
*/
public enum DifferenceOperator
implements com.google.protobuf.ProtocolMessageEnum {
/**
* <code>INSERTION = 1;</code>
*/
INSERTION(0, 1),
/**
* <code>DELETION = 2;</code>
*/
DELETION(1, 2),
/**
* <code>MISMATCH = 3;</code>
*/
MISMATCH(2, 3),
/**
* <code>SKIPPED_REGION = 4;</code>
*/
SKIPPED_REGION(3, 4),
/**
* <code>SOFT_CLIPPING = 5;</code>
*/
SOFT_CLIPPING(4, 5),
/**
* <code>HARD_CLIPPING = 6;</code>
*/
HARD_CLIPPING(5, 6),
/**
* <code>PADDING = 7;</code>
*/
PADDING(6, 7),
;
/**
* <code>INSERTION = 1;</code>
*/
public static final int INSERTION_VALUE = 1;
/**
* <code>DELETION = 2;</code>
*/
public static final int DELETION_VALUE = 2;
/**
* <code>MISMATCH = 3;</code>
*/
public static final int MISMATCH_VALUE = 3;
/**
* <code>SKIPPED_REGION = 4;</code>
*/
public static final int SKIPPED_REGION_VALUE = 4;
/**
* <code>SOFT_CLIPPING = 5;</code>
*/
public static final int SOFT_CLIPPING_VALUE = 5;
/**
* <code>HARD_CLIPPING = 6;</code>
*/
public static final int HARD_CLIPPING_VALUE = 6;
/**
* <code>PADDING = 7;</code>
*/
public static final int PADDING_VALUE = 7;
public final int getNumber() { return value; }
public static DifferenceOperator valueOf(int value) {
switch (value) {
case 1: return INSERTION;
case 2: return DELETION;
case 3: return MISMATCH;
case 4: return SKIPPED_REGION;
case 5: return SOFT_CLIPPING;
case 6: return HARD_CLIPPING;
case 7: return PADDING;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap<DifferenceOperator>
internalGetValueMap() {
return internalValueMap;
}
private static com.google.protobuf.Internal.EnumLiteMap<DifferenceOperator>
internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap<DifferenceOperator>() {
public DifferenceOperator findValueByNumber(int number) {
return DifferenceOperator.valueOf(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(index);
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.getDescriptor().getEnumTypes().get(0);
}
private static final DifferenceOperator[] VALUES = values();
public static DifferenceOperator valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
return VALUES[desc.getIndex()];
}
private final int index;
private final int value;
private DifferenceOperator(int index, int value) {
this.index = index;
this.value = value;
}
// @@protoc_insertion_point(enum_scope:org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator)
}
private int bitField0_;
// required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;
public static final int OPERATOR_FIELD_NUMBER = 1;
private org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator operator_;
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public boolean hasOperator() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator getOperator() {
return operator_;
}
// optional uint32 pos = 2;
public static final int POS_FIELD_NUMBER = 2;
private int pos_;
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public boolean hasPos() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public int getPos() {
return pos_;
}
// optional uint32 length = 3;
public static final int LENGTH_FIELD_NUMBER = 3;
private int length_;
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public boolean hasLength() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public int getLength() {
return length_;
}
// optional bytes sequence = 4;
public static final int SEQUENCE_FIELD_NUMBER = 4;
private com.google.protobuf.ByteString sequence_;
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public boolean hasSequence() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public com.google.protobuf.ByteString getSequence() {
return sequence_;
}
private void initFields() {
operator_ = org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator.INSERTION;
pos_ = 0;
length_ = 0;
sequence_ = com.google.protobuf.ByteString.EMPTY;
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasOperator()) {
memoizedIsInitialized = 0;
return false;
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeEnum(1, operator_.getNumber());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, pos_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
output.writeUInt32(3, length_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
output.writeBytes(4, sequence_);
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeEnumSize(1, operator_.getNumber());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, pos_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(3, length_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(4, sequence_);
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference 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.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Difference}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Difference_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
operator_ = org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator.INSERTION;
bitField0_ = (bitField0_ & ~0x00000001);
pos_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
length_ = 0;
bitField0_ = (bitField0_ & ~0x00000004);
sequence_ = com.google.protobuf.ByteString.EMPTY;
bitField0_ = (bitField0_ & ~0x00000008);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.operator_ = operator_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.pos_ = pos_;
if (((from_bitField0_ & 0x00000004) == 0x00000004)) {
to_bitField0_ |= 0x00000004;
}
result.length_ = length_;
if (((from_bitField0_ & 0x00000008) == 0x00000008)) {
to_bitField0_ |= 0x00000008;
}
result.sequence_ = sequence_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.getDefaultInstance()) return this;
if (other.hasOperator()) {
setOperator(other.getOperator());
}
if (other.hasPos()) {
setPos(other.getPos());
}
if (other.hasLength()) {
setLength(other.getLength());
}
if (other.hasSequence()) {
setSequence(other.getSequence());
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasOperator()) {
return false;
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;
private org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator operator_ = org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator.INSERTION;
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public boolean hasOperator() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator getOperator() {
return operator_;
}
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public Builder setOperator(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000001;
operator_ = value;
onChanged();
return this;
}
/**
* <code>required .org.opencb.opencga.storage.alignment.proto.Difference.DifferenceOperator operator = 1;</code>
*
* <pre>
*TODO: Default op? Summary, Bucket or Alignment level?
* </pre>
*/
public Builder clearOperator() {
bitField0_ = (bitField0_ & ~0x00000001);
operator_ = org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.DifferenceOperator.INSERTION;
onChanged();
return this;
}
// optional uint32 pos = 2;
private int pos_ ;
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public boolean hasPos() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public int getPos() {
return pos_;
}
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public Builder setPos(int value) {
bitField0_ |= 0x00000002;
pos_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 pos = 2;</code>
*
* <pre>
*If missing, starts at the end of the last difference.
* </pre>
*/
public Builder clearPos() {
bitField0_ = (bitField0_ & ~0x00000002);
pos_ = 0;
onChanged();
return this;
}
// optional uint32 length = 3;
private int length_ ;
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public boolean hasLength() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public int getLength() {
return length_;
}
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public Builder setLength(int value) {
bitField0_ |= 0x00000004;
length_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 length = 3;</code>
*
* <pre>
*If missing, length is length of sequence. If missing too, length is 1 //TODO: defaultDiffLength?
* </pre>
*/
public Builder clearLength() {
bitField0_ = (bitField0_ & ~0x00000004);
length_ = 0;
onChanged();
return this;
}
// optional bytes sequence = 4;
private com.google.protobuf.ByteString sequence_ = com.google.protobuf.ByteString.EMPTY;
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public boolean hasSequence() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public com.google.protobuf.ByteString getSequence() {
return sequence_;
}
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public Builder setSequence(com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000008;
sequence_ = value;
onChanged();
return this;
}
/**
* <code>optional bytes sequence = 4;</code>
*
* <pre>
*If missing, take from the reference sequence.
* </pre>
*/
public Builder clearSequence() {
bitField0_ = (bitField0_ & ~0x00000008);
sequence_ = getDefaultInstance().getSequence();
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Difference)
}
static {
defaultInstance = new Difference(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Difference)
}
public interface AlignmentRecordOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required string name = 1;
/**
* <code>required string name = 1;</code>
*/
boolean hasName();
/**
* <code>required string name = 1;</code>
*/
java.lang.String getName();
/**
* <code>required string name = 1;</code>
*/
com.google.protobuf.ByteString
getNameBytes();
// required uint32 pos = 2;
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
boolean hasPos();
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
int getPos();
// optional uint32 flags = 3;
/**
* <code>optional uint32 flags = 3;</code>
*/
boolean hasFlags();
/**
* <code>optional uint32 flags = 3;</code>
*/
int getFlags();
// optional uint32 len = 4;
/**
* <code>optional uint32 len = 4;</code>
*/
boolean hasLen();
/**
* <code>optional uint32 len = 4;</code>
*/
int getLen();
// required uint32 mapq = 5;
/**
* <code>required uint32 mapq = 5;</code>
*/
boolean hasMapq();
/**
* <code>required uint32 mapq = 5;</code>
*/
int getMapq();
// required string qualities = 6;
/**
* <code>required string qualities = 6;</code>
*/
boolean hasQualities();
/**
* <code>required string qualities = 6;</code>
*/
java.lang.String getQualities();
/**
* <code>required string qualities = 6;</code>
*/
com.google.protobuf.ByteString
getQualitiesBytes();
// optional string rnext = 7;
/**
* <code>optional string rnext = 7;</code>
*/
boolean hasRnext();
/**
* <code>optional string rnext = 7;</code>
*/
java.lang.String getRnext();
/**
* <code>optional string rnext = 7;</code>
*/
com.google.protobuf.ByteString
getRnextBytes();
// required sint32 relativePnext = 8;
/**
* <code>required sint32 relativePnext = 8;</code>
*/
boolean hasRelativePnext();
/**
* <code>required sint32 relativePnext = 8;</code>
*/
int getRelativePnext();
// required sint32 inferredInsertSize = 9;
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
boolean hasInferredInsertSize();
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
int getInferredInsertSize();
// repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference>
getDiffsList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference getDiffs(int index);
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
int getDiffsCount();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder>
getDiffsOrBuilderList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder getDiffsOrBuilder(
int index);
// repeated uint32 tags = 11 [packed = true];
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getTagsList();
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
int getTagsCount();
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
int getTags(int index);
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.AlignmentRecord}
*/
public static final class AlignmentRecord extends
com.google.protobuf.GeneratedMessage
implements AlignmentRecordOrBuilder {
// Use AlignmentRecord.newBuilder() to construct.
private AlignmentRecord(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private AlignmentRecord(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final AlignmentRecord defaultInstance;
public static AlignmentRecord getDefaultInstance() {
return defaultInstance;
}
public AlignmentRecord getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private AlignmentRecord(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 10: {
bitField0_ |= 0x00000001;
name_ = input.readBytes();
break;
}
case 16: {
bitField0_ |= 0x00000002;
pos_ = input.readUInt32();
break;
}
case 24: {
bitField0_ |= 0x00000004;
flags_ = input.readUInt32();
break;
}
case 32: {
bitField0_ |= 0x00000008;
len_ = input.readUInt32();
break;
}
case 40: {
bitField0_ |= 0x00000010;
mapq_ = input.readUInt32();
break;
}
case 50: {
bitField0_ |= 0x00000020;
qualities_ = input.readBytes();
break;
}
case 58: {
bitField0_ |= 0x00000040;
rnext_ = input.readBytes();
break;
}
case 64: {
bitField0_ |= 0x00000080;
relativePnext_ = input.readSInt32();
break;
}
case 72: {
bitField0_ |= 0x00000100;
inferredInsertSize_ = input.readSInt32();
break;
}
case 82: {
if (!((mutable_bitField0_ & 0x00000200) == 0x00000200)) {
diffs_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference>();
mutable_bitField0_ |= 0x00000200;
}
diffs_.add(input.readMessage(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.PARSER, extensionRegistry));
break;
}
case 88: {
if (!((mutable_bitField0_ & 0x00000400) == 0x00000400)) {
tags_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000400;
}
tags_.add(input.readUInt32());
break;
}
case 90: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000400) == 0x00000400) && input.getBytesUntilLimit() > 0) {
tags_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000400;
}
while (input.getBytesUntilLimit() > 0) {
tags_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000200) == 0x00000200)) {
diffs_ = java.util.Collections.unmodifiableList(diffs_);
}
if (((mutable_bitField0_ & 0x00000400) == 0x00000400)) {
tags_ = java.util.Collections.unmodifiableList(tags_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder.class);
}
public static com.google.protobuf.Parser<AlignmentRecord> PARSER =
new com.google.protobuf.AbstractParser<AlignmentRecord>() {
public AlignmentRecord parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new AlignmentRecord(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<AlignmentRecord> getParserForType() {
return PARSER;
}
private int bitField0_;
// required string name = 1;
public static final int NAME_FIELD_NUMBER = 1;
private java.lang.Object name_;
/**
* <code>required string name = 1;</code>
*/
public boolean hasName() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required string name = 1;</code>
*/
public java.lang.String getName() {
java.lang.Object ref = name_;
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();
if (bs.isValidUtf8()) {
name_ = s;
}
return s;
}
}
/**
* <code>required string name = 1;</code>
*/
public com.google.protobuf.ByteString
getNameBytes() {
java.lang.Object ref = name_;
if (ref instanceof java.lang.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;
}
}
// required uint32 pos = 2;
public static final int POS_FIELD_NUMBER = 2;
private int pos_;
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public boolean hasPos() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public int getPos() {
return pos_;
}
// optional uint32 flags = 3;
public static final int FLAGS_FIELD_NUMBER = 3;
private int flags_;
/**
* <code>optional uint32 flags = 3;</code>
*/
public boolean hasFlags() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional uint32 flags = 3;</code>
*/
public int getFlags() {
return flags_;
}
// optional uint32 len = 4;
public static final int LEN_FIELD_NUMBER = 4;
