-
-
-
-
+ * An alignment from minimap2 sent to the server + *+ * + * Protobuf type {@code assembly.AlignmentMsg} + */ +public final class AlignmentMsg extends + com.google.protobuf.GeneratedMessageV3 implements + // @@protoc_insertion_point(message_implements:assembly.AlignmentMsg) + AlignmentMsgOrBuilder { +private static final long serialVersionUID = 0L; + // Use AlignmentMsg.newBuilder() to construct. + private AlignmentMsg(com.google.protobuf.GeneratedMessageV3.Builder builder) { + super(builder); + } + private AlignmentMsg() { + queryName_ = ""; + targetName_ = ""; + } + + @java.lang.Override + @SuppressWarnings({"unused"}) + protected java.lang.Object newInstance( + UnusedPrivateParameter unused) { + return new AlignmentMsg(); + } + + @java.lang.Override + public final com.google.protobuf.UnknownFieldSet + getUnknownFields() { + return this.unknownFields; + } + private AlignmentMsg( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException { + this(); + if (extensionRegistry == null) { + throw new java.lang.NullPointerException(); + } + com.google.protobuf.UnknownFieldSet.Builder unknownFields = + com.google.protobuf.UnknownFieldSet.newBuilder(); + try { + boolean done = false; + while (!done) { + int tag = input.readTag(); + switch (tag) { + case 0: + done = true; + break; + case 10: { + java.lang.String s = input.readStringRequireUtf8(); + + queryName_ = s; + break; + } + case 16: { + + queryLength_ = input.readInt32(); + break; + } + case 24: { + + queryStart_ = input.readInt32(); + break; + } + case 32: { + + queryEnd_ = input.readInt32(); + break; + } + case 40: { + + strand_ = input.readBool(); + break; + } + case 50: { + java.lang.String s = input.readStringRequireUtf8(); + + targetName_ = s; + break; + } + case 56: { + + targetLength_ = input.readInt32(); + break; + } + case 64: { + + targetStart_ = input.readInt32(); + break; + } + case 72: { + + targetEnd_ = input.readInt32(); + break; + } + case 80: { + + quality_ = input.readInt32(); + break; + } + case 88: { + + score_ = input.readInt32(); + break; + } + default: { + if (!parseUnknownField( + input, unknownFields, extensionRegistry, tag)) { + done = true; + } + break; + } + } + } + } catch (com.google.protobuf.InvalidProtocolBufferException e) { + throw e.setUnfinishedMessage(this); + } catch (java.io.IOException e) { + throw new com.google.protobuf.InvalidProtocolBufferException( + e).setUnfinishedMessage(this); + } finally { + this.unknownFields = unknownFields.build(); + makeExtensionsImmutable(); + } + } + public static final com.google.protobuf.Descriptors.Descriptor + getDescriptor() { + return org.rtassembly.npgraph.grpc.AssemblyGuideProto.internal_static_assembly_AlignmentMsg_descriptor; + } + + @java.lang.Override + protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable + internalGetFieldAccessorTable() { + return org.rtassembly.npgraph.grpc.AssemblyGuideProto.internal_static_assembly_AlignmentMsg_fieldAccessorTable + .ensureFieldAccessorsInitialized( + org.rtassembly.npgraph.grpc.AlignmentMsg.class, org.rtassembly.npgraph.grpc.AlignmentMsg.Builder.class); + } + + public static final int QUERY_NAME_FIELD_NUMBER = 1; + private volatile java.lang.Object queryName_; + /** + *
string query_name = 1;
+ * @return The queryName.
+ */
+ public java.lang.String getQueryName() {
+ java.lang.Object ref = queryName_;
+ 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();
+ queryName_ = s;
+ return s;
+ }
+ }
+ /**
+ * string query_name = 1;
+ * @return The bytes for queryName.
+ */
+ public com.google.protobuf.ByteString
+ getQueryNameBytes() {
+ java.lang.Object ref = queryName_;
+ if (ref instanceof java.lang.String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ queryName_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+
+ public static final int QUERY_LENGTH_FIELD_NUMBER = 2;
+ private int queryLength_;
+ /**
+ * int32 query_length = 2;
+ * @return The queryLength.
+ */
+ public int getQueryLength() {
+ return queryLength_;
+ }
+
+ public static final int QUERY_START_FIELD_NUMBER = 3;
+ private int queryStart_;
+ /**
+ * int32 query_start = 3;
+ * @return The queryStart.
+ */
+ public int getQueryStart() {
+ return queryStart_;
+ }
+
+ public static final int QUERY_END_FIELD_NUMBER = 4;
+ private int queryEnd_;
+ /**
+ * int32 query_end = 4;
+ * @return The queryEnd.
+ */
+ public int getQueryEnd() {
+ return queryEnd_;
+ }
+
+ public static final int STRAND_FIELD_NUMBER = 5;
+ private boolean strand_;
+ /**
+ * bool strand = 5;
+ * @return The strand.
+ */
+ public boolean getStrand() {
+ return strand_;
+ }
+
+ public static final int TARGET_NAME_FIELD_NUMBER = 6;
+ private volatile java.lang.Object targetName_;
+ /**
+ * string target_name = 6;
+ * @return The targetName.
+ */
+ public java.lang.String getTargetName() {
+ java.lang.Object ref = targetName_;
+ 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();
+ targetName_ = s;
+ return s;
+ }
+ }
+ /**
+ * string target_name = 6;
+ * @return The bytes for targetName.
+ */
+ public com.google.protobuf.ByteString
+ getTargetNameBytes() {
+ java.lang.Object ref = targetName_;
+ if (ref instanceof java.lang.String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ targetName_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+
+ public static final int TARGET_LENGTH_FIELD_NUMBER = 7;
+ private int targetLength_;
+ /**
+ * int32 target_length = 7;
+ * @return The targetLength.
+ */
+ public int getTargetLength() {
+ return targetLength_;
+ }
+
+ public static final int TARGET_START_FIELD_NUMBER = 8;
+ private int targetStart_;
+ /**
+ * int32 target_start = 8;
+ * @return The targetStart.
+ */
+ public int getTargetStart() {
+ return targetStart_;
+ }
+
+ public static final int TARGET_END_FIELD_NUMBER = 9;
+ private int targetEnd_;
+ /**
+ * int32 target_end = 9;
+ * @return The targetEnd.
+ */
+ public int getTargetEnd() {
+ return targetEnd_;
+ }
+
+ public static final int QUALITY_FIELD_NUMBER = 10;
+ private int quality_;
+ /**
+ * int32 quality = 10;
+ * @return The quality.
+ */
+ public int getQuality() {
+ return quality_;
+ }
+
+ public static final int SCORE_FIELD_NUMBER = 11;
+ private int score_;
+ /**
+ * int32 score = 11;
+ * @return The score.
+ */
+ public int getScore() {
+ return score_;
+ }
+
+ private byte memoizedIsInitialized = -1;
+ @java.lang.Override
+ public final boolean isInitialized() {
+ byte isInitialized = memoizedIsInitialized;
+ if (isInitialized == 1) return true;
+ if (isInitialized == 0) return false;
+
+ memoizedIsInitialized = 1;
+ return true;
+ }
+
+ @java.lang.Override
+ public void writeTo(com.google.protobuf.CodedOutputStream output)
+ throws java.io.IOException {
+ if (!getQueryNameBytes().isEmpty()) {
+ com.google.protobuf.GeneratedMessageV3.writeString(output, 1, queryName_);
+ }
+ if (queryLength_ != 0) {
+ output.writeInt32(2, queryLength_);
+ }
+ if (queryStart_ != 0) {
+ output.writeInt32(3, queryStart_);
+ }
+ if (queryEnd_ != 0) {
+ output.writeInt32(4, queryEnd_);
+ }
+ if (strand_ != false) {
+ output.writeBool(5, strand_);
+ }
+ if (!getTargetNameBytes().isEmpty()) {
+ com.google.protobuf.GeneratedMessageV3.writeString(output, 6, targetName_);
+ }
+ if (targetLength_ != 0) {
+ output.writeInt32(7, targetLength_);
+ }
+ if (targetStart_ != 0) {
+ output.writeInt32(8, targetStart_);
+ }
+ if (targetEnd_ != 0) {
+ output.writeInt32(9, targetEnd_);
+ }
+ if (quality_ != 0) {
+ output.writeInt32(10, quality_);
+ }
+ if (score_ != 0) {
+ output.writeInt32(11, score_);
+ }
+ unknownFields.writeTo(output);
+ }
+
+ @java.lang.Override
+ public int getSerializedSize() {
+ int size = memoizedSize;
+ if (size != -1) return size;
+
+ size = 0;
+ if (!getQueryNameBytes().isEmpty()) {
+ size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, queryName_);
+ }
+ if (queryLength_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(2, queryLength_);
+ }
+ if (queryStart_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(3, queryStart_);
+ }
+ if (queryEnd_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(4, queryEnd_);
+ }
+ if (strand_ != false) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeBoolSize(5, strand_);
+ }
+ if (!getTargetNameBytes().isEmpty()) {
+ size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, targetName_);
+ }
+ if (targetLength_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(7, targetLength_);
+ }
+ if (targetStart_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(8, targetStart_);
+ }
+ if (targetEnd_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(9, targetEnd_);
+ }
+ if (quality_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(10, quality_);
+ }
+ if (score_ != 0) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeInt32Size(11, score_);
+ }
+ size += unknownFields.getSerializedSize();
+ memoizedSize = size;
+ return size;
+ }
+
+ @java.lang.Override
+ public boolean equals(final java.lang.Object obj) {
+ if (obj == this) {
+ return true;
+ }
+ if (!(obj instanceof org.rtassembly.npgraph.grpc.AlignmentMsg)) {
+ return super.equals(obj);
+ }
+ org.rtassembly.npgraph.grpc.AlignmentMsg other = (org.rtassembly.npgraph.grpc.AlignmentMsg) obj;
+
+ if (!getQueryName()
+ .equals(other.getQueryName())) return false;
+ if (getQueryLength()
+ != other.getQueryLength()) return false;
+ if (getQueryStart()
+ != other.getQueryStart()) return false;
+ if (getQueryEnd()
+ != other.getQueryEnd()) return false;
+ if (getStrand()
+ != other.getStrand()) return false;
+ if (!getTargetName()
+ .equals(other.getTargetName())) return false;
+ if (getTargetLength()
+ != other.getTargetLength()) return false;
+ if (getTargetStart()
+ != other.getTargetStart()) return false;
+ if (getTargetEnd()
+ != other.getTargetEnd()) return false;
+ if (getQuality()
+ != other.getQuality()) return false;
+ if (getScore()
+ != other.getScore()) return false;
+ if (!unknownFields.equals(other.unknownFields)) return false;
+ return true;
+ }
+
+ @java.lang.Override
+ public int hashCode() {
+ if (memoizedHashCode != 0) {
+ return memoizedHashCode;
+ }
+ int hash = 41;
+ hash = (19 * hash) + getDescriptor().hashCode();
+ hash = (37 * hash) + QUERY_NAME_FIELD_NUMBER;
+ hash = (53 * hash) + getQueryName().hashCode();
+ hash = (37 * hash) + QUERY_LENGTH_FIELD_NUMBER;
+ hash = (53 * hash) + getQueryLength();
+ hash = (37 * hash) + QUERY_START_FIELD_NUMBER;
+ hash = (53 * hash) + getQueryStart();
+ hash = (37 * hash) + QUERY_END_FIELD_NUMBER;
+ hash = (53 * hash) + getQueryEnd();
+ hash = (37 * hash) + STRAND_FIELD_NUMBER;
+ hash = (53 * hash) + com.google.protobuf.Internal.hashBoolean(
+ getStrand());
+ hash = (37 * hash) + TARGET_NAME_FIELD_NUMBER;
+ hash = (53 * hash) + getTargetName().hashCode();
+ hash = (37 * hash) + TARGET_LENGTH_FIELD_NUMBER;
+ hash = (53 * hash) + getTargetLength();
+ hash = (37 * hash) + TARGET_START_FIELD_NUMBER;
+ hash = (53 * hash) + getTargetStart();
+ hash = (37 * hash) + TARGET_END_FIELD_NUMBER;
+ hash = (53 * hash) + getTargetEnd();
+ hash = (37 * hash) + QUALITY_FIELD_NUMBER;
+ hash = (53 * hash) + getQuality();
+ hash = (37 * hash) + SCORE_FIELD_NUMBER;
+ hash = (53 * hash) + getScore();
+ hash = (29 * hash) + unknownFields.hashCode();
+ memoizedHashCode = hash;
+ return hash;
+ }
+
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ java.nio.ByteBuffer data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ java.nio.ByteBuffer data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ com.google.protobuf.ByteString data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ com.google.protobuf.ByteString data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(byte[] data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ byte[] data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseDelimitedFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseDelimitedFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ com.google.protobuf.CodedInputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg parseFrom(
+ com.google.protobuf.CodedInputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+
+ @java.lang.Override
+ public Builder newBuilderForType() { return newBuilder(); }
+ public static Builder newBuilder() {
+ return DEFAULT_INSTANCE.toBuilder();
+ }
+ public static Builder newBuilder(org.rtassembly.npgraph.grpc.AlignmentMsg prototype) {
+ return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
+ }
+ @java.lang.Override
+ public Builder toBuilder() {
+ return this == DEFAULT_INSTANCE
+ ? new Builder() : new Builder().mergeFrom(this);
+ }
+
+ @java.lang.Override
+ protected Builder newBuilderForType(
+ com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
+ Builder builder = new Builder(parent);
+ return builder;
+ }
+ /**
+ * + * An alignment from minimap2 sent to the server + *+ * + * Protobuf type {@code assembly.AlignmentMsg} + */ + public static final class Builder extends + com.google.protobuf.GeneratedMessageV3.Builder
string query_name = 1;
+ * @return The queryName.