private int len_;
/**
* <code>optional uint32 len = 4;</code>
*/
public boolean hasLen() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional uint32 len = 4;</code>
*/
public int getLen() {
return len_;
}
// required uint32 mapq = 5;
public static final int MAPQ_FIELD_NUMBER = 5;
private int mapq_;
/**
* <code>required uint32 mapq = 5;</code>
*/
public boolean hasMapq() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>required uint32 mapq = 5;</code>
*/
public int getMapq() {
return mapq_;
}
// required string qualities = 6;
public static final int QUALITIES_FIELD_NUMBER = 6;
private java.lang.Object qualities_;
/**
* <code>required string qualities = 6;</code>
*/
public boolean hasQualities() {
return ((bitField0_ & 0x00000020) == 0x00000020);
}
/**
* <code>required string qualities = 6;</code>
*/
public java.lang.String getQualities() {
java.lang.Object ref = qualities_;
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();
if (bs.isValidUtf8()) {
qualities_ = s;
}
return s;
}
}
/**
* <code>required string qualities = 6;</code>
*/
public com.google.protobuf.ByteString
getQualitiesBytes() {
java.lang.Object ref = qualities_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
qualities_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
// optional string rnext = 7;
public static final int RNEXT_FIELD_NUMBER = 7;
private java.lang.Object rnext_;
/**
* <code>optional string rnext = 7;</code>
*/
public boolean hasRnext() {
return ((bitField0_ & 0x00000040) == 0x00000040);
}
/**
* <code>optional string rnext = 7;</code>
*/
public java.lang.String getRnext() {
java.lang.Object ref = rnext_;
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();
if (bs.isValidUtf8()) {
rnext_ = s;
}
return s;
}
}
/**
* <code>optional string rnext = 7;</code>
*/
public com.google.protobuf.ByteString
getRnextBytes() {
java.lang.Object ref = rnext_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
rnext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
// required sint32 relativePnext = 8;
public static final int RELATIVEPNEXT_FIELD_NUMBER = 8;
private int relativePnext_;
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public boolean hasRelativePnext() {
return ((bitField0_ & 0x00000080) == 0x00000080);
}
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public int getRelativePnext() {
return relativePnext_;
}
// required sint32 inferredInsertSize = 9;
public static final int INFERREDINSERTSIZE_FIELD_NUMBER = 9;
private int inferredInsertSize_;
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public boolean hasInferredInsertSize() {
return ((bitField0_ & 0x00000100) == 0x00000100);
}
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public int getInferredInsertSize() {
return inferredInsertSize_;
}
// repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;
public static final int DIFFS_FIELD_NUMBER = 10;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference> diffs_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference> getDiffsList() {
return diffs_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder>
getDiffsOrBuilderList() {
return diffs_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public int getDiffsCount() {
return diffs_.size();
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference getDiffs(int index) {
return diffs_.get(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder getDiffsOrBuilder(
int index) {
return diffs_.get(index);
}
// repeated uint32 tags = 11 [packed = true];
public static final int TAGS_FIELD_NUMBER = 11;
private java.util.List<java.lang.Integer> tags_;
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getTagsList() {
return tags_;
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public int getTagsCount() {
return tags_.size();
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public int getTags(int index) {
return tags_.get(index);
}
private int tagsMemoizedSerializedSize = -1;
private void initFields() {
name_ = "";
pos_ = 0;
flags_ = 0;
len_ = 0;
mapq_ = 0;
qualities_ = "";
rnext_ = "";
relativePnext_ = 0;
inferredInsertSize_ = 0;
diffs_ = java.util.Collections.emptyList();
tags_ = java.util.Collections.emptyList();
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasName()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasPos()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasMapq()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasQualities()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasRelativePnext()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasInferredInsertSize()) {
memoizedIsInitialized = 0;
return false;
}
for (int i = 0; i < getDiffsCount(); i++) {
if (!getDiffs(i).isInitialized()) {
memoizedIsInitialized = 0;
return false;
}
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeBytes(1, getNameBytes());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, pos_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
output.writeUInt32(3, flags_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
output.writeUInt32(4, len_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
output.writeUInt32(5, mapq_);
}
if (((bitField0_ & 0x00000020) == 0x00000020)) {
output.writeBytes(6, getQualitiesBytes());
}
if (((bitField0_ & 0x00000040) == 0x00000040)) {
output.writeBytes(7, getRnextBytes());
}
if (((bitField0_ & 0x00000080) == 0x00000080)) {
output.writeSInt32(8, relativePnext_);
}
if (((bitField0_ & 0x00000100) == 0x00000100)) {
output.writeSInt32(9, inferredInsertSize_);
}
for (int i = 0; i < diffs_.size(); i++) {
output.writeMessage(10, diffs_.get(i));
}
if (getTagsList().size() > 0) {
output.writeRawVarint32(90);
output.writeRawVarint32(tagsMemoizedSerializedSize);
}
for (int i = 0; i < tags_.size(); i++) {
output.writeUInt32NoTag(tags_.get(i));
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(1, getNameBytes());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, pos_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(3, flags_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(4, len_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(5, mapq_);
}
if (((bitField0_ & 0x00000020) == 0x00000020)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(6, getQualitiesBytes());
}
if (((bitField0_ & 0x00000040) == 0x00000040)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(7, getRnextBytes());
}
if (((bitField0_ & 0x00000080) == 0x00000080)) {
size += com.google.protobuf.CodedOutputStream
.computeSInt32Size(8, relativePnext_);
}
if (((bitField0_ & 0x00000100) == 0x00000100)) {
size += com.google.protobuf.CodedOutputStream
.computeSInt32Size(9, inferredInsertSize_);
}
for (int i = 0; i < diffs_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(10, diffs_.get(i));
}
{
int dataSize = 0;
for (int i = 0; i < tags_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(tags_.get(i));
}
size += dataSize;
if (!getTagsList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
tagsMemoizedSerializedSize = dataSize;
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord 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.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.AlignmentRecord}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
getDiffsFieldBuilder();
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
name_ = "";
bitField0_ = (bitField0_ & ~0x00000001);
pos_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
flags_ = 0;
bitField0_ = (bitField0_ & ~0x00000004);
len_ = 0;
bitField0_ = (bitField0_ & ~0x00000008);
mapq_ = 0;
bitField0_ = (bitField0_ & ~0x00000010);
qualities_ = "";
bitField0_ = (bitField0_ & ~0x00000020);
rnext_ = "";
bitField0_ = (bitField0_ & ~0x00000040);
relativePnext_ = 0;
bitField0_ = (bitField0_ & ~0x00000080);
inferredInsertSize_ = 0;
bitField0_ = (bitField0_ & ~0x00000100);
if (diffsBuilder_ == null) {
diffs_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000200);
} else {
diffsBuilder_.clear();
}
tags_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000400);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.name_ = name_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.pos_ = pos_;
if (((from_bitField0_ & 0x00000004) == 0x00000004)) {
to_bitField0_ |= 0x00000004;
}
result.flags_ = flags_;
if (((from_bitField0_ & 0x00000008) == 0x00000008)) {
to_bitField0_ |= 0x00000008;
}
result.len_ = len_;
if (((from_bitField0_ & 0x00000010) == 0x00000010)) {
to_bitField0_ |= 0x00000010;
}
result.mapq_ = mapq_;
if (((from_bitField0_ & 0x00000020) == 0x00000020)) {
to_bitField0_ |= 0x00000020;
}
result.qualities_ = qualities_;
if (((from_bitField0_ & 0x00000040) == 0x00000040)) {
to_bitField0_ |= 0x00000040;
}
result.rnext_ = rnext_;
if (((from_bitField0_ & 0x00000080) == 0x00000080)) {
to_bitField0_ |= 0x00000080;
}
result.relativePnext_ = relativePnext_;
if (((from_bitField0_ & 0x00000100) == 0x00000100)) {
to_bitField0_ |= 0x00000100;
}
result.inferredInsertSize_ = inferredInsertSize_;
if (diffsBuilder_ == null) {
if (((bitField0_ & 0x00000200) == 0x00000200)) {
diffs_ = java.util.Collections.unmodifiableList(diffs_);
bitField0_ = (bitField0_ & ~0x00000200);
}
result.diffs_ = diffs_;
} else {
result.diffs_ = diffsBuilder_.build();
}
if (((bitField0_ & 0x00000400) == 0x00000400)) {
tags_ = java.util.Collections.unmodifiableList(tags_);
bitField0_ = (bitField0_ & ~0x00000400);
}
result.tags_ = tags_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.getDefaultInstance()) return this;
if (other.hasName()) {
bitField0_ |= 0x00000001;
name_ = other.name_;
onChanged();
}
if (other.hasPos()) {
setPos(other.getPos());
}
if (other.hasFlags()) {
setFlags(other.getFlags());
}
if (other.hasLen()) {
setLen(other.getLen());
}
if (other.hasMapq()) {
setMapq(other.getMapq());
}
if (other.hasQualities()) {
bitField0_ |= 0x00000020;
qualities_ = other.qualities_;
onChanged();
}
if (other.hasRnext()) {
bitField0_ |= 0x00000040;
rnext_ = other.rnext_;
onChanged();
}
if (other.hasRelativePnext()) {
setRelativePnext(other.getRelativePnext());
}
if (other.hasInferredInsertSize()) {
setInferredInsertSize(other.getInferredInsertSize());
}
if (diffsBuilder_ == null) {
if (!other.diffs_.isEmpty()) {
if (diffs_.isEmpty()) {
diffs_ = other.diffs_;
bitField0_ = (bitField0_ & ~0x00000200);
} else {
ensureDiffsIsMutable();
diffs_.addAll(other.diffs_);
}
onChanged();
}
} else {
if (!other.diffs_.isEmpty()) {
if (diffsBuilder_.isEmpty()) {
diffsBuilder_.dispose();
diffsBuilder_ = null;
diffs_ = other.diffs_;
bitField0_ = (bitField0_ & ~0x00000200);
diffsBuilder_ =
com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders ?
getDiffsFieldBuilder() : null;
} else {
diffsBuilder_.addAllMessages(other.diffs_);
}
}
}
if (!other.tags_.isEmpty()) {
if (tags_.isEmpty()) {
tags_ = other.tags_;
bitField0_ = (bitField0_ & ~0x00000400);
} else {
ensureTagsIsMutable();
tags_.addAll(other.tags_);
}
onChanged();
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasName()) {
return false;
}
if (!hasPos()) {
return false;
}
if (!hasMapq()) {
return false;
}
if (!hasQualities()) {
return false;
}
if (!hasRelativePnext()) {
return false;
}
if (!hasInferredInsertSize()) {
return false;
}
for (int i = 0; i < getDiffsCount(); i++) {
if (!getDiffs(i).isInitialized()) {
return false;
}
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required string name = 1;
private java.lang.Object name_ = "";
/**
* <code>required string name = 1;</code>
*/
public boolean hasName() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required string name = 1;</code>
*/
public java.lang.String getName() {
java.lang.Object ref = name_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
name_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>required string name = 1;</code>
*/
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;
}
}
/**
* <code>required string name = 1;</code>
*/
public Builder setName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000001;
name_ = value;
onChanged();
return this;
}
/**
* <code>required string name = 1;</code>
*/
public Builder clearName() {
bitField0_ = (bitField0_ & ~0x00000001);
name_ = getDefaultInstance().getName();
onChanged();
return this;
}
/**
* <code>required string name = 1;</code>
*/
public Builder setNameBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000001;
name_ = value;
onChanged();
return this;
}
// required uint32 pos = 2;
private int pos_ ;
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public boolean hasPos() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public int getPos() {
return pos_;
}
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public Builder setPos(int value) {
bitField0_ |= 0x00000002;
pos_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 pos = 2;</code>
*
* <pre>
* position relative to the alignment region
* </pre>
*/
public Builder clearPos() {
bitField0_ = (bitField0_ & ~0x00000002);
pos_ = 0;
onChanged();
return this;
}
// optional uint32 flags = 3;
private int flags_ ;
/**
* <code>optional uint32 flags = 3;</code>
*/
public boolean hasFlags() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional uint32 flags = 3;</code>
*/
public int getFlags() {
return flags_;
}
/**
* <code>optional uint32 flags = 3;</code>
*/
public Builder setFlags(int value) {
bitField0_ |= 0x00000004;
flags_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 flags = 3;</code>
*/
public Builder clearFlags() {
bitField0_ = (bitField0_ & ~0x00000004);
flags_ = 0;
onChanged();
return this;
}
// optional uint32 len = 4;
private int len_ ;
/**
* <code>optional uint32 len = 4;</code>
*/
public boolean hasLen() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional uint32 len = 4;</code>
*/
public int getLen() {
return len_;
}
/**
* <code>optional uint32 len = 4;</code>
*/
public Builder setLen(int value) {
bitField0_ |= 0x00000008;
len_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 len = 4;</code>
*/
public Builder clearLen() {
bitField0_ = (bitField0_ & ~0x00000008);
len_ = 0;
onChanged();
return this;
}
// required uint32 mapq = 5;
private int mapq_ ;
/**
* <code>required uint32 mapq = 5;</code>
*/
public boolean hasMapq() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>required uint32 mapq = 5;</code>
*/
public int getMapq() {
return mapq_;
}
/**
* <code>required uint32 mapq = 5;</code>
*/
public Builder setMapq(int value) {
bitField0_ |= 0x00000010;
mapq_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 mapq = 5;</code>
*/
public Builder clearMapq() {
bitField0_ = (bitField0_ & ~0x00000010);
mapq_ = 0;
onChanged();
return this;
}
// required string qualities = 6;
private java.lang.Object qualities_ = "";
/**
* <code>required string qualities = 6;</code>
*/
public boolean hasQualities() {
return ((bitField0_ & 0x00000020) == 0x00000020);
}
/**
* <code>required string qualities = 6;</code>
*/
public java.lang.String getQualities() {
java.lang.Object ref = qualities_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
qualities_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>required string qualities = 6;</code>
*/
public com.google.protobuf.ByteString
getQualitiesBytes() {
java.lang.Object ref = qualities_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
qualities_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>required string qualities = 6;</code>
*/
public Builder setQualities(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000020;
qualities_ = value;
onChanged();
return this;
}
/**
* <code>required string qualities = 6;</code>
*/
public Builder clearQualities() {
bitField0_ = (bitField0_ & ~0x00000020);
qualities_ = getDefaultInstance().getQualities();
onChanged();
return this;
}
/**
* <code>required string qualities = 6;</code>
*/
public Builder setQualitiesBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000020;