+ */
+ public java.lang.String getQueryName() {
+ java.lang.Object ref = queryName_;
+ if (!(ref instanceof java.lang.String)) {
+ com.google.protobuf.ByteString bs =
+ (com.google.protobuf.ByteString) ref;
+ java.lang.String s = bs.toStringUtf8();
+ queryName_ = s;
+ return s;
+ } else {
+ return (java.lang.String) ref;
+ }
+ }
+ /**
+ * string query_name = 1;
+ * @return The bytes for queryName.
+ */
+ public com.google.protobuf.ByteString
+ getQueryNameBytes() {
+ java.lang.Object ref = queryName_;
+ if (ref instanceof String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ queryName_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+ /**
+ * string query_name = 1;
+ * @param value The queryName to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQueryName(
+ java.lang.String value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+
+ queryName_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * string query_name = 1;
+ * @return This builder for chaining.
+ */
+ public Builder clearQueryName() {
+
+ queryName_ = getDefaultInstance().getQueryName();
+ onChanged();
+ return this;
+ }
+ /**
+ * string query_name = 1;
+ * @param value The bytes for queryName to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQueryNameBytes(
+ com.google.protobuf.ByteString value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ checkByteStringIsUtf8(value);
+
+ queryName_ = value;
+ onChanged();
+ return this;
+ }
+
+ private int queryLength_ ;
+ /**
+ * int32 query_length = 2;
+ * @return The queryLength.
+ */
+ public int getQueryLength() {
+ return queryLength_;
+ }
+ /**
+ * int32 query_length = 2;
+ * @param value The queryLength to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQueryLength(int value) {
+
+ queryLength_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 query_length = 2;
+ * @return This builder for chaining.
+ */
+ public Builder clearQueryLength() {
+
+ queryLength_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int queryStart_ ;
+ /**
+ * int32 query_start = 3;
+ * @return The queryStart.
+ */
+ public int getQueryStart() {
+ return queryStart_;
+ }
+ /**
+ * int32 query_start = 3;
+ * @param value The queryStart to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQueryStart(int value) {
+
+ queryStart_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 query_start = 3;
+ * @return This builder for chaining.
+ */
+ public Builder clearQueryStart() {
+
+ queryStart_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int queryEnd_ ;
+ /**
+ * int32 query_end = 4;
+ * @return The queryEnd.
+ */
+ public int getQueryEnd() {
+ return queryEnd_;
+ }
+ /**
+ * int32 query_end = 4;
+ * @param value The queryEnd to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQueryEnd(int value) {
+
+ queryEnd_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 query_end = 4;
+ * @return This builder for chaining.
+ */
+ public Builder clearQueryEnd() {
+
+ queryEnd_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private boolean strand_ ;
+ /**
+ * bool strand = 5;
+ * @return The strand.
+ */
+ public boolean getStrand() {
+ return strand_;
+ }
+ /**
+ * bool strand = 5;
+ * @param value The strand to set.
+ * @return This builder for chaining.
+ */
+ public Builder setStrand(boolean value) {
+
+ strand_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * bool strand = 5;
+ * @return This builder for chaining.
+ */
+ public Builder clearStrand() {
+
+ strand_ = false;
+ onChanged();
+ return this;
+ }
+
+ private java.lang.Object targetName_ = "";
+ /**
+ * string target_name = 6;
+ * @return The targetName.
+ */
+ public java.lang.String getTargetName() {
+ java.lang.Object ref = targetName_;
+ if (!(ref instanceof java.lang.String)) {
+ com.google.protobuf.ByteString bs =
+ (com.google.protobuf.ByteString) ref;
+ java.lang.String s = bs.toStringUtf8();
+ targetName_ = s;
+ return s;
+ } else {
+ return (java.lang.String) ref;
+ }
+ }
+ /**
+ * string target_name = 6;
+ * @return The bytes for targetName.
+ */
+ public com.google.protobuf.ByteString
+ getTargetNameBytes() {
+ java.lang.Object ref = targetName_;
+ if (ref instanceof String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ targetName_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+ /**
+ * string target_name = 6;
+ * @param value The targetName to set.
+ * @return This builder for chaining.
+ */
+ public Builder setTargetName(
+ java.lang.String value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+
+ targetName_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * string target_name = 6;
+ * @return This builder for chaining.
+ */
+ public Builder clearTargetName() {
+
+ targetName_ = getDefaultInstance().getTargetName();
+ onChanged();
+ return this;
+ }
+ /**
+ * string target_name = 6;
+ * @param value The bytes for targetName to set.
+ * @return This builder for chaining.
+ */
+ public Builder setTargetNameBytes(
+ com.google.protobuf.ByteString value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ checkByteStringIsUtf8(value);
+
+ targetName_ = value;
+ onChanged();
+ return this;
+ }
+
+ private int targetLength_ ;
+ /**
+ * int32 target_length = 7;
+ * @return The targetLength.
+ */
+ public int getTargetLength() {
+ return targetLength_;
+ }
+ /**
+ * int32 target_length = 7;
+ * @param value The targetLength to set.
+ * @return This builder for chaining.
+ */
+ public Builder setTargetLength(int value) {
+
+ targetLength_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 target_length = 7;
+ * @return This builder for chaining.
+ */
+ public Builder clearTargetLength() {
+
+ targetLength_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int targetStart_ ;
+ /**
+ * int32 target_start = 8;
+ * @return The targetStart.
+ */
+ public int getTargetStart() {
+ return targetStart_;
+ }
+ /**
+ * int32 target_start = 8;
+ * @param value The targetStart to set.
+ * @return This builder for chaining.
+ */
+ public Builder setTargetStart(int value) {
+
+ targetStart_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 target_start = 8;
+ * @return This builder for chaining.
+ */
+ public Builder clearTargetStart() {
+
+ targetStart_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int targetEnd_ ;
+ /**
+ * int32 target_end = 9;
+ * @return The targetEnd.
+ */
+ public int getTargetEnd() {
+ return targetEnd_;
+ }
+ /**
+ * int32 target_end = 9;
+ * @param value The targetEnd to set.
+ * @return This builder for chaining.
+ */
+ public Builder setTargetEnd(int value) {
+
+ targetEnd_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 target_end = 9;
+ * @return This builder for chaining.
+ */
+ public Builder clearTargetEnd() {
+
+ targetEnd_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int quality_ ;
+ /**
+ * int32 quality = 10;
+ * @return The quality.
+ */
+ public int getQuality() {
+ return quality_;
+ }
+ /**
+ * int32 quality = 10;
+ * @param value The quality to set.
+ * @return This builder for chaining.
+ */
+ public Builder setQuality(int value) {
+
+ quality_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 quality = 10;
+ * @return This builder for chaining.
+ */
+ public Builder clearQuality() {
+
+ quality_ = 0;
+ onChanged();
+ return this;
+ }
+
+ private int score_ ;
+ /**
+ * int32 score = 11;
+ * @return The score.
+ */
+ public int getScore() {
+ return score_;
+ }
+ /**
+ * int32 score = 11;
+ * @param value The score to set.
+ * @return This builder for chaining.
+ */
+ public Builder setScore(int value) {
+
+ score_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * int32 score = 11;
+ * @return This builder for chaining.
+ */
+ public Builder clearScore() {
+
+ score_ = 0;
+ onChanged();
+ return this;
+ }
+ @java.lang.Override
+ public final Builder setUnknownFields(
+ final com.google.protobuf.UnknownFieldSet unknownFields) {
+ return super.setUnknownFields(unknownFields);
+ }
+
+ @java.lang.Override
+ public final Builder mergeUnknownFields(
+ final com.google.protobuf.UnknownFieldSet unknownFields) {
+ return super.mergeUnknownFields(unknownFields);
+ }
+
+
+ // @@protoc_insertion_point(builder_scope:assembly.AlignmentMsg)
+ }
+
+ // @@protoc_insertion_point(class_scope:assembly.AlignmentMsg)
+ private static final org.rtassembly.npgraph.grpc.AlignmentMsg DEFAULT_INSTANCE;
+ static {
+ DEFAULT_INSTANCE = new org.rtassembly.npgraph.grpc.AlignmentMsg();
+ }
+
+ public static org.rtassembly.npgraph.grpc.AlignmentMsg getDefaultInstance() {
+ return DEFAULT_INSTANCE;
+ }
+
+ private static final com.google.protobuf.Parserstring query_name = 1;
+ * @return The queryName.
+ */
+ java.lang.String getQueryName();
+ /**
+ * string query_name = 1;
+ * @return The bytes for queryName.
+ */
+ com.google.protobuf.ByteString
+ getQueryNameBytes();
+
+ /**
+ * int32 query_length = 2;
+ * @return The queryLength.
+ */
+ int getQueryLength();
+
+ /**
+ * int32 query_start = 3;
+ * @return The queryStart.
+ */
+ int getQueryStart();
+
+ /**
+ * int32 query_end = 4;
+ * @return The queryEnd.
+ */
+ int getQueryEnd();
+
+ /**
+ * bool strand = 5;
+ * @return The strand.
+ */
+ boolean getStrand();
+
+ /**
+ * string target_name = 6;
+ * @return The targetName.
+ */
+ java.lang.String getTargetName();
+ /**
+ * string target_name = 6;
+ * @return The bytes for targetName.
+ */
+ com.google.protobuf.ByteString
+ getTargetNameBytes();
+
+ /**
+ * int32 target_length = 7;
+ * @return The targetLength.
+ */
+ int getTargetLength();
+
+ /**
+ * int32 target_start = 8;
+ * @return The targetStart.
+ */
+ int getTargetStart();
+
+ /**
+ * int32 target_end = 9;
+ * @return The targetEnd.
+ */
+ int getTargetEnd();
+
+ /**
+ * int32 quality = 10;
+ * @return The quality.
+ */
+ int getQuality();
+
+ /**
+ * int32 score = 11;
+ * @return The score.