qualities_ = value;
onChanged();
return this;
}
// optional string rnext = 7;
private java.lang.Object rnext_ = "";
/**
* <code>optional string rnext = 7;</code>
*/
public boolean hasRnext() {
return ((bitField0_ & 0x00000040) == 0x00000040);
}
/**
* <code>optional string rnext = 7;</code>
*/
public java.lang.String getRnext() {
java.lang.Object ref = rnext_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
rnext_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>optional string rnext = 7;</code>
*/
public com.google.protobuf.ByteString
getRnextBytes() {
java.lang.Object ref = rnext_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
rnext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>optional string rnext = 7;</code>
*/
public Builder setRnext(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000040;
rnext_ = value;
onChanged();
return this;
}
/**
* <code>optional string rnext = 7;</code>
*/
public Builder clearRnext() {
bitField0_ = (bitField0_ & ~0x00000040);
rnext_ = getDefaultInstance().getRnext();
onChanged();
return this;
}
/**
* <code>optional string rnext = 7;</code>
*/
public Builder setRnextBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000040;
rnext_ = value;
onChanged();
return this;
}
// required sint32 relativePnext = 8;
private int relativePnext_ ;
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public boolean hasRelativePnext() {
return ((bitField0_ & 0x00000080) == 0x00000080);
}
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public int getRelativePnext() {
return relativePnext_;
}
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public Builder setRelativePnext(int value) {
bitField0_ |= 0x00000080;
relativePnext_ = value;
onChanged();
return this;
}
/**
* <code>required sint32 relativePnext = 8;</code>
*/
public Builder clearRelativePnext() {
bitField0_ = (bitField0_ & ~0x00000080);
relativePnext_ = 0;
onChanged();
return this;
}
// required sint32 inferredInsertSize = 9;
private int inferredInsertSize_ ;
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public boolean hasInferredInsertSize() {
return ((bitField0_ & 0x00000100) == 0x00000100);
}
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public int getInferredInsertSize() {
return inferredInsertSize_;
}
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public Builder setInferredInsertSize(int value) {
bitField0_ |= 0x00000100;
inferredInsertSize_ = value;
onChanged();
return this;
}
/**
* <code>required sint32 inferredInsertSize = 9;</code>
*/
public Builder clearInferredInsertSize() {
bitField0_ = (bitField0_ & ~0x00000100);
inferredInsertSize_ = 0;
onChanged();
return this;
}
// repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference> diffs_ =
java.util.Collections.emptyList();
private void ensureDiffsIsMutable() {
if (!((bitField0_ & 0x00000200) == 0x00000200)) {
diffs_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference>(diffs_);
bitField0_ |= 0x00000200;
}
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder> diffsBuilder_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference> getDiffsList() {
if (diffsBuilder_ == null) {
return java.util.Collections.unmodifiableList(diffs_);
} else {
return diffsBuilder_.getMessageList();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public int getDiffsCount() {
if (diffsBuilder_ == null) {
return diffs_.size();
} else {
return diffsBuilder_.getCount();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference getDiffs(int index) {
if (diffsBuilder_ == null) {
return diffs_.get(index);
} else {
return diffsBuilder_.getMessage(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder setDiffs(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference value) {
if (diffsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiffsIsMutable();
diffs_.set(index, value);
onChanged();
} else {
diffsBuilder_.setMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder setDiffs(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder builderForValue) {
if (diffsBuilder_ == null) {
ensureDiffsIsMutable();
diffs_.set(index, builderForValue.build());
onChanged();
} else {
diffsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder addDiffs(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference value) {
if (diffsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiffsIsMutable();
diffs_.add(value);
onChanged();
} else {
diffsBuilder_.addMessage(value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder addDiffs(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference value) {
if (diffsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureDiffsIsMutable();
diffs_.add(index, value);
onChanged();
} else {
diffsBuilder_.addMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder addDiffs(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder builderForValue) {
if (diffsBuilder_ == null) {
ensureDiffsIsMutable();
diffs_.add(builderForValue.build());
onChanged();
} else {
diffsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder addDiffs(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder builderForValue) {
if (diffsBuilder_ == null) {
ensureDiffsIsMutable();
diffs_.add(index, builderForValue.build());
onChanged();
} else {
diffsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder addAllDiffs(
java.lang.Iterable<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference> values) {
if (diffsBuilder_ == null) {
ensureDiffsIsMutable();
super.addAll(values, diffs_);
onChanged();
} else {
diffsBuilder_.addAllMessages(values);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder clearDiffs() {
if (diffsBuilder_ == null) {
diffs_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000200);
onChanged();
} else {
diffsBuilder_.clear();
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public Builder removeDiffs(int index) {
if (diffsBuilder_ == null) {
ensureDiffsIsMutable();
diffs_.remove(index);
onChanged();
} else {
diffsBuilder_.remove(index);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder getDiffsBuilder(
int index) {
return getDiffsFieldBuilder().getBuilder(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder getDiffsOrBuilder(
int index) {
if (diffsBuilder_ == null) {
return diffs_.get(index); } else {
return diffsBuilder_.getMessageOrBuilder(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder>
getDiffsOrBuilderList() {
if (diffsBuilder_ != null) {
return diffsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(diffs_);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder addDiffsBuilder() {
return getDiffsFieldBuilder().addBuilder(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder addDiffsBuilder(
int index) {
return getDiffsFieldBuilder().addBuilder(
index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Difference diffs = 10;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder>
getDiffsBuilderList() {
return getDiffsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder>
getDiffsFieldBuilder() {
if (diffsBuilder_ == null) {
diffsBuilder_ = new com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Difference.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.DifferenceOrBuilder>(
diffs_,
((bitField0_ & 0x00000200) == 0x00000200),
getParentForChildren(),
isClean());
diffs_ = null;
}
return diffsBuilder_;
}
// repeated uint32 tags = 11 [packed = true];
private java.util.List<java.lang.Integer> tags_ = java.util.Collections.emptyList();
private void ensureTagsIsMutable() {
if (!((bitField0_ & 0x00000400) == 0x00000400)) {
tags_ = new java.util.ArrayList<java.lang.Integer>(tags_);
bitField0_ |= 0x00000400;
}
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getTagsList() {
return java.util.Collections.unmodifiableList(tags_);
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public int getTagsCount() {
return tags_.size();
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public int getTags(int index) {
return tags_.get(index);
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public Builder setTags(
int index, int value) {
ensureTagsIsMutable();
tags_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public Builder addTags(int value) {
ensureTagsIsMutable();
tags_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public Builder addAllTags(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureTagsIsMutable();
super.addAll(values, tags_);
onChanged();
return this;
}
/**
* <code>repeated uint32 tags = 11 [packed = true];</code>
*/
public Builder clearTags() {
tags_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000400);
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.AlignmentRecord)
}
static {
defaultInstance = new AlignmentRecord(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.AlignmentRecord)
}
public interface AlignmentBucketOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required uint32 summaryIndex = 1;
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
boolean hasSummaryIndex();
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
int getSummaryIndex();
// optional uint32 overlapped = 2;
/**
* <code>optional uint32 overlapped = 2;</code>
*/
boolean hasOverlapped();
/**
* <code>optional uint32 overlapped = 2;</code>
*/
int getOverlapped();
// repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord>
getAlignmentRecordsList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord getAlignmentRecords(int index);
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
int getAlignmentRecordsCount();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder>
getAlignmentRecordsOrBuilderList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder getAlignmentRecordsOrBuilder(
int index);
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.AlignmentBucket}
*/
public static final class AlignmentBucket extends
com.google.protobuf.GeneratedMessage
implements AlignmentBucketOrBuilder {
// Use AlignmentBucket.newBuilder() to construct.
private AlignmentBucket(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private AlignmentBucket(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final AlignmentBucket defaultInstance;
public static AlignmentBucket getDefaultInstance() {
return defaultInstance;
}
public AlignmentBucket getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private AlignmentBucket(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 8: {
bitField0_ |= 0x00000001;
summaryIndex_ = input.readUInt32();
break;
}
case 16: {
bitField0_ |= 0x00000002;
overlapped_ = input.readUInt32();
break;
}
case 74: {
if (!((mutable_bitField0_ & 0x00000004) == 0x00000004)) {
alignmentRecords_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord>();
mutable_bitField0_ |= 0x00000004;
}
alignmentRecords_.add(input.readMessage(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.PARSER, extensionRegistry));
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000004) == 0x00000004)) {
alignmentRecords_ = java.util.Collections.unmodifiableList(alignmentRecords_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.Builder.class);
}
public static com.google.protobuf.Parser<AlignmentBucket> PARSER =
new com.google.protobuf.AbstractParser<AlignmentBucket>() {
public AlignmentBucket parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new AlignmentBucket(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<AlignmentBucket> getParserForType() {
return PARSER;
}
private int bitField0_;
// required uint32 summaryIndex = 1;
public static final int SUMMARYINDEX_FIELD_NUMBER = 1;
private int summaryIndex_;
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public boolean hasSummaryIndex() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public int getSummaryIndex() {
return summaryIndex_;
}
// optional uint32 overlapped = 2;
public static final int OVERLAPPED_FIELD_NUMBER = 2;
private int overlapped_;
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public boolean hasOverlapped() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public int getOverlapped() {
return overlapped_;
}
// repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;
public static final int ALIGNMENTRECORDS_FIELD_NUMBER = 9;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord> alignmentRecords_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord> getAlignmentRecordsList() {
return alignmentRecords_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder>
getAlignmentRecordsOrBuilderList() {
return alignmentRecords_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public int getAlignmentRecordsCount() {
return alignmentRecords_.size();
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord getAlignmentRecords(int index) {
return alignmentRecords_.get(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder getAlignmentRecordsOrBuilder(
int index) {
return alignmentRecords_.get(index);
}
private void initFields() {
summaryIndex_ = 0;
overlapped_ = 0;
alignmentRecords_ = java.util.Collections.emptyList();
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasSummaryIndex()) {
memoizedIsInitialized = 0;
return false;
}
for (int i = 0; i < getAlignmentRecordsCount(); i++) {
if (!getAlignmentRecords(i).isInitialized()) {
memoizedIsInitialized = 0;
return false;
}
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeUInt32(1, summaryIndex_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, overlapped_);
}
for (int i = 0; i < alignmentRecords_.size(); i++) {
output.writeMessage(9, alignmentRecords_.get(i));
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(1, summaryIndex_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, overlapped_);
}
for (int i = 0; i < alignmentRecords_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, alignmentRecords_.get(i));
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket 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.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.AlignmentBucket}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucketOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
getAlignmentRecordsFieldBuilder();
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
summaryIndex_ = 0;
bitField0_ = (bitField0_ & ~0x00000001);
overlapped_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
if (alignmentRecordsBuilder_ == null) {
alignmentRecords_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
} else {
alignmentRecordsBuilder_.clear();
}
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.summaryIndex_ = summaryIndex_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.overlapped_ = overlapped_;
if (alignmentRecordsBuilder_ == null) {
if (((bitField0_ & 0x00000004) == 0x00000004)) {
alignmentRecords_ = java.util.Collections.unmodifiableList(alignmentRecords_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.alignmentRecords_ = alignmentRecords_;
} else {
result.alignmentRecords_ = alignmentRecordsBuilder_.build();
}
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket.getDefaultInstance()) return this;
if (other.hasSummaryIndex()) {
setSummaryIndex(other.getSummaryIndex());
}
if (other.hasOverlapped()) {
setOverlapped(other.getOverlapped());
}
if (alignmentRecordsBuilder_ == null) {
if (!other.alignmentRecords_.isEmpty()) {
if (alignmentRecords_.isEmpty()) {
alignmentRecords_ = other.alignmentRecords_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureAlignmentRecordsIsMutable();
alignmentRecords_.addAll(other.alignmentRecords_);
}
onChanged();
}
} else {
if (!other.alignmentRecords_.isEmpty()) {
if (alignmentRecordsBuilder_.isEmpty()) {
alignmentRecordsBuilder_.dispose();
alignmentRecordsBuilder_ = null;
alignmentRecords_ = other.alignmentRecords_;
bitField0_ = (bitField0_ & ~0x00000004);
alignmentRecordsBuilder_ =
com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders ?