+ */
+ int getScore();
+}
diff --git a/src/main/java/org/rtassembly/npgraph/grpc/AssemblyGuideGrpc.java b/src/main/java/org/rtassembly/npgraph/grpc/AssemblyGuideGrpc.java
new file mode 100644
index 0000000..62d8eb8
--- /dev/null
+++ b/src/main/java/org/rtassembly/npgraph/grpc/AssemblyGuideGrpc.java
@@ -0,0 +1,303 @@
+package org.rtassembly.npgraph.grpc;
+
+import static io.grpc.MethodDescriptor.generateFullMethodName;
+import static io.grpc.stub.ClientCalls.asyncBidiStreamingCall;
+import static io.grpc.stub.ClientCalls.asyncClientStreamingCall;
+import static io.grpc.stub.ClientCalls.asyncServerStreamingCall;
+import static io.grpc.stub.ClientCalls.asyncUnaryCall;
+import static io.grpc.stub.ClientCalls.blockingServerStreamingCall;
+import static io.grpc.stub.ClientCalls.blockingUnaryCall;
+import static io.grpc.stub.ClientCalls.futureUnaryCall;
+import static io.grpc.stub.ServerCalls.asyncBidiStreamingCall;
+import static io.grpc.stub.ServerCalls.asyncClientStreamingCall;
+import static io.grpc.stub.ServerCalls.asyncServerStreamingCall;
+import static io.grpc.stub.ServerCalls.asyncUnaryCall;
+import static io.grpc.stub.ServerCalls.asyncUnimplementedStreamingCall;
+import static io.grpc.stub.ServerCalls.asyncUnimplementedUnaryCall;
+
+/**
+ * + * Interface exported by the server. + *+ */ +@javax.annotation.Generated( + value = "by gRPC proto compiler (version 1.28.0)", + comments = "Source: npgraph_service.proto") +public final class AssemblyGuideGrpc { + + private AssemblyGuideGrpc() {} + + public static final String SERVICE_NAME = "assembly.AssemblyGuide"; + + // Static method descriptors that strictly reflect the proto. + private static volatile io.grpc.MethodDescriptor
+ * Interface exported by the server. + *+ */ + public static abstract class AssemblyGuideImplBase implements io.grpc.BindableService { + + /** + */ + public void getAssemblyContribution(org.rtassembly.npgraph.grpc.RequestAssembly request, + io.grpc.stub.StreamObserver
+ * Interface exported by the server. + *+ */ + public static final class AssemblyGuideStub extends io.grpc.stub.AbstractAsyncStub
+ * Interface exported by the server. + *+ */ + public static final class AssemblyGuideBlockingStub extends io.grpc.stub.AbstractBlockingStub
+ * Interface exported by the server. + *+ */ + public static final class AssemblyGuideFutureStub extends io.grpc.stub.AbstractFutureStub
See src/main/proto/npgraph_service.proto for details of the methods.
+ */
+ private static class AssemblyGuideService extends AssemblyGuideGrpc.AssemblyGuideImplBase {
+ private static final HashMap
+ * Client sent all hits from a chunk simultaneously
+ *
+ *
+ * Protobuf type {@code assembly.RequestAssembly}
+ */
+public final class RequestAssembly extends
+ com.google.protobuf.GeneratedMessageV3 implements
+ // @@protoc_insertion_point(message_implements:assembly.RequestAssembly)
+ RequestAssemblyOrBuilder {
+private static final long serialVersionUID = 0L;
+ // Use RequestAssembly.newBuilder() to construct.
+ private RequestAssembly(com.google.protobuf.GeneratedMessageV3.Builder builder) {
+ super(builder);
+ }
+ private RequestAssembly() {
+ readId_ = "";
+ hitsList_ = java.util.Collections.emptyList();
+ }
+
+ @java.lang.Override
+ @SuppressWarnings({"unused"})
+ protected java.lang.Object newInstance(
+ UnusedPrivateParameter unused) {
+ return new RequestAssembly();
+ }
+
+ @java.lang.Override
+ public final com.google.protobuf.UnknownFieldSet
+ getUnknownFields() {
+ return this.unknownFields;
+ }
+ private RequestAssembly(
+ com.google.protobuf.CodedInputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ this();
+ if (extensionRegistry == null) {
+ throw new java.lang.NullPointerException();
+ }
+ int mutable_bitField0_ = 0;
+ com.google.protobuf.UnknownFieldSet.Builder unknownFields =
+ com.google.protobuf.UnknownFieldSet.newBuilder();
+ try {
+ boolean done = false;
+ while (!done) {
+ int tag = input.readTag();
+ switch (tag) {
+ case 0:
+ done = true;
+ break;
+ case 10: {
+ java.lang.String s = input.readStringRequireUtf8();
+
+ readId_ = s;
+ break;
+ }
+ case 18: {
+ if (!((mutable_bitField0_ & 0x00000001) != 0)) {
+ hitsList_ = new java.util.ArrayListstring read_id = 1;
+ * @return The readId.
+ */
+ public java.lang.String getReadId() {
+ java.lang.Object ref = readId_;
+ 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();
+ readId_ = s;
+ return s;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ public com.google.protobuf.ByteString
+ getReadIdBytes() {
+ java.lang.Object ref = readId_;
+ if (ref instanceof java.lang.String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ readId_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+
+ public static final int HITS_LIST_FIELD_NUMBER = 2;
+ private java.util.Listrepeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public java.util.Listrepeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public java.util.List
+ getHitsListOrBuilderList() {
+ return hitsList_;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public int getHitsListCount() {
+ return hitsList_.size();
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsg getHitsList(int index) {
+ return hitsList_.get(index);
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsgOrBuilder getHitsListOrBuilder(
+ int index) {
+ return hitsList_.get(index);
+ }
+
+ private byte memoizedIsInitialized = -1;
+ @java.lang.Override
+ public final boolean isInitialized() {
+ byte isInitialized = memoizedIsInitialized;
+ if (isInitialized == 1) return true;
+ if (isInitialized == 0) return false;
+
+ memoizedIsInitialized = 1;
+ return true;
+ }
+
+ @java.lang.Override
+ public void writeTo(com.google.protobuf.CodedOutputStream output)
+ throws java.io.IOException {
+ if (!getReadIdBytes().isEmpty()) {
+ com.google.protobuf.GeneratedMessageV3.writeString(output, 1, readId_);
+ }
+ for (int i = 0; i < hitsList_.size(); i++) {
+ output.writeMessage(2, hitsList_.get(i));
+ }
+ unknownFields.writeTo(output);
+ }
+
+ @java.lang.Override
+ public int getSerializedSize() {
+ int size = memoizedSize;
+ if (size != -1) return size;
+
+ size = 0;
+ if (!getReadIdBytes().isEmpty()) {
+ size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, readId_);
+ }
+ for (int i = 0; i < hitsList_.size(); i++) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeMessageSize(2, hitsList_.get(i));