getAlignmentRecordsFieldBuilder() : null;
} else {
alignmentRecordsBuilder_.addAllMessages(other.alignmentRecords_);
}
}
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasSummaryIndex()) {
return false;
}
for (int i = 0; i < getAlignmentRecordsCount(); i++) {
if (!getAlignmentRecords(i).isInitialized()) {
return false;
}
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentBucket) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required uint32 summaryIndex = 1;
private int summaryIndex_ ;
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public boolean hasSummaryIndex() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public int getSummaryIndex() {
return summaryIndex_;
}
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public Builder setSummaryIndex(int value) {
bitField0_ |= 0x00000001;
summaryIndex_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 summaryIndex = 1;</code>
*/
public Builder clearSummaryIndex() {
bitField0_ = (bitField0_ & ~0x00000001);
summaryIndex_ = 0;
onChanged();
return this;
}
// optional uint32 overlapped = 2;
private int overlapped_ ;
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public boolean hasOverlapped() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public int getOverlapped() {
return overlapped_;
}
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public Builder setOverlapped(int value) {
bitField0_ |= 0x00000002;
overlapped_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 overlapped = 2;</code>
*/
public Builder clearOverlapped() {
bitField0_ = (bitField0_ & ~0x00000002);
overlapped_ = 0;
onChanged();
return this;
}
// repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord> alignmentRecords_ =
java.util.Collections.emptyList();
private void ensureAlignmentRecordsIsMutable() {
if (!((bitField0_ & 0x00000004) == 0x00000004)) {
alignmentRecords_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord>(alignmentRecords_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder> alignmentRecordsBuilder_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord> getAlignmentRecordsList() {
if (alignmentRecordsBuilder_ == null) {
return java.util.Collections.unmodifiableList(alignmentRecords_);
} else {
return alignmentRecordsBuilder_.getMessageList();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public int getAlignmentRecordsCount() {
if (alignmentRecordsBuilder_ == null) {
return alignmentRecords_.size();
} else {
return alignmentRecordsBuilder_.getCount();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord getAlignmentRecords(int index) {
if (alignmentRecordsBuilder_ == null) {
return alignmentRecords_.get(index);
} else {
return alignmentRecordsBuilder_.getMessage(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder setAlignmentRecords(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord value) {
if (alignmentRecordsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAlignmentRecordsIsMutable();
alignmentRecords_.set(index, value);
onChanged();
} else {
alignmentRecordsBuilder_.setMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder setAlignmentRecords(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder builderForValue) {
if (alignmentRecordsBuilder_ == null) {
ensureAlignmentRecordsIsMutable();
alignmentRecords_.set(index, builderForValue.build());
onChanged();
} else {
alignmentRecordsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder addAlignmentRecords(org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord value) {
if (alignmentRecordsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAlignmentRecordsIsMutable();
alignmentRecords_.add(value);
onChanged();
} else {
alignmentRecordsBuilder_.addMessage(value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder addAlignmentRecords(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord value) {
if (alignmentRecordsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAlignmentRecordsIsMutable();
alignmentRecords_.add(index, value);
onChanged();
} else {
alignmentRecordsBuilder_.addMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder addAlignmentRecords(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder builderForValue) {
if (alignmentRecordsBuilder_ == null) {
ensureAlignmentRecordsIsMutable();
alignmentRecords_.add(builderForValue.build());
onChanged();
} else {
alignmentRecordsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder addAlignmentRecords(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder builderForValue) {
if (alignmentRecordsBuilder_ == null) {
ensureAlignmentRecordsIsMutable();
alignmentRecords_.add(index, builderForValue.build());
onChanged();
} else {
alignmentRecordsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder addAllAlignmentRecords(
java.lang.Iterable<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord> values) {
if (alignmentRecordsBuilder_ == null) {
ensureAlignmentRecordsIsMutable();
super.addAll(values, alignmentRecords_);
onChanged();
} else {
alignmentRecordsBuilder_.addAllMessages(values);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder clearAlignmentRecords() {
if (alignmentRecordsBuilder_ == null) {
alignmentRecords_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
alignmentRecordsBuilder_.clear();
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public Builder removeAlignmentRecords(int index) {
if (alignmentRecordsBuilder_ == null) {
ensureAlignmentRecordsIsMutable();
alignmentRecords_.remove(index);
onChanged();
} else {
alignmentRecordsBuilder_.remove(index);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder getAlignmentRecordsBuilder(
int index) {
return getAlignmentRecordsFieldBuilder().getBuilder(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder getAlignmentRecordsOrBuilder(
int index) {
if (alignmentRecordsBuilder_ == null) {
return alignmentRecords_.get(index); } else {
return alignmentRecordsBuilder_.getMessageOrBuilder(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder>
getAlignmentRecordsOrBuilderList() {
if (alignmentRecordsBuilder_ != null) {
return alignmentRecordsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(alignmentRecords_);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder addAlignmentRecordsBuilder() {
return getAlignmentRecordsFieldBuilder().addBuilder(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder addAlignmentRecordsBuilder(
int index) {
return getAlignmentRecordsFieldBuilder().addBuilder(
index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.AlignmentRecord alignmentRecords = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder>
getAlignmentRecordsBuilderList() {
return getAlignmentRecordsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder>
getAlignmentRecordsFieldBuilder() {
if (alignmentRecordsBuilder_ == null) {
alignmentRecordsBuilder_ = new com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecord.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.AlignmentRecordOrBuilder>(
alignmentRecords_,
((bitField0_ & 0x00000004) == 0x00000004),
getParentForChildren(),
isClean());
alignmentRecords_ = null;
}
return alignmentRecordsBuilder_;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.AlignmentBucket)
}
static {
defaultInstance = new AlignmentBucket(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.AlignmentBucket)
}
public interface SummaryOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required uint32 defaultFlag = 1;
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
boolean hasDefaultFlag();
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
int getDefaultFlag();
// required uint32 defaultLen = 2;
/**
* <code>required uint32 defaultLen = 2;</code>
*/
boolean hasDefaultLen();
/**
* <code>required uint32 defaultLen = 2;</code>
*/
int getDefaultLen();
// required string defaultRNext = 3;
/**
* <code>required string defaultRNext = 3;</code>
*/
boolean hasDefaultRNext();
/**
* <code>required string defaultRNext = 3;</code>
*/
java.lang.String getDefaultRNext();
/**
* <code>required string defaultRNext = 3;</code>
*/
com.google.protobuf.ByteString
getDefaultRNextBytes();
// required uint32 defaultOverlapped = 4;
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
boolean hasDefaultOverlapped();
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
int getDefaultOverlapped();
// required string keys = 8;
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
boolean hasKeys();
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
java.lang.String getKeys();
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
com.google.protobuf.ByteString
getKeysBytes();
// repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair>
getValuesList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair getValues(int index);
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
int getValuesCount();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder>
getValuesOrBuilderList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder getValuesOrBuilder(
int index);
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Summary}
*/
public static final class Summary extends
com.google.protobuf.GeneratedMessage
implements SummaryOrBuilder {
// Use Summary.newBuilder() to construct.
private Summary(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Summary(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Summary defaultInstance;
public static Summary getDefaultInstance() {
return defaultInstance;
}
public Summary getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Summary(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 8: {
bitField0_ |= 0x00000001;
defaultFlag_ = input.readUInt32();
break;
}
case 16: {
bitField0_ |= 0x00000002;
defaultLen_ = input.readUInt32();
break;
}
case 26: {
bitField0_ |= 0x00000004;
defaultRNext_ = input.readBytes();
break;
}
case 32: {
bitField0_ |= 0x00000008;
defaultOverlapped_ = input.readUInt32();
break;
}
case 66: {
bitField0_ |= 0x00000010;
keys_ = input.readBytes();
break;
}
case 74: {
if (!((mutable_bitField0_ & 0x00000020) == 0x00000020)) {
values_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair>();
mutable_bitField0_ |= 0x00000020;
}
values_.add(input.readMessage(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.PARSER, extensionRegistry));
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000020) == 0x00000020)) {
values_ = java.util.Collections.unmodifiableList(values_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Builder.class);
}
public static com.google.protobuf.Parser<Summary> PARSER =
new com.google.protobuf.AbstractParser<Summary>() {
public Summary parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Summary(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Summary> getParserForType() {
return PARSER;
}
public interface PairOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required uint32 key = 1;
/**
* <code>required uint32 key = 1;</code>
*/
boolean hasKey();
/**
* <code>required uint32 key = 1;</code>
*/
int getKey();
// optional uint32 avalue = 2;
/**
* <code>optional uint32 avalue = 2;</code>
*/
boolean hasAvalue();
/**
* <code>optional uint32 avalue = 2;</code>
*/
int getAvalue();
// optional sint32 ivalue = 3;
/**
* <code>optional sint32 ivalue = 3;</code>
*/
boolean hasIvalue();
/**
* <code>optional sint32 ivalue = 3;</code>
*/
int getIvalue();
// optional float fvalue = 4;
/**
* <code>optional float fvalue = 4;</code>
*/
boolean hasFvalue();
/**
* <code>optional float fvalue = 4;</code>
*/
float getFvalue();
// optional string zvalue = 5;
/**
* <code>optional string zvalue = 5;</code>
*/
boolean hasZvalue();
/**
* <code>optional string zvalue = 5;</code>
*/
java.lang.String getZvalue();
/**
* <code>optional string zvalue = 5;</code>
*/
com.google.protobuf.ByteString
getZvalueBytes();
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Summary.Pair}
*/
public static final class Pair extends
com.google.protobuf.GeneratedMessage
implements PairOrBuilder {
// Use Pair.newBuilder() to construct.
private Pair(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Pair(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Pair defaultInstance;
public static Pair getDefaultInstance() {
return defaultInstance;
}
public Pair getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Pair(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 8: {
bitField0_ |= 0x00000001;
key_ = input.readUInt32();
break;
}
case 16: {
bitField0_ |= 0x00000002;
avalue_ = input.readUInt32();
break;
}
case 24: {
bitField0_ |= 0x00000004;
ivalue_ = input.readSInt32();
break;
}
case 37: {
bitField0_ |= 0x00000008;
fvalue_ = input.readFloat();
break;
}
case 42: {
bitField0_ |= 0x00000010;
zvalue_ = input.readBytes();
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder.class);
}
public static com.google.protobuf.Parser<Pair> PARSER =
new com.google.protobuf.AbstractParser<Pair>() {
public Pair parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Pair(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Pair> getParserForType() {
return PARSER;
}
private int bitField0_;
// required uint32 key = 1;
public static final int KEY_FIELD_NUMBER = 1;
private int key_;
/**
* <code>required uint32 key = 1;</code>
*/
public boolean hasKey() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 key = 1;</code>
*/
public int getKey() {
return key_;
}
// optional uint32 avalue = 2;
public static final int AVALUE_FIELD_NUMBER = 2;
private int avalue_;
/**
* <code>optional uint32 avalue = 2;</code>
*/
public boolean hasAvalue() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 avalue = 2;</code>
*/
public int getAvalue() {
return avalue_;
}
// optional sint32 ivalue = 3;
public static final int IVALUE_FIELD_NUMBER = 3;
private int ivalue_;
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public boolean hasIvalue() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public int getIvalue() {
return ivalue_;
}
// optional float fvalue = 4;
public static final int FVALUE_FIELD_NUMBER = 4;
private float fvalue_;
/**
* <code>optional float fvalue = 4;</code>
*/
public boolean hasFvalue() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional float fvalue = 4;</code>
*/
public float getFvalue() {
return fvalue_;
}
// optional string zvalue = 5;
public static final int ZVALUE_FIELD_NUMBER = 5;
private java.lang.Object zvalue_;
/**
* <code>optional string zvalue = 5;</code>
*/
public boolean hasZvalue() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>optional string zvalue = 5;</code>
*/
public java.lang.String getZvalue() {
java.lang.Object ref = zvalue_;
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();
if (bs.isValidUtf8()) {
zvalue_ = s;
}
return s;
}
}
/**
* <code>optional string zvalue = 5;</code>
*/
public com.google.protobuf.ByteString
getZvalueBytes() {
java.lang.Object ref = zvalue_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
zvalue_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
private void initFields() {
key_ = 0;
avalue_ = 0;
ivalue_ = 0;
fvalue_ = 0F;
zvalue_ = "";
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasKey()) {
memoizedIsInitialized = 0;
return false;
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeUInt32(1, key_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, avalue_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
output.writeSInt32(3, ivalue_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
output.writeFloat(4, fvalue_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
output.writeBytes(5, getZvalueBytes());
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(1, key_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, avalue_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
size += com.google.protobuf.CodedOutputStream
.computeSInt32Size(3, ivalue_);
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
size += com.google.protobuf.CodedOutputStream
.computeFloatSize(4, fvalue_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(5, getZvalueBytes());
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair 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.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Summary.Pair}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
key_ = 0;
bitField0_ = (bitField0_ & ~0x00000001);
avalue_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
ivalue_ = 0;
bitField0_ = (bitField0_ & ~0x00000004);
fvalue_ = 0F;
bitField0_ = (bitField0_ & ~0x00000008);
zvalue_ = "";
bitField0_ = (bitField0_ & ~0x00000010);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.key_ = key_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.avalue_ = avalue_;
if (((from_bitField0_ & 0x00000004) == 0x00000004)) {
to_bitField0_ |= 0x00000004;
}
result.ivalue_ = ivalue_;
if (((from_bitField0_ & 0x00000008) == 0x00000008)) {
to_bitField0_ |= 0x00000008;
}
result.fvalue_ = fvalue_;
if (((from_bitField0_ & 0x00000010) == 0x00000010)) {
to_bitField0_ |= 0x00000010;
}
result.zvalue_ = zvalue_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.getDefaultInstance()) return this;
if (other.hasKey()) {
setKey(other.getKey());
}
if (other.hasAvalue()) {
setAvalue(other.getAvalue());
}
if (other.hasIvalue()) {
setIvalue(other.getIvalue());
}
if (other.hasFvalue()) {
setFvalue(other.getFvalue());
}
if (other.hasZvalue()) {
bitField0_ |= 0x00000010;
zvalue_ = other.zvalue_;
onChanged();
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasKey()) {
return false;
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required uint32 key = 1;
private int key_ ;
/**
* <code>required uint32 key = 1;</code>
*/
public boolean hasKey() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 key = 1;</code>
*/
public int getKey() {
return key_;
}
/**
* <code>required uint32 key = 1;</code>
*/
public Builder setKey(int value) {
bitField0_ |= 0x00000001;
key_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 key = 1;</code>
*/
public Builder clearKey() {
bitField0_ = (bitField0_ & ~0x00000001);
key_ = 0;
onChanged();
return this;
}
// optional uint32 avalue = 2;
private int avalue_ ;
/**
* <code>optional uint32 avalue = 2;</code>
*/
public boolean hasAvalue() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional uint32 avalue = 2;</code>
*/
public int getAvalue() {
return avalue_;
}
/**
* <code>optional uint32 avalue = 2;</code>
*/
public Builder setAvalue(int value) {
bitField0_ |= 0x00000002;
avalue_ = value;
onChanged();
return this;
}
/**
* <code>optional uint32 avalue = 2;</code>
*/
public Builder clearAvalue() {
bitField0_ = (bitField0_ & ~0x00000002);
avalue_ = 0;
onChanged();
return this;
}
// optional sint32 ivalue = 3;
private int ivalue_ ;
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public boolean hasIvalue() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public int getIvalue() {
return ivalue_;
}
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public Builder setIvalue(int value) {
bitField0_ |= 0x00000004;
ivalue_ = value;
onChanged();
return this;
}
/**
* <code>optional sint32 ivalue = 3;</code>
*/
public Builder clearIvalue() {
bitField0_ = (bitField0_ & ~0x00000004);
ivalue_ = 0;
onChanged();
return this;
}
// optional float fvalue = 4;
private float fvalue_ ;
/**
* <code>optional float fvalue = 4;</code>
*/
public boolean hasFvalue() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>optional float fvalue = 4;</code>
*/
public float getFvalue() {
return fvalue_;
}
/**
* <code>optional float fvalue = 4;</code>
*/
public Builder setFvalue(float value) {
bitField0_ |= 0x00000008;
fvalue_ = value;
onChanged();
return this;
}
/**
* <code>optional float fvalue = 4;</code>
*/
public Builder clearFvalue() {
bitField0_ = (bitField0_ & ~0x00000008);
fvalue_ = 0F;
onChanged();
return this;
}
// optional string zvalue = 5;
private java.lang.Object zvalue_ = "";
/**
* <code>optional string zvalue = 5;</code>
*/
public boolean hasZvalue() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>optional string zvalue = 5;</code>
*/
public java.lang.String getZvalue() {
java.lang.Object ref = zvalue_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
zvalue_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>optional string zvalue = 5;</code>
*/
public com.google.protobuf.ByteString
getZvalueBytes() {
java.lang.Object ref = zvalue_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
zvalue_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>optional string zvalue = 5;</code>
*/
public Builder setZvalue(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000010;
zvalue_ = value;
onChanged();
return this;
}
/**
* <code>optional string zvalue = 5;</code>
*/
public Builder clearZvalue() {
bitField0_ = (bitField0_ & ~0x00000010);
zvalue_ = getDefaultInstance().getZvalue();
onChanged();
return this;
}
/**
* <code>optional string zvalue = 5;</code>
*/
public Builder setZvalueBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000010;
zvalue_ = value;
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Summary.Pair)
}
static {
defaultInstance = new Pair(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Summary.Pair)
}
private int bitField0_;
// required uint32 defaultFlag = 1;
public static final int DEFAULTFLAG_FIELD_NUMBER = 1;
private int defaultFlag_;
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public boolean hasDefaultFlag() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public int getDefaultFlag() {
return defaultFlag_;
}
// required uint32 defaultLen = 2;
public static final int DEFAULTLEN_FIELD_NUMBER = 2;
private int defaultLen_;
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public boolean hasDefaultLen() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public int getDefaultLen() {
return defaultLen_;
}
// required string defaultRNext = 3;
public static final int DEFAULTRNEXT_FIELD_NUMBER = 3;
private java.lang.Object defaultRNext_;
/**
* <code>required string defaultRNext = 3;</code>
*/
public boolean hasDefaultRNext() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public java.lang.String getDefaultRNext() {
java.lang.Object ref = defaultRNext_;
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();
if (bs.isValidUtf8()) {
defaultRNext_ = s;
}
return s;
}
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public com.google.protobuf.ByteString
getDefaultRNextBytes() {
java.lang.Object ref = defaultRNext_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
defaultRNext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
// required uint32 defaultOverlapped = 4;
public static final int DEFAULTOVERLAPPED_FIELD_NUMBER = 4;
private int defaultOverlapped_;
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public boolean hasDefaultOverlapped() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public int getDefaultOverlapped() {
return defaultOverlapped_;
}
// required string keys = 8;
public static final int KEYS_FIELD_NUMBER = 8;
private java.lang.Object keys_;
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public boolean hasKeys() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public java.lang.String getKeys() {
java.lang.Object ref = keys_;
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();
if (bs.isValidUtf8()) {
keys_ = s;
}
return s;
}
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public com.google.protobuf.ByteString
getKeysBytes() {
java.lang.Object ref = keys_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
keys_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
// repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;
public static final int VALUES_FIELD_NUMBER = 9;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair> values_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair> getValuesList() {
return values_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder>
getValuesOrBuilderList() {
return values_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public int getValuesCount() {
return values_.size();
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair getValues(int index) {
return values_.get(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder getValuesOrBuilder(
int index) {
return values_.get(index);
}
private void initFields() {
defaultFlag_ = 0;
defaultLen_ = 0;
defaultRNext_ = "";
defaultOverlapped_ = 0;
keys_ = "";
values_ = java.util.Collections.emptyList();
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasDefaultFlag()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasDefaultLen()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasDefaultRNext()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasDefaultOverlapped()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasKeys()) {
memoizedIsInitialized = 0;
return false;
}
for (int i = 0; i < getValuesCount(); i++) {
if (!getValues(i).isInitialized()) {
memoizedIsInitialized = 0;
return false;
}
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeUInt32(1, defaultFlag_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, defaultLen_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
output.writeBytes(3, getDefaultRNextBytes());
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
output.writeUInt32(4, defaultOverlapped_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
output.writeBytes(8, getKeysBytes());
}
for (int i = 0; i < values_.size(); i++) {
output.writeMessage(9, values_.get(i));
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(1, defaultFlag_);
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, defaultLen_);
}
if (((bitField0_ & 0x00000004) == 0x00000004)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(3, getDefaultRNextBytes());
}
if (((bitField0_ & 0x00000008) == 0x00000008)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(4, defaultOverlapped_);
}
if (((bitField0_ & 0x00000010) == 0x00000010)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(8, getKeysBytes());
}
for (int i = 0; i < values_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(9, values_.get(i));
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary 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.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Summary}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.SummaryOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
getValuesFieldBuilder();
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
defaultFlag_ = 0;
bitField0_ = (bitField0_ & ~0x00000001);
defaultLen_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
defaultRNext_ = "";
bitField0_ = (bitField0_ & ~0x00000004);
defaultOverlapped_ = 0;
bitField0_ = (bitField0_ & ~0x00000008);
keys_ = "";
bitField0_ = (bitField0_ & ~0x00000010);
if (valuesBuilder_ == null) {
values_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000020);
} else {
valuesBuilder_.clear();
}
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.defaultFlag_ = defaultFlag_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.defaultLen_ = defaultLen_;
if (((from_bitField0_ & 0x00000004) == 0x00000004)) {
to_bitField0_ |= 0x00000004;
}
result.defaultRNext_ = defaultRNext_;
if (((from_bitField0_ & 0x00000008) == 0x00000008)) {
to_bitField0_ |= 0x00000008;
}
result.defaultOverlapped_ = defaultOverlapped_;
if (((from_bitField0_ & 0x00000010) == 0x00000010)) {
to_bitField0_ |= 0x00000010;
}
result.keys_ = keys_;
if (valuesBuilder_ == null) {
if (((bitField0_ & 0x00000020) == 0x00000020)) {
values_ = java.util.Collections.unmodifiableList(values_);
bitField0_ = (bitField0_ & ~0x00000020);
}
result.values_ = values_;
} else {
result.values_ = valuesBuilder_.build();
}
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.getDefaultInstance()) return this;
if (other.hasDefaultFlag()) {
setDefaultFlag(other.getDefaultFlag());
}
if (other.hasDefaultLen()) {
setDefaultLen(other.getDefaultLen());
}
if (other.hasDefaultRNext()) {
bitField0_ |= 0x00000004;
defaultRNext_ = other.defaultRNext_;
onChanged();
}
if (other.hasDefaultOverlapped()) {
setDefaultOverlapped(other.getDefaultOverlapped());
}
if (other.hasKeys()) {
bitField0_ |= 0x00000010;
keys_ = other.keys_;
onChanged();
}
if (valuesBuilder_ == null) {
if (!other.values_.isEmpty()) {
if (values_.isEmpty()) {
values_ = other.values_;
bitField0_ = (bitField0_ & ~0x00000020);
} else {
ensureValuesIsMutable();
values_.addAll(other.values_);
}
onChanged();
}
} else {
if (!other.values_.isEmpty()) {
if (valuesBuilder_.isEmpty()) {
valuesBuilder_.dispose();
valuesBuilder_ = null;
values_ = other.values_;
bitField0_ = (bitField0_ & ~0x00000020);
valuesBuilder_ =
com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders ?
getValuesFieldBuilder() : null;
} else {
valuesBuilder_.addAllMessages(other.values_);
}
}
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasDefaultFlag()) {
return false;
}
if (!hasDefaultLen()) {
return false;
}
if (!hasDefaultRNext()) {
return false;
}
if (!hasDefaultOverlapped()) {
return false;
}
if (!hasKeys()) {
return false;
}
for (int i = 0; i < getValuesCount(); i++) {
if (!getValues(i).isInitialized()) {
return false;
}
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required uint32 defaultFlag = 1;
private int defaultFlag_ ;
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public boolean hasDefaultFlag() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public int getDefaultFlag() {
return defaultFlag_;
}
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public Builder setDefaultFlag(int value) {
bitField0_ |= 0x00000001;
defaultFlag_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 defaultFlag = 1;</code>
*/
public Builder clearDefaultFlag() {
bitField0_ = (bitField0_ & ~0x00000001);
defaultFlag_ = 0;
onChanged();
return this;
}
// required uint32 defaultLen = 2;
private int defaultLen_ ;
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public boolean hasDefaultLen() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public int getDefaultLen() {
return defaultLen_;
}
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public Builder setDefaultLen(int value) {
bitField0_ |= 0x00000002;
defaultLen_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 defaultLen = 2;</code>
*/
public Builder clearDefaultLen() {
bitField0_ = (bitField0_ & ~0x00000002);
defaultLen_ = 0;
onChanged();
return this;
}
// required string defaultRNext = 3;
private java.lang.Object defaultRNext_ = "";
/**
* <code>required string defaultRNext = 3;</code>
*/
public boolean hasDefaultRNext() {
return ((bitField0_ & 0x00000004) == 0x00000004);
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public java.lang.String getDefaultRNext() {
java.lang.Object ref = defaultRNext_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
defaultRNext_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public com.google.protobuf.ByteString
getDefaultRNextBytes() {
java.lang.Object ref = defaultRNext_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
defaultRNext_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public Builder setDefaultRNext(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000004;
defaultRNext_ = value;
onChanged();
return this;
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public Builder clearDefaultRNext() {
bitField0_ = (bitField0_ & ~0x00000004);
defaultRNext_ = getDefaultInstance().getDefaultRNext();
onChanged();
return this;
}
/**
* <code>required string defaultRNext = 3;</code>
*/
public Builder setDefaultRNextBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000004;
defaultRNext_ = value;
onChanged();
return this;
}
// required uint32 defaultOverlapped = 4;
private int defaultOverlapped_ ;
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public boolean hasDefaultOverlapped() {
return ((bitField0_ & 0x00000008) == 0x00000008);
}
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public int getDefaultOverlapped() {
return defaultOverlapped_;
}
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public Builder setDefaultOverlapped(int value) {
bitField0_ |= 0x00000008;
defaultOverlapped_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 defaultOverlapped = 4;</code>
*/
public Builder clearDefaultOverlapped() {
bitField0_ = (bitField0_ & ~0x00000008);
defaultOverlapped_ = 0;
onChanged();
return this;
}
// required string keys = 8;
private java.lang.Object keys_ = "";
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public boolean hasKeys() {
return ((bitField0_ & 0x00000010) == 0x00000010);
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public java.lang.String getKeys() {
java.lang.Object ref = keys_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
keys_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public com.google.protobuf.ByteString
getKeysBytes() {
java.lang.Object ref = keys_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
keys_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public Builder setKeys(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000010;
keys_ = value;
onChanged();
return this;
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public Builder clearKeys() {
bitField0_ = (bitField0_ & ~0x00000010);
keys_ = getDefaultInstance().getKeys();
onChanged();
return this;
}
/**
* <code>required string keys = 8;</code>
*
* <pre>
*Concatenated tags.
* </pre>
*/
public Builder setKeysBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000010;
keys_ = value;
onChanged();
return this;
}
// repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair> values_ =
java.util.Collections.emptyList();
private void ensureValuesIsMutable() {
if (!((bitField0_ & 0x00000020) == 0x00000020)) {
values_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair>(values_);
bitField0_ |= 0x00000020;
}
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder> valuesBuilder_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair> getValuesList() {
if (valuesBuilder_ == null) {
return java.util.Collections.unmodifiableList(values_);
} else {
return valuesBuilder_.getMessageList();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public int getValuesCount() {
if (valuesBuilder_ == null) {
return values_.size();
} else {
return valuesBuilder_.getCount();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair getValues(int index) {
if (valuesBuilder_ == null) {
return values_.get(index);
} else {
return valuesBuilder_.getMessage(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder setValues(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair value) {
if (valuesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureValuesIsMutable();
values_.set(index, value);
onChanged();
} else {
valuesBuilder_.setMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder setValues(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder builderForValue) {
if (valuesBuilder_ == null) {
ensureValuesIsMutable();
values_.set(index, builderForValue.build());
onChanged();
} else {
valuesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder addValues(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair value) {
if (valuesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureValuesIsMutable();
values_.add(value);
onChanged();
} else {
valuesBuilder_.addMessage(value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder addValues(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair value) {
if (valuesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureValuesIsMutable();
values_.add(index, value);
onChanged();
} else {
valuesBuilder_.addMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder addValues(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder builderForValue) {
if (valuesBuilder_ == null) {
ensureValuesIsMutable();
values_.add(builderForValue.build());
onChanged();
} else {
valuesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder addValues(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder builderForValue) {
if (valuesBuilder_ == null) {
ensureValuesIsMutable();
values_.add(index, builderForValue.build());
onChanged();
} else {
valuesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder addAllValues(
java.lang.Iterable<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair> values) {
if (valuesBuilder_ == null) {
ensureValuesIsMutable();
super.addAll(values, values_);
onChanged();
} else {
valuesBuilder_.addAllMessages(values);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder clearValues() {
if (valuesBuilder_ == null) {
values_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000020);
onChanged();
} else {
valuesBuilder_.clear();
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public Builder removeValues(int index) {
if (valuesBuilder_ == null) {
ensureValuesIsMutable();
values_.remove(index);
onChanged();
} else {
valuesBuilder_.remove(index);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder getValuesBuilder(
int index) {
return getValuesFieldBuilder().getBuilder(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder getValuesOrBuilder(
int index) {
if (valuesBuilder_ == null) {
return values_.get(index); } else {
return valuesBuilder_.getMessageOrBuilder(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder>
getValuesOrBuilderList() {
if (valuesBuilder_ != null) {
return valuesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(values_);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder addValuesBuilder() {
return getValuesFieldBuilder().addBuilder(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder addValuesBuilder(
int index) {
return getValuesFieldBuilder().addBuilder(
index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Summary.Pair values = 9;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder>
getValuesBuilderList() {
return getValuesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder>
getValuesFieldBuilder() {
if (valuesBuilder_ == null) {
valuesBuilder_ = new com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.Pair.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Summary.PairOrBuilder>(
values_,
((bitField0_ & 0x00000020) == 0x00000020),
getParentForChildren(),
isClean());
values_ = null;
}
return valuesBuilder_;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Summary)
}
static {
defaultInstance = new Summary(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Summary)
}
public interface HeaderOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region>
getRegionsList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region getRegions(int index);
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
int getRegionsCount();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder>
getRegionsOrBuilderList();
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder getRegionsOrBuilder(
int index);
// optional bytes SamHeader = 2;
/**
* <code>optional bytes SamHeader = 2;</code>
*/
boolean hasSamHeader();
/**
* <code>optional bytes SamHeader = 2;</code>
*/
com.google.protobuf.ByteString getSamHeader();
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Header}
*/
public static final class Header extends
com.google.protobuf.GeneratedMessage
implements HeaderOrBuilder {
// Use Header.newBuilder() to construct.