+ }
+ size += unknownFields.getSerializedSize();
+ memoizedSize = size;
+ return size;
+ }
+
+ @java.lang.Override
+ public boolean equals(final java.lang.Object obj) {
+ if (obj == this) {
+ return true;
+ }
+ if (!(obj instanceof org.rtassembly.npgraph.grpc.RequestAssembly)) {
+ return super.equals(obj);
+ }
+ org.rtassembly.npgraph.grpc.RequestAssembly other = (org.rtassembly.npgraph.grpc.RequestAssembly) obj;
+
+ if (!getReadId()
+ .equals(other.getReadId())) return false;
+ if (!getHitsListList()
+ .equals(other.getHitsListList())) return false;
+ if (!unknownFields.equals(other.unknownFields)) return false;
+ return true;
+ }
+
+ @java.lang.Override
+ public int hashCode() {
+ if (memoizedHashCode != 0) {
+ return memoizedHashCode;
+ }
+ int hash = 41;
+ hash = (19 * hash) + getDescriptor().hashCode();
+ hash = (37 * hash) + READ_ID_FIELD_NUMBER;
+ hash = (53 * hash) + getReadId().hashCode();
+ if (getHitsListCount() > 0) {
+ hash = (37 * hash) + HITS_LIST_FIELD_NUMBER;
+ hash = (53 * hash) + getHitsListList().hashCode();
+ }
+ hash = (29 * hash) + unknownFields.hashCode();
+ memoizedHashCode = hash;
+ return hash;
+ }
+
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ java.nio.ByteBuffer data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ java.nio.ByteBuffer data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ com.google.protobuf.ByteString data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ com.google.protobuf.ByteString data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(byte[] data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ byte[] data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseDelimitedFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseDelimitedFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ com.google.protobuf.CodedInputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.RequestAssembly parseFrom(
+ com.google.protobuf.CodedInputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+
+ @java.lang.Override
+ public Builder newBuilderForType() { return newBuilder(); }
+ public static Builder newBuilder() {
+ return DEFAULT_INSTANCE.toBuilder();
+ }
+ public static Builder newBuilder(org.rtassembly.npgraph.grpc.RequestAssembly prototype) {
+ return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
+ }
+ @java.lang.Override
+ public Builder toBuilder() {
+ return this == DEFAULT_INSTANCE
+ ? new Builder() : new Builder().mergeFrom(this);
+ }
+
+ @java.lang.Override
+ protected Builder newBuilderForType(
+ com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
+ Builder builder = new Builder(parent);
+ return builder;
+ }
+ /**
+ *
+ * Client sent all hits from a chunk simultaneously
+ *
+ *
+ * Protobuf type {@code assembly.RequestAssembly}
+ */
+ public static final class Builder extends
+ com.google.protobuf.GeneratedMessageV3.Builderstring read_id = 1;
+ * @return The readId.
+ */
+ public java.lang.String getReadId() {
+ java.lang.Object ref = readId_;
+ if (!(ref instanceof java.lang.String)) {
+ com.google.protobuf.ByteString bs =
+ (com.google.protobuf.ByteString) ref;
+ java.lang.String s = bs.toStringUtf8();
+ readId_ = s;
+ return s;
+ } else {
+ return (java.lang.String) ref;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ public com.google.protobuf.ByteString
+ getReadIdBytes() {
+ java.lang.Object ref = readId_;
+ if (ref instanceof String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ readId_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @param value The readId to set.
+ * @return This builder for chaining.
+ */
+ public Builder setReadId(
+ java.lang.String value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+
+ readId_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * string read_id = 1;
+ * @return This builder for chaining.
+ */
+ public Builder clearReadId() {
+
+ readId_ = getDefaultInstance().getReadId();
+ onChanged();
+ return this;
+ }
+ /**
+ * string read_id = 1;
+ * @param value The bytes for readId to set.
+ * @return This builder for chaining.
+ */
+ public Builder setReadIdBytes(
+ com.google.protobuf.ByteString value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ checkByteStringIsUtf8(value);
+
+ readId_ = value;
+ onChanged();
+ return this;
+ }
+
+ private java.util.Listrepeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public java.util.Listrepeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public int getHitsListCount() {
+ if (hitsListBuilder_ == null) {
+ return hitsList_.size();
+ } else {
+ return hitsListBuilder_.getCount();
+ }
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsg getHitsList(int index) {
+ if (hitsListBuilder_ == null) {
+ return hitsList_.get(index);
+ } else {
+ return hitsListBuilder_.getMessage(index);
+ }
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder setHitsList(
+ int index, org.rtassembly.npgraph.grpc.AlignmentMsg value) {
+ if (hitsListBuilder_ == null) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ ensureHitsListIsMutable();
+ hitsList_.set(index, value);
+ onChanged();
+ } else {
+ hitsListBuilder_.setMessage(index, value);
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder setHitsList(
+ int index, org.rtassembly.npgraph.grpc.AlignmentMsg.Builder builderForValue) {
+ if (hitsListBuilder_ == null) {
+ ensureHitsListIsMutable();
+ hitsList_.set(index, builderForValue.build());
+ onChanged();
+ } else {
+ hitsListBuilder_.setMessage(index, builderForValue.build());
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder addHitsList(org.rtassembly.npgraph.grpc.AlignmentMsg value) {
+ if (hitsListBuilder_ == null) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ ensureHitsListIsMutable();
+ hitsList_.add(value);
+ onChanged();
+ } else {
+ hitsListBuilder_.addMessage(value);
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder addHitsList(
+ int index, org.rtassembly.npgraph.grpc.AlignmentMsg value) {
+ if (hitsListBuilder_ == null) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ ensureHitsListIsMutable();
+ hitsList_.add(index, value);
+ onChanged();
+ } else {
+ hitsListBuilder_.addMessage(index, value);
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder addHitsList(
+ org.rtassembly.npgraph.grpc.AlignmentMsg.Builder builderForValue) {
+ if (hitsListBuilder_ == null) {
+ ensureHitsListIsMutable();