private Header(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Header(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Header defaultInstance;
public static Header getDefaultInstance() {
return defaultInstance;
}
public Header getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Header(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 10: {
if (!((mutable_bitField0_ & 0x00000001) == 0x00000001)) {
regions_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region>();
mutable_bitField0_ |= 0x00000001;
}
regions_.add(input.readMessage(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.PARSER, extensionRegistry));
break;
}
case 18: {
bitField0_ |= 0x00000001;
samHeader_ = input.readBytes();
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000001) == 0x00000001)) {
regions_ = java.util.Collections.unmodifiableList(regions_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Builder.class);
}
public static com.google.protobuf.Parser<Header> PARSER =
new com.google.protobuf.AbstractParser<Header>() {
public Header parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Header(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Header> getParserForType() {
return PARSER;
}
public interface RegionOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required string chromosomeName = 1;
/**
* <code>required string chromosomeName = 1;</code>
*/
boolean hasChromosomeName();
/**
* <code>required string chromosomeName = 1;</code>
*/
java.lang.String getChromosomeName();
/**
* <code>required string chromosomeName = 1;</code>
*/
com.google.protobuf.ByteString
getChromosomeNameBytes();
// required uint32 maxValue = 2;
/**
* <code>required uint32 maxValue = 2;</code>
*/
boolean hasMaxValue();
/**
* <code>required uint32 maxValue = 2;</code>
*/
int getMaxValue();
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Header.Region}
*/
public static final class Region extends
com.google.protobuf.GeneratedMessage
implements RegionOrBuilder {
// Use Region.newBuilder() to construct.
private Region(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Region(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Region defaultInstance;
public static Region getDefaultInstance() {
return defaultInstance;
}
public Region getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Region(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 10: {
bitField0_ |= 0x00000001;
chromosomeName_ = input.readBytes();
break;
}
case 16: {
bitField0_ |= 0x00000002;
maxValue_ = input.readUInt32();
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder.class);
}
public static com.google.protobuf.Parser<Region> PARSER =
new com.google.protobuf.AbstractParser<Region>() {
public Region parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Region(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Region> getParserForType() {
return PARSER;
}
private int bitField0_;
// required string chromosomeName = 1;
public static final int CHROMOSOMENAME_FIELD_NUMBER = 1;
private java.lang.Object chromosomeName_;
/**
* <code>required string chromosomeName = 1;</code>
*/
public boolean hasChromosomeName() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public java.lang.String getChromosomeName() {
java.lang.Object ref = chromosomeName_;
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();
if (bs.isValidUtf8()) {
chromosomeName_ = s;
}
return s;
}
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public com.google.protobuf.ByteString
getChromosomeNameBytes() {
java.lang.Object ref = chromosomeName_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chromosomeName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
// required uint32 maxValue = 2;
public static final int MAXVALUE_FIELD_NUMBER = 2;
private int maxValue_;
/**
* <code>required uint32 maxValue = 2;</code>
*/
public boolean hasMaxValue() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 maxValue = 2;</code>
*/
public int getMaxValue() {
return maxValue_;
}
private void initFields() {
chromosomeName_ = "";
maxValue_ = 0;
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasChromosomeName()) {
memoizedIsInitialized = 0;
return false;
}
if (!hasMaxValue()) {
memoizedIsInitialized = 0;
return false;
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeBytes(1, getChromosomeNameBytes());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
output.writeUInt32(2, maxValue_);
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(1, getChromosomeNameBytes());
}
if (((bitField0_ & 0x00000002) == 0x00000002)) {
size += com.google.protobuf.CodedOutputStream
.computeUInt32Size(2, maxValue_);
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region 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.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Header.Region}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
chromosomeName_ = "";
bitField0_ = (bitField0_ & ~0x00000001);
maxValue_ = 0;
bitField0_ = (bitField0_ & ~0x00000002);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.chromosomeName_ = chromosomeName_;
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000002;
}
result.maxValue_ = maxValue_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.getDefaultInstance()) return this;
if (other.hasChromosomeName()) {
bitField0_ |= 0x00000001;
chromosomeName_ = other.chromosomeName_;
onChanged();
}
if (other.hasMaxValue()) {
setMaxValue(other.getMaxValue());
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasChromosomeName()) {
return false;
}
if (!hasMaxValue()) {
return false;
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required string chromosomeName = 1;
private java.lang.Object chromosomeName_ = "";
/**
* <code>required string chromosomeName = 1;</code>
*/
public boolean hasChromosomeName() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public java.lang.String getChromosomeName() {
java.lang.Object ref = chromosomeName_;
if (!(ref instanceof java.lang.String)) {
java.lang.String s = ((com.google.protobuf.ByteString) ref)
.toStringUtf8();
chromosomeName_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public com.google.protobuf.ByteString
getChromosomeNameBytes() {
java.lang.Object ref = chromosomeName_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
chromosomeName_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public Builder setChromosomeName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000001;
chromosomeName_ = value;
onChanged();
return this;
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public Builder clearChromosomeName() {
bitField0_ = (bitField0_ & ~0x00000001);
chromosomeName_ = getDefaultInstance().getChromosomeName();
onChanged();
return this;
}
/**
* <code>required string chromosomeName = 1;</code>
*/
public Builder setChromosomeNameBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000001;
chromosomeName_ = value;
onChanged();
return this;
}
// required uint32 maxValue = 2;
private int maxValue_ ;
/**
* <code>required uint32 maxValue = 2;</code>
*/
public boolean hasMaxValue() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>required uint32 maxValue = 2;</code>
*/
public int getMaxValue() {
return maxValue_;
}
/**
* <code>required uint32 maxValue = 2;</code>
*/
public Builder setMaxValue(int value) {
bitField0_ |= 0x00000002;
maxValue_ = value;
onChanged();
return this;
}
/**
* <code>required uint32 maxValue = 2;</code>
*/
public Builder clearMaxValue() {
bitField0_ = (bitField0_ & ~0x00000002);
maxValue_ = 0;
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Header.Region)
}
static {
defaultInstance = new Region(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Header.Region)
}
private int bitField0_;
// repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;
public static final int REGIONS_FIELD_NUMBER = 1;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region> regions_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region> getRegionsList() {
return regions_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder>
getRegionsOrBuilderList() {
return regions_;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public int getRegionsCount() {
return regions_.size();
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region getRegions(int index) {
return regions_.get(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder getRegionsOrBuilder(
int index) {
return regions_.get(index);
}
// optional bytes SamHeader = 2;
public static final int SAMHEADER_FIELD_NUMBER = 2;
private com.google.protobuf.ByteString samHeader_;
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public boolean hasSamHeader() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public com.google.protobuf.ByteString getSamHeader() {
return samHeader_;
}
private void initFields() {
regions_ = java.util.Collections.emptyList();
samHeader_ = com.google.protobuf.ByteString.EMPTY;
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
for (int i = 0; i < getRegionsCount(); i++) {
if (!getRegions(i).isInitialized()) {
memoizedIsInitialized = 0;
return false;
}
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
for (int i = 0; i < regions_.size(); i++) {
output.writeMessage(1, regions_.get(i));
}
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeBytes(2, samHeader_);
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
for (int i = 0; i < regions_.size(); i++) {
size += com.google.protobuf.CodedOutputStream
.computeMessageSize(1, regions_.get(i));
}
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeBytesSize(2, samHeader_);
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header 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.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Header}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.HeaderOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
getRegionsFieldBuilder();
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
if (regionsBuilder_ == null) {
regions_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
} else {
regionsBuilder_.clear();
}
samHeader_ = com.google.protobuf.ByteString.EMPTY;
bitField0_ = (bitField0_ & ~0x00000002);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (regionsBuilder_ == null) {
if (((bitField0_ & 0x00000001) == 0x00000001)) {
regions_ = java.util.Collections.unmodifiableList(regions_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.regions_ = regions_;
} else {
result.regions_ = regionsBuilder_.build();
}
if (((from_bitField0_ & 0x00000002) == 0x00000002)) {
to_bitField0_ |= 0x00000001;
}
result.samHeader_ = samHeader_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.getDefaultInstance()) return this;
if (regionsBuilder_ == null) {
if (!other.regions_.isEmpty()) {
if (regions_.isEmpty()) {
regions_ = other.regions_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureRegionsIsMutable();
regions_.addAll(other.regions_);
}
onChanged();
}
} else {
if (!other.regions_.isEmpty()) {
if (regionsBuilder_.isEmpty()) {
regionsBuilder_.dispose();
regionsBuilder_ = null;
regions_ = other.regions_;
bitField0_ = (bitField0_ & ~0x00000001);
regionsBuilder_ =
com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders ?
getRegionsFieldBuilder() : null;
} else {
regionsBuilder_.addAllMessages(other.regions_);
}
}
}
if (other.hasSamHeader()) {
setSamHeader(other.getSamHeader());
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
for (int i = 0; i < getRegionsCount(); i++) {
if (!getRegions(i).isInitialized()) {
return false;
}
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;
private java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region> regions_ =
java.util.Collections.emptyList();
private void ensureRegionsIsMutable() {
if (!((bitField0_ & 0x00000001) == 0x00000001)) {
regions_ = new java.util.ArrayList<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region>(regions_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder> regionsBuilder_;
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region> getRegionsList() {
if (regionsBuilder_ == null) {
return java.util.Collections.unmodifiableList(regions_);
} else {
return regionsBuilder_.getMessageList();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public int getRegionsCount() {
if (regionsBuilder_ == null) {
return regions_.size();
} else {
return regionsBuilder_.getCount();
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region getRegions(int index) {
if (regionsBuilder_ == null) {
return regions_.get(index);
} else {
return regionsBuilder_.getMessage(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder setRegions(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region value) {
if (regionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRegionsIsMutable();
regions_.set(index, value);
onChanged();
} else {
regionsBuilder_.setMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder setRegions(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder builderForValue) {
if (regionsBuilder_ == null) {
ensureRegionsIsMutable();
regions_.set(index, builderForValue.build());
onChanged();
} else {
regionsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder addRegions(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region value) {
if (regionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRegionsIsMutable();
regions_.add(value);
onChanged();
} else {
regionsBuilder_.addMessage(value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder addRegions(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region value) {
if (regionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureRegionsIsMutable();
regions_.add(index, value);
onChanged();
} else {
regionsBuilder_.addMessage(index, value);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder addRegions(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder builderForValue) {
if (regionsBuilder_ == null) {
ensureRegionsIsMutable();
regions_.add(builderForValue.build());
onChanged();
} else {
regionsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder addRegions(
int index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder builderForValue) {
if (regionsBuilder_ == null) {
ensureRegionsIsMutable();
regions_.add(index, builderForValue.build());
onChanged();
} else {
regionsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder addAllRegions(
java.lang.Iterable<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region> values) {
if (regionsBuilder_ == null) {
ensureRegionsIsMutable();
super.addAll(values, regions_);
onChanged();
} else {
regionsBuilder_.addAllMessages(values);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder clearRegions() {
if (regionsBuilder_ == null) {
regions_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
regionsBuilder_.clear();
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public Builder removeRegions(int index) {
if (regionsBuilder_ == null) {
ensureRegionsIsMutable();
regions_.remove(index);
onChanged();
} else {
regionsBuilder_.remove(index);
}
return this;
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder getRegionsBuilder(
int index) {
return getRegionsFieldBuilder().getBuilder(index);
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder getRegionsOrBuilder(
int index) {
if (regionsBuilder_ == null) {
return regions_.get(index); } else {
return regionsBuilder_.getMessageOrBuilder(index);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public java.util.List<? extends org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder>
getRegionsOrBuilderList() {
if (regionsBuilder_ != null) {
return regionsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(regions_);
}
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder addRegionsBuilder() {
return getRegionsFieldBuilder().addBuilder(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder addRegionsBuilder(
int index) {
return getRegionsFieldBuilder().addBuilder(
index, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.getDefaultInstance());
}
/**
* <code>repeated .org.opencb.opencga.storage.alignment.proto.Header.Region regions = 1;</code>
*/
public java.util.List<org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder>
getRegionsBuilderList() {
return getRegionsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder>
getRegionsFieldBuilder() {
if (regionsBuilder_ == null) {
regionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilder<
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.Region.Builder, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Header.RegionOrBuilder>(
regions_,
((bitField0_ & 0x00000001) == 0x00000001),
getParentForChildren(),
isClean());
regions_ = null;
}
return regionsBuilder_;
}
// optional bytes SamHeader = 2;
private com.google.protobuf.ByteString samHeader_ = com.google.protobuf.ByteString.EMPTY;
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public boolean hasSamHeader() {
return ((bitField0_ & 0x00000002) == 0x00000002);
}
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public com.google.protobuf.ByteString getSamHeader() {
return samHeader_;
}
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public Builder setSamHeader(com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
bitField0_ |= 0x00000002;
samHeader_ = value;
onChanged();
return this;
}
/**
* <code>optional bytes SamHeader = 2;</code>
*/
public Builder clearSamHeader() {
bitField0_ = (bitField0_ & ~0x00000002);
samHeader_ = getDefaultInstance().getSamHeader();
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Header)
}
static {
defaultInstance = new Header(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Header)
}
public interface MeanCoverageOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// required float coverage = 1;
/**
* <code>required float coverage = 1;</code>
*/
boolean hasCoverage();
/**
* <code>required float coverage = 1;</code>
*/
float getCoverage();
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.MeanCoverage}
*/
public static final class MeanCoverage extends
com.google.protobuf.GeneratedMessage
implements MeanCoverageOrBuilder {
// Use MeanCoverage.newBuilder() to construct.