+ hitsList_.add(builderForValue.build());
+ onChanged();
+ } else {
+ hitsListBuilder_.addMessage(builderForValue.build());
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder addHitsList(
+ int index, org.rtassembly.npgraph.grpc.AlignmentMsg.Builder builderForValue) {
+ if (hitsListBuilder_ == null) {
+ ensureHitsListIsMutable();
+ hitsList_.add(index, builderForValue.build());
+ onChanged();
+ } else {
+ hitsListBuilder_.addMessage(index, builderForValue.build());
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder addAllHitsList(
+ java.lang.Iterable values) {
+ if (hitsListBuilder_ == null) {
+ ensureHitsListIsMutable();
+ com.google.protobuf.AbstractMessageLite.Builder.addAll(
+ values, hitsList_);
+ onChanged();
+ } else {
+ hitsListBuilder_.addAllMessages(values);
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder clearHitsList() {
+ if (hitsListBuilder_ == null) {
+ hitsList_ = java.util.Collections.emptyList();
+ bitField0_ = (bitField0_ & ~0x00000001);
+ onChanged();
+ } else {
+ hitsListBuilder_.clear();
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public Builder removeHitsList(int index) {
+ if (hitsListBuilder_ == null) {
+ ensureHitsListIsMutable();
+ hitsList_.remove(index);
+ onChanged();
+ } else {
+ hitsListBuilder_.remove(index);
+ }
+ return this;
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsg.Builder getHitsListBuilder(
+ int index) {
+ return getHitsListFieldBuilder().getBuilder(index);
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsgOrBuilder getHitsListOrBuilder(
+ int index) {
+ if (hitsListBuilder_ == null) {
+ return hitsList_.get(index); } else {
+ return hitsListBuilder_.getMessageOrBuilder(index);
+ }
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public java.util.List
+ getHitsListOrBuilderList() {
+ if (hitsListBuilder_ != null) {
+ return hitsListBuilder_.getMessageOrBuilderList();
+ } else {
+ return java.util.Collections.unmodifiableList(hitsList_);
+ }
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsg.Builder addHitsListBuilder() {
+ return getHitsListFieldBuilder().addBuilder(
+ org.rtassembly.npgraph.grpc.AlignmentMsg.getDefaultInstance());
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public org.rtassembly.npgraph.grpc.AlignmentMsg.Builder addHitsListBuilder(
+ int index) {
+ return getHitsListFieldBuilder().addBuilder(
+ index, org.rtassembly.npgraph.grpc.AlignmentMsg.getDefaultInstance());
+ }
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ public java.util.Liststring read_id = 1;
+ * @return The readId.
+ */
+ java.lang.String getReadId();
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ com.google.protobuf.ByteString
+ getReadIdBytes();
+
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ java.util.Listrepeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ org.rtassembly.npgraph.grpc.AlignmentMsg getHitsList(int index);
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ int getHitsListCount();
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ java.util.List
+ getHitsListOrBuilderList();
+ /**
+ * repeated .assembly.AlignmentMsg hits_list = 2;
+ */
+ org.rtassembly.npgraph.grpc.AlignmentMsgOrBuilder getHitsListOrBuilder(
+ int index);
+}
diff --git a/src/main/java/org/rtassembly/npgraph/grpc/ResponseAssembly.java b/src/main/java/org/rtassembly/npgraph/grpc/ResponseAssembly.java
new file mode 100644
index 0000000..c1566c7
--- /dev/null
+++ b/src/main/java/org/rtassembly/npgraph/grpc/ResponseAssembly.java
@@ -0,0 +1,626 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: npgraph_service.proto
+
+package org.rtassembly.npgraph.grpc;
+
+/**
+ *
+ * Response from the assembly guide service: useful or not
+ *
+ *
+ * Protobuf type {@code assembly.ResponseAssembly}
+ */
+public final class ResponseAssembly extends
+ com.google.protobuf.GeneratedMessageV3 implements
+ // @@protoc_insertion_point(message_implements:assembly.ResponseAssembly)
+ ResponseAssemblyOrBuilder {
+private static final long serialVersionUID = 0L;
+ // Use ResponseAssembly.newBuilder() to construct.
+ private ResponseAssembly(com.google.protobuf.GeneratedMessageV3.Builder builder) {
+ super(builder);
+ }
+ private ResponseAssembly() {
+ readId_ = "";
+ }
+
+ @java.lang.Override
+ @SuppressWarnings({"unused"})
+ protected java.lang.Object newInstance(
+ UnusedPrivateParameter unused) {
+ return new ResponseAssembly();
+ }
+
+ @java.lang.Override
+ public final com.google.protobuf.UnknownFieldSet
+ getUnknownFields() {
+ return this.unknownFields;
+ }
+ private ResponseAssembly(
+ com.google.protobuf.CodedInputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ this();
+ if (extensionRegistry == null) {
+ throw new java.lang.NullPointerException();
+ }
+ com.google.protobuf.UnknownFieldSet.Builder unknownFields =
+ com.google.protobuf.UnknownFieldSet.newBuilder();
+ try {
+ boolean done = false;
+ while (!done) {
+ int tag = input.readTag();
+ switch (tag) {
+ case 0:
+ done = true;
+ break;
+ case 10: {
+ java.lang.String s = input.readStringRequireUtf8();
+
+ readId_ = s;
+ break;
+ }
+ case 16: {
+
+ usefulness_ = input.readBool();
+ break;
+ }
+ default: {
+ if (!parseUnknownField(
+ input, unknownFields, extensionRegistry, tag)) {
+ done = true;
+ }
+ break;
+ }
+ }
+ }
+ } catch (com.google.protobuf.InvalidProtocolBufferException e) {
+ throw e.setUnfinishedMessage(this);
+ } catch (java.io.IOException e) {
+ throw new com.google.protobuf.InvalidProtocolBufferException(
+ e).setUnfinishedMessage(this);
+ } finally {
+ this.unknownFields = unknownFields.build();
+ makeExtensionsImmutable();
+ }
+ }
+ public static final com.google.protobuf.Descriptors.Descriptor
+ getDescriptor() {
+ return org.rtassembly.npgraph.grpc.AssemblyGuideProto.internal_static_assembly_ResponseAssembly_descriptor;
+ }
+
+ @java.lang.Override
+ protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
+ internalGetFieldAccessorTable() {
+ return org.rtassembly.npgraph.grpc.AssemblyGuideProto.internal_static_assembly_ResponseAssembly_fieldAccessorTable
+ .ensureFieldAccessorsInitialized(
+ org.rtassembly.npgraph.grpc.ResponseAssembly.class, org.rtassembly.npgraph.grpc.ResponseAssembly.Builder.class);
+ }
+
+ public static final int READ_ID_FIELD_NUMBER = 1;
+ private volatile java.lang.Object readId_;
+ /**
+ * string read_id = 1;
+ * @return The readId.
+ */
+ public java.lang.String getReadId() {
+ java.lang.Object ref = readId_;
+ 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();
+ readId_ = s;
+ return s;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ public com.google.protobuf.ByteString
+ getReadIdBytes() {
+ java.lang.Object ref = readId_;
+ if (ref instanceof java.lang.String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ readId_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+
+ public static final int USEFULNESS_FIELD_NUMBER = 2;
+ private boolean usefulness_;
+ /**
+ * bool usefulness = 2;
+ * @return The usefulness.
+ */
+ public boolean getUsefulness() {
+ return usefulness_;
+ }
+
+ private byte memoizedIsInitialized = -1;
+ @java.lang.Override
+ public final boolean isInitialized() {
+ byte isInitialized = memoizedIsInitialized;
+ if (isInitialized == 1) return true;
+ if (isInitialized == 0) return false;
+
+ memoizedIsInitialized = 1;
+ return true;
+ }
+
+ @java.lang.Override
+ public void writeTo(com.google.protobuf.CodedOutputStream output)
+ throws java.io.IOException {
+ if (!getReadIdBytes().isEmpty()) {
+ com.google.protobuf.GeneratedMessageV3.writeString(output, 1, readId_);
+ }
+ if (usefulness_ != false) {
+ output.writeBool(2, usefulness_);
+ }
+ unknownFields.writeTo(output);
+ }
+
+ @java.lang.Override
+ public int getSerializedSize() {
+ int size = memoizedSize;
+ if (size != -1) return size;
+
+ size = 0;
+ if (!getReadIdBytes().isEmpty()) {
+ size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, readId_);
+ }
+ if (usefulness_ != false) {
+ size += com.google.protobuf.CodedOutputStream
+ .computeBoolSize(2, usefulness_);
+ }
+ size += unknownFields.getSerializedSize();
+ memoizedSize = size;
+ return size;
+ }
+
+ @java.lang.Override
+ public boolean equals(final java.lang.Object obj) {
+ if (obj == this) {
+ return true;
+ }
+ if (!(obj instanceof org.rtassembly.npgraph.grpc.ResponseAssembly)) {
+ return super.equals(obj);
+ }
+ org.rtassembly.npgraph.grpc.ResponseAssembly other = (org.rtassembly.npgraph.grpc.ResponseAssembly) obj;
+
+ if (!getReadId()
+ .equals(other.getReadId())) return false;
+ if (getUsefulness()
+ != other.getUsefulness()) return false;
+ if (!unknownFields.equals(other.unknownFields)) return false;
+ return true;
+ }
+
+ @java.lang.Override
+ public int hashCode() {
+ if (memoizedHashCode != 0) {
+ return memoizedHashCode;
+ }
+ int hash = 41;
+ hash = (19 * hash) + getDescriptor().hashCode();
+ hash = (37 * hash) + READ_ID_FIELD_NUMBER;
+ hash = (53 * hash) + getReadId().hashCode();
+ hash = (37 * hash) + USEFULNESS_FIELD_NUMBER;
+ hash = (53 * hash) + com.google.protobuf.Internal.hashBoolean(
+ getUsefulness());
+ hash = (29 * hash) + unknownFields.hashCode();
+ memoizedHashCode = hash;
+ return hash;
+ }
+
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ java.nio.ByteBuffer data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ java.nio.ByteBuffer data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ com.google.protobuf.ByteString data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ com.google.protobuf.ByteString data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(byte[] data)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ byte[] data,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws com.google.protobuf.InvalidProtocolBufferException {
+ return PARSER.parseFrom(data, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseDelimitedFrom(java.io.InputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseDelimitedFrom(
+ java.io.InputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseDelimitedWithIOException(PARSER, input, extensionRegistry);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ com.google.protobuf.CodedInputStream input)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input);
+ }
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly parseFrom(
+ com.google.protobuf.CodedInputStream input,
+ com.google.protobuf.ExtensionRegistryLite extensionRegistry)
+ throws java.io.IOException {
+ return com.google.protobuf.GeneratedMessageV3
+ .parseWithIOException(PARSER, input, extensionRegistry);
+ }
+
+ @java.lang.Override
+ public Builder newBuilderForType() { return newBuilder(); }
+ public static Builder newBuilder() {
+ return DEFAULT_INSTANCE.toBuilder();
+ }
+ public static Builder newBuilder(org.rtassembly.npgraph.grpc.ResponseAssembly prototype) {
+ return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
+ }
+ @java.lang.Override
+ public Builder toBuilder() {
+ return this == DEFAULT_INSTANCE
+ ? new Builder() : new Builder().mergeFrom(this);
+ }
+
+ @java.lang.Override
+ protected Builder newBuilderForType(
+ com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
+ Builder builder = new Builder(parent);
+ return builder;
+ }
+ /**
+ *
+ * Response from the assembly guide service: useful or not
+ *
+ *
+ * Protobuf type {@code assembly.ResponseAssembly}
+ */
+ public static final class Builder extends
+ com.google.protobuf.GeneratedMessageV3.Builderstring read_id = 1;
+ * @return The readId.
+ */
+ public java.lang.String getReadId() {
+ java.lang.Object ref = readId_;
+ if (!(ref instanceof java.lang.String)) {
+ com.google.protobuf.ByteString bs =
+ (com.google.protobuf.ByteString) ref;
+ java.lang.String s = bs.toStringUtf8();
+ readId_ = s;
+ return s;
+ } else {
+ return (java.lang.String) ref;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ public com.google.protobuf.ByteString
+ getReadIdBytes() {
+ java.lang.Object ref = readId_;
+ if (ref instanceof String) {
+ com.google.protobuf.ByteString b =
+ com.google.protobuf.ByteString.copyFromUtf8(
+ (java.lang.String) ref);
+ readId_ = b;
+ return b;
+ } else {
+ return (com.google.protobuf.ByteString) ref;
+ }
+ }
+ /**
+ * string read_id = 