private MeanCoverage(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private MeanCoverage(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final MeanCoverage defaultInstance;
public static MeanCoverage getDefaultInstance() {
return defaultInstance;
}
public MeanCoverage getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private MeanCoverage(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 13: {
bitField0_ |= 0x00000001;
coverage_ = input.readFloat();
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.Builder.class);
}
public static com.google.protobuf.Parser<MeanCoverage> PARSER =
new com.google.protobuf.AbstractParser<MeanCoverage>() {
public MeanCoverage parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new MeanCoverage(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<MeanCoverage> getParserForType() {
return PARSER;
}
private int bitField0_;
// required float coverage = 1;
public static final int COVERAGE_FIELD_NUMBER = 1;
private float coverage_;
/**
* <code>required float coverage = 1;</code>
*/
public boolean hasCoverage() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required float coverage = 1;</code>
*/
public float getCoverage() {
return coverage_;
}
private void initFields() {
coverage_ = 0F;
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
if (!hasCoverage()) {
memoizedIsInitialized = 0;
return false;
}
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (((bitField0_ & 0x00000001) == 0x00000001)) {
output.writeFloat(1, coverage_);
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
size += com.google.protobuf.CodedOutputStream
.computeFloatSize(1, coverage_);
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage 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.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.MeanCoverage}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverageOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
coverage_ = 0F;
bitField0_ = (bitField0_ & ~0x00000001);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage(this);
int from_bitField0_ = bitField0_;
int to_bitField0_ = 0;
if (((from_bitField0_ & 0x00000001) == 0x00000001)) {
to_bitField0_ |= 0x00000001;
}
result.coverage_ = coverage_;
result.bitField0_ = to_bitField0_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage.getDefaultInstance()) return this;
if (other.hasCoverage()) {
setCoverage(other.getCoverage());
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
if (!hasCoverage()) {
return false;
}
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.MeanCoverage) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// required float coverage = 1;
private float coverage_ ;
/**
* <code>required float coverage = 1;</code>
*/
public boolean hasCoverage() {
return ((bitField0_ & 0x00000001) == 0x00000001);
}
/**
* <code>required float coverage = 1;</code>
*/
public float getCoverage() {
return coverage_;
}
/**
* <code>required float coverage = 1;</code>
*/
public Builder setCoverage(float value) {
bitField0_ |= 0x00000001;
coverage_ = value;
onChanged();
return this;
}
/**
* <code>required float coverage = 1;</code>
*/
public Builder clearCoverage() {
bitField0_ = (bitField0_ & ~0x00000001);
coverage_ = 0F;
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.MeanCoverage)
}
static {
defaultInstance = new MeanCoverage(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.MeanCoverage)
}
public interface CoverageOrBuilder
extends com.google.protobuf.MessageOrBuilder {
// repeated uint32 all = 1 [packed = true];
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getAllList();
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
int getAllCount();
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
int getAll(int index);
// repeated uint32 a = 2 [packed = true];
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getAList();
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
int getACount();
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
int getA(int index);
// repeated uint32 c = 3 [packed = true];
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getCList();
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
int getCCount();
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
int getC(int index);
// repeated uint32 g = 4 [packed = true];
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getGList();
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
int getGCount();
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
int getG(int index);
// repeated uint32 t = 5 [packed = true];
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
java.util.List<java.lang.Integer> getTList();
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
int getTCount();
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
int getT(int index);
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Coverage}
*/
public static final class Coverage extends
com.google.protobuf.GeneratedMessage
implements CoverageOrBuilder {
// Use Coverage.newBuilder() to construct.
private Coverage(com.google.protobuf.GeneratedMessage.Builder<?> builder) {
super(builder);
this.unknownFields = builder.getUnknownFields();
}
private Coverage(boolean noInit) { this.unknownFields = com.google.protobuf.UnknownFieldSet.getDefaultInstance(); }
private static final Coverage defaultInstance;
public static Coverage getDefaultInstance() {
return defaultInstance;
}
public Coverage getDefaultInstanceForType() {
return defaultInstance;
}
private final com.google.protobuf.UnknownFieldSet unknownFields;
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private Coverage(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
initFields();
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;
default: {
if (!parseUnknownField(input, unknownFields,
extensionRegistry, tag)) {
done = true;
}
break;
}
case 8: {
if (!((mutable_bitField0_ & 0x00000001) == 0x00000001)) {
all_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000001;
}
all_.add(input.readUInt32());
break;
}
case 10: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000001) == 0x00000001) && input.getBytesUntilLimit() > 0) {
all_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000001;
}
while (input.getBytesUntilLimit() > 0) {
all_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
case 16: {
if (!((mutable_bitField0_ & 0x00000002) == 0x00000002)) {
a_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000002;
}
a_.add(input.readUInt32());
break;
}
case 18: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000002) == 0x00000002) && input.getBytesUntilLimit() > 0) {
a_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000002;
}
while (input.getBytesUntilLimit() > 0) {
a_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
case 24: {
if (!((mutable_bitField0_ & 0x00000004) == 0x00000004)) {
c_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000004;
}
c_.add(input.readUInt32());
break;
}
case 26: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000004) == 0x00000004) && input.getBytesUntilLimit() > 0) {
c_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000004;
}
while (input.getBytesUntilLimit() > 0) {
c_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
case 32: {
if (!((mutable_bitField0_ & 0x00000008) == 0x00000008)) {
g_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000008;
}
g_.add(input.readUInt32());
break;
}
case 34: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000008) == 0x00000008) && input.getBytesUntilLimit() > 0) {
g_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000008;
}
while (input.getBytesUntilLimit() > 0) {
g_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
case 40: {
if (!((mutable_bitField0_ & 0x00000010) == 0x00000010)) {
t_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000010;
}
t_.add(input.readUInt32());
break;
}
case 42: {
int length = input.readRawVarint32();
int limit = input.pushLimit(length);
if (!((mutable_bitField0_ & 0x00000010) == 0x00000010) && input.getBytesUntilLimit() > 0) {
t_ = new java.util.ArrayList<java.lang.Integer>();
mutable_bitField0_ |= 0x00000010;
}
while (input.getBytesUntilLimit() > 0) {
t_.add(input.readUInt32());
}
input.popLimit(limit);
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e.getMessage()).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000001) == 0x00000001)) {
all_ = java.util.Collections.unmodifiableList(all_);
}
if (((mutable_bitField0_ & 0x00000002) == 0x00000002)) {
a_ = java.util.Collections.unmodifiableList(a_);
}
if (((mutable_bitField0_ & 0x00000004) == 0x00000004)) {
c_ = java.util.Collections.unmodifiableList(c_);
}
if (((mutable_bitField0_ & 0x00000008) == 0x00000008)) {
g_ = java.util.Collections.unmodifiableList(g_);
}
if (((mutable_bitField0_ & 0x00000010) == 0x00000010)) {
t_ = java.util.Collections.unmodifiableList(t_);
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.Builder.class);
}
public static com.google.protobuf.Parser<Coverage> PARSER =
new com.google.protobuf.AbstractParser<Coverage>() {
public Coverage parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Coverage(input, extensionRegistry);
}
};
@java.lang.Override
public com.google.protobuf.Parser<Coverage> getParserForType() {
return PARSER;
}
// repeated uint32 all = 1 [packed = true];
public static final int ALL_FIELD_NUMBER = 1;
private java.util.List<java.lang.Integer> all_;
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getAllList() {
return all_;
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public int getAllCount() {
return all_.size();
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public int getAll(int index) {
return all_.get(index);
}
private int allMemoizedSerializedSize = -1;
// repeated uint32 a = 2 [packed = true];
public static final int A_FIELD_NUMBER = 2;
private java.util.List<java.lang.Integer> a_;
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getAList() {
return a_;
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public int getACount() {
return a_.size();
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public int getA(int index) {
return a_.get(index);
}
private int aMemoizedSerializedSize = -1;
// repeated uint32 c = 3 [packed = true];
public static final int C_FIELD_NUMBER = 3;
private java.util.List<java.lang.Integer> c_;
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getCList() {
return c_;
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public int getCCount() {
return c_.size();
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public int getC(int index) {
return c_.get(index);
}
private int cMemoizedSerializedSize = -1;
// repeated uint32 g = 4 [packed = true];
public static final int G_FIELD_NUMBER = 4;
private java.util.List<java.lang.Integer> g_;
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getGList() {
return g_;
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public int getGCount() {
return g_.size();
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public int getG(int index) {
return g_.get(index);
}
private int gMemoizedSerializedSize = -1;
// repeated uint32 t = 5 [packed = true];
public static final int T_FIELD_NUMBER = 5;
private java.util.List<java.lang.Integer> t_;
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getTList() {
return t_;
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public int getTCount() {
return t_.size();
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public int getT(int index) {
return t_.get(index);
}
private int tMemoizedSerializedSize = -1;
private void initFields() {
all_ = java.util.Collections.emptyList();
a_ = java.util.Collections.emptyList();
c_ = java.util.Collections.emptyList();
g_ = java.util.Collections.emptyList();
t_ = java.util.Collections.emptyList();
}
private byte memoizedIsInitialized = -1;
public final boolean isInitialized() {
byte isInitialized = memoizedIsInitialized;
if (isInitialized != -1) return isInitialized == 1;
memoizedIsInitialized = 1;
return true;
}
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
getSerializedSize();
if (getAllList().size() > 0) {
output.writeRawVarint32(10);
output.writeRawVarint32(allMemoizedSerializedSize);
}
for (int i = 0; i < all_.size(); i++) {
output.writeUInt32NoTag(all_.get(i));
}
if (getAList().size() > 0) {
output.writeRawVarint32(18);
output.writeRawVarint32(aMemoizedSerializedSize);
}
for (int i = 0; i < a_.size(); i++) {
output.writeUInt32NoTag(a_.get(i));
}
if (getCList().size() > 0) {
output.writeRawVarint32(26);
output.writeRawVarint32(cMemoizedSerializedSize);
}
for (int i = 0; i < c_.size(); i++) {
output.writeUInt32NoTag(c_.get(i));
}
if (getGList().size() > 0) {
output.writeRawVarint32(34);
output.writeRawVarint32(gMemoizedSerializedSize);
}
for (int i = 0; i < g_.size(); i++) {
output.writeUInt32NoTag(g_.get(i));
}
if (getTList().size() > 0) {
output.writeRawVarint32(42);
output.writeRawVarint32(tMemoizedSerializedSize);
}
for (int i = 0; i < t_.size(); i++) {
output.writeUInt32NoTag(t_.get(i));
}
getUnknownFields().writeTo(output);
}
private int memoizedSerializedSize = -1;
public int getSerializedSize() {
int size = memoizedSerializedSize;
if (size != -1) return size;
size = 0;
{
int dataSize = 0;
for (int i = 0; i < all_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(all_.get(i));
}
size += dataSize;
if (!getAllList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
allMemoizedSerializedSize = dataSize;
}
{
int dataSize = 0;
for (int i = 0; i < a_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(a_.get(i));
}
size += dataSize;
if (!getAList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
aMemoizedSerializedSize = dataSize;
}
{
int dataSize = 0;
for (int i = 0; i < c_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(c_.get(i));
}
size += dataSize;
if (!getCList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
cMemoizedSerializedSize = dataSize;
}
{
int dataSize = 0;
for (int i = 0; i < g_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(g_.get(i));
}
size += dataSize;
if (!getGList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
gMemoizedSerializedSize = dataSize;
}
{
int dataSize = 0;
for (int i = 0; i < t_.size(); i++) {
dataSize += com.google.protobuf.CodedOutputStream
.computeUInt32SizeNoTag(t_.get(i));
}
size += dataSize;
if (!getTList().isEmpty()) {
size += 1;
size += com.google.protobuf.CodedOutputStream
.computeInt32SizeNoTag(dataSize);
}
tMemoizedSerializedSize = dataSize;
}
size += getUnknownFields().getSerializedSize();
memoizedSerializedSize = size;
return size;
}
private static final long serialVersionUID = 0L;
@java.lang.Override
protected java.lang.Object writeReplace()
throws java.io.ObjectStreamException {
return super.writeReplace();
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage 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.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseDelimitedFrom(input, extensionRegistry);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return PARSER.parseFrom(input);
}
public static org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return PARSER.parseFrom(input, extensionRegistry);
}
public static Builder newBuilder() { return Builder.create(); }
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage prototype) {
return newBuilder().mergeFrom(prototype);
}
public Builder toBuilder() { return newBuilder(this); }
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
* Protobuf type {@code org.opencb.opencga.storage.alignment.proto.Coverage}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessage.Builder<Builder>
implements org.opencb.opencga.storage.alignment.proto.AlignmentProto.CoverageOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor;
}
protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.class, org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.Builder.class);
}
// Construct using org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessage.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessage.alwaysUseFieldBuilders) {
}
}
private static Builder create() {
return new Builder();
}
public Builder clear() {
super.clear();
all_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
a_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
c_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
g_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
t_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
return this;
}
public Builder clone() {
return create().mergeFrom(buildPartial());
}
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage getDefaultInstanceForType() {
return org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.getDefaultInstance();
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage build() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
public org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage buildPartial() {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage result = new org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage(this);
int from_bitField0_ = bitField0_;
if (((bitField0_ & 0x00000001) == 0x00000001)) {
all_ = java.util.Collections.unmodifiableList(all_);
bitField0_ = (bitField0_ & ~0x00000001);
}
result.all_ = all_;
if (((bitField0_ & 0x00000002) == 0x00000002)) {
a_ = java.util.Collections.unmodifiableList(a_);
bitField0_ = (bitField0_ & ~0x00000002);
}
result.a_ = a_;
if (((bitField0_ & 0x00000004) == 0x00000004)) {
c_ = java.util.Collections.unmodifiableList(c_);
bitField0_ = (bitField0_ & ~0x00000004);
}
result.c_ = c_;
if (((bitField0_ & 0x00000008) == 0x00000008)) {
g_ = java.util.Collections.unmodifiableList(g_);
bitField0_ = (bitField0_ & ~0x00000008);
}
result.g_ = g_;
if (((bitField0_ & 0x00000010) == 0x00000010)) {
t_ = java.util.Collections.unmodifiableList(t_);
bitField0_ = (bitField0_ & ~0x00000010);
}
result.t_ = t_;
onBuilt();
return result;
}
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage) {
return mergeFrom((org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage other) {
if (other == org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage.getDefaultInstance()) return this;
if (!other.all_.isEmpty()) {
if (all_.isEmpty()) {
all_ = other.all_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureAllIsMutable();
all_.addAll(other.all_);
}
onChanged();
}
if (!other.a_.isEmpty()) {
if (a_.isEmpty()) {
a_ = other.a_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureAIsMutable();
a_.addAll(other.a_);
}
onChanged();
}
if (!other.c_.isEmpty()) {
if (c_.isEmpty()) {
c_ = other.c_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureCIsMutable();
c_.addAll(other.c_);
}
onChanged();
}
if (!other.g_.isEmpty()) {
if (g_.isEmpty()) {
g_ = other.g_;
bitField0_ = (bitField0_ & ~0x00000008);
} else {
ensureGIsMutable();
g_.addAll(other.g_);
}
onChanged();
}
if (!other.t_.isEmpty()) {
if (t_.isEmpty()) {
t_ = other.t_;
bitField0_ = (bitField0_ & ~0x00000010);
} else {
ensureTIsMutable();
t_.addAll(other.t_);
}
onChanged();
}
this.mergeUnknownFields(other.getUnknownFields());
return this;
}
public final boolean isInitialized() {
return true;
}
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.opencga.storage.alignment.proto.AlignmentProto.Coverage) e.getUnfinishedMessage();
throw e;
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
// repeated uint32 all = 1 [packed = true];
private java.util.List<java.lang.Integer> all_ = java.util.Collections.emptyList();
private void ensureAllIsMutable() {
if (!((bitField0_ & 0x00000001) == 0x00000001)) {
all_ = new java.util.ArrayList<java.lang.Integer>(all_);
bitField0_ |= 0x00000001;
}
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getAllList() {
return java.util.Collections.unmodifiableList(all_);
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public int getAllCount() {
return all_.size();
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public int getAll(int index) {
return all_.get(index);
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public Builder setAll(
int index, int value) {
ensureAllIsMutable();
all_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public Builder addAll(int value) {
ensureAllIsMutable();
all_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public Builder addAllAll(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureAllIsMutable();
super.addAll(values, all_);
onChanged();
return this;
}
/**
* <code>repeated uint32 all = 1 [packed = true];</code>
*/
public Builder clearAll() {
all_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
return this;
}
// repeated uint32 a = 2 [packed = true];
private java.util.List<java.lang.Integer> a_ = java.util.Collections.emptyList();
private void ensureAIsMutable() {
if (!((bitField0_ & 0x00000002) == 0x00000002)) {
a_ = new java.util.ArrayList<java.lang.Integer>(a_);
bitField0_ |= 0x00000002;
}
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getAList() {
return java.util.Collections.unmodifiableList(a_);
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public int getACount() {
return a_.size();
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public int getA(int index) {
return a_.get(index);
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public Builder setA(
int index, int value) {
ensureAIsMutable();
a_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public Builder addA(int value) {
ensureAIsMutable();
a_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public Builder addAllA(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureAIsMutable();
super.addAll(values, a_);
onChanged();
return this;
}
/**
* <code>repeated uint32 a = 2 [packed = true];</code>
*/
public Builder clearA() {
a_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
return this;
}
// repeated uint32 c = 3 [packed = true];
private java.util.List<java.lang.Integer> c_ = java.util.Collections.emptyList();
private void ensureCIsMutable() {
if (!((bitField0_ & 0x00000004) == 0x00000004)) {
c_ = new java.util.ArrayList<java.lang.Integer>(c_);
bitField0_ |= 0x00000004;
}
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getCList() {
return java.util.Collections.unmodifiableList(c_);
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public int getCCount() {
return c_.size();
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public int getC(int index) {
return c_.get(index);
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public Builder setC(
int index, int value) {
ensureCIsMutable();
c_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public Builder addC(int value) {
ensureCIsMutable();
c_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public Builder addAllC(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureCIsMutable();
super.addAll(values, c_);
onChanged();
return this;
}
/**
* <code>repeated uint32 c = 3 [packed = true];</code>
*/
public Builder clearC() {
c_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
return this;
}
// repeated uint32 g = 4 [packed = true];
private java.util.List<java.lang.Integer> g_ = java.util.Collections.emptyList();
private void ensureGIsMutable() {
if (!((bitField0_ & 0x00000008) == 0x00000008)) {
g_ = new java.util.ArrayList<java.lang.Integer>(g_);
bitField0_ |= 0x00000008;
}
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getGList() {
return java.util.Collections.unmodifiableList(g_);
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public int getGCount() {
return g_.size();
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public int getG(int index) {
return g_.get(index);
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public Builder setG(
int index, int value) {
ensureGIsMutable();
g_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public Builder addG(int value) {
ensureGIsMutable();
g_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public Builder addAllG(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureGIsMutable();
super.addAll(values, g_);
onChanged();
return this;
}
/**
* <code>repeated uint32 g = 4 [packed = true];</code>
*/
public Builder clearG() {
g_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
onChanged();
return this;
}
// repeated uint32 t = 5 [packed = true];
private java.util.List<java.lang.Integer> t_ = java.util.Collections.emptyList();
private void ensureTIsMutable() {
if (!((bitField0_ & 0x00000010) == 0x00000010)) {
t_ = new java.util.ArrayList<java.lang.Integer>(t_);
bitField0_ |= 0x00000010;
}
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public java.util.List<java.lang.Integer>
getTList() {
return java.util.Collections.unmodifiableList(t_);
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public int getTCount() {
return t_.size();
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public int getT(int index) {
return t_.get(index);
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public Builder setT(
int index, int value) {
ensureTIsMutable();
t_.set(index, value);
onChanged();
return this;
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public Builder addT(int value) {
ensureTIsMutable();
t_.add(value);
onChanged();
return this;
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public Builder addAllT(
java.lang.Iterable<? extends java.lang.Integer> values) {
ensureTIsMutable();
super.addAll(values, t_);
onChanged();
return this;
}
/**
* <code>repeated uint32 t = 5 [packed = true];</code>
*/
public Builder clearT() {
t_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
onChanged();
return this;
}
// @@protoc_insertion_point(builder_scope:org.opencb.opencga.storage.alignment.proto.Coverage)
}
static {
defaultInstance = new Coverage(true);
defaultInstance.initFields();
}
// @@protoc_insertion_point(class_scope:org.opencb.opencga.storage.alignment.proto.Coverage)
}
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Difference_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Header_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_fieldAccessorTable;
private static com.google.protobuf.Descriptors.Descriptor
internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor;
private static
com.google.protobuf.GeneratedMessage.FieldAccessorTable
internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_fieldAccessorTable;
public static com.google.protobuf.Descriptors.FileDescriptor
getDescriptor() {
return descriptor;
}
private static com.google.protobuf.Descriptors.FileDescriptor
descriptor;
static {
java.lang.String[] descriptorData = {
"\n\017Alignment.proto\022*org.opencb.opencga.st" +
"orage.alignment.proto\"\241\002\n\nDifference\022[\n\010" +
"operator\030\001 \002(\0162I.org.opencb.opencga.stor" +
"age.alignment.proto.Difference.Differenc" +
"eOperator\022\013\n\003pos\030\002 \001(\r\022\016\n\006length\030\003 \001(\r\022\020" +
"\n\010sequence\030\004 \001(\014\"\206\001\n\022DifferenceOperator\022" +
"\r\n\tINSERTION\020\001\022\014\n\010DELETION\020\002\022\014\n\010MISMATCH" +
"\020\003\022\022\n\016SKIPPED_REGION\020\004\022\021\n\rSOFT_CLIPPING\020" +
"\005\022\021\n\rHARD_CLIPPING\020\006\022\013\n\007PADDING\020\007\"\204\002\n\017Al" +
"ignmentRecord\022\014\n\004name\030\001 \002(\t\022\013\n\003pos\030\002 \002(\r",
"\022\r\n\005flags\030\003 \001(\r\022\013\n\003len\030\004 \001(\r\022\014\n\004mapq\030\005 \002" +
"(\r\022\021\n\tqualities\030\006 \002(\t\022\r\n\005rnext\030\007 \001(\t\022\025\n\r" +
"relativePnext\030\010 \002(\021\022\032\n\022inferredInsertSiz" +
"e\030\t \002(\021\022E\n\005diffs\030\n \003(\01326.org.opencb.open" +
"cga.storage.alignment.proto.Difference\022\020" +
"\n\004tags\030\013 \003(\rB\002\020\001\"\222\001\n\017AlignmentBucket\022\024\n\014" +
"summaryIndex\030\001 \002(\r\022\022\n\noverlapped\030\002 \001(\r\022U" +
"\n\020alignmentRecords\030\t \003(\0132;.org.opencb.op" +
"encga.storage.alignment.proto.AlignmentR" +
"ecord\"\220\002\n\007Summary\022\023\n\013defaultFlag\030\001 \002(\r\022\022",
"\n\ndefaultLen\030\002 \002(\r\022\024\n\014defaultRNext\030\003 \002(\t" +
"\022\031\n\021defaultOverlapped\030\004 \002(\r\022\014\n\004keys\030\010 \002(" +
"\t\022H\n\006values\030\t \003(\01328.org.opencb.opencga.s" +
"torage.alignment.proto.Summary.Pair\032S\n\004P" +
"air\022\013\n\003key\030\001 \002(\r\022\016\n\006avalue\030\002 \001(\r\022\016\n\006ival" +
"ue\030\003 \001(\021\022\016\n\006fvalue\030\004 \001(\002\022\016\n\006zvalue\030\005 \001(\t" +
"\"\233\001\n\006Header\022J\n\007regions\030\001 \003(\01329.org.openc" +
"b.opencga.storage.alignment.proto.Header" +
".Region\022\021\n\tSamHeader\030\002 \001(\014\0322\n\006Region\022\026\n\016" +
"chromosomeName\030\001 \002(\t\022\020\n\010maxValue\030\002 \002(\r\" ",
"\n\014MeanCoverage\022\020\n\010coverage\030\001 \002(\002\"W\n\010Cove" +
"rage\022\017\n\003all\030\001 \003(\rB\002\020\001\022\r\n\001a\030\002 \003(\rB\002\020\001\022\r\n\001" +
"c\030\003 \003(\rB\002\020\001\022\r\n\001g\030\004 \003(\rB\002\020\001\022\r\n\001t\030\005 \003(\rB\002\020" +
"\001B\020B\016AlignmentProto"
};
com.google.protobuf.Descriptors.FileDescriptor.InternalDescriptorAssigner assigner =
new com.google.protobuf.Descriptors.FileDescriptor.InternalDescriptorAssigner() {
public com.google.protobuf.ExtensionRegistry assignDescriptors(
com.google.protobuf.Descriptors.FileDescriptor root) {
descriptor = root;
internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor =
getDescriptor().getMessageTypes().get(0);
internal_static_org_opencb_opencga_storage_alignment_proto_Difference_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Difference_descriptor,
new java.lang.String[] { "Operator", "Pos", "Length", "Sequence", });
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor =
getDescriptor().getMessageTypes().get(1);
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentRecord_descriptor,
new java.lang.String[] { "Name", "Pos", "Flags", "Len", "Mapq", "Qualities", "Rnext", "RelativePnext", "InferredInsertSize", "Diffs", "Tags", });
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor =
getDescriptor().getMessageTypes().get(2);
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_AlignmentBucket_descriptor,
new java.lang.String[] { "SummaryIndex", "Overlapped", "AlignmentRecords", });
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor =
getDescriptor().getMessageTypes().get(3);
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor,
new java.lang.String[] { "DefaultFlag", "DefaultLen", "DefaultRNext", "DefaultOverlapped", "Keys", "Values", });
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor =
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_descriptor.getNestedTypes().get(0);
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Summary_Pair_descriptor,
new java.lang.String[] { "Key", "Avalue", "Ivalue", "Fvalue", "Zvalue", });
internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor =
getDescriptor().getMessageTypes().get(4);
internal_static_org_opencb_opencga_storage_alignment_proto_Header_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor,
new java.lang.String[] { "Regions", "SamHeader", });
internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor =
internal_static_org_opencb_opencga_storage_alignment_proto_Header_descriptor.getNestedTypes().get(0);
internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Header_Region_descriptor,
new java.lang.String[] { "ChromosomeName", "MaxValue", });
internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor =
getDescriptor().getMessageTypes().get(5);
internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_MeanCoverage_descriptor,
new java.lang.String[] { "Coverage", });
internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor =
getDescriptor().getMessageTypes().get(6);
internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_fieldAccessorTable = new
com.google.protobuf.GeneratedMessage.FieldAccessorTable(
internal_static_org_opencb_opencga_storage_alignment_proto_Coverage_descriptor,
new java.lang.String[] { "All", "A", "C", "G", "T", });
return null;
}
};
com.google.protobuf.Descriptors.FileDescriptor
.internalBuildGeneratedFileFrom(descriptorData,
new com.google.protobuf.Descriptors.FileDescriptor[] {
}, assigner);
}
// @@protoc_insertion_point(outer_class_scope)
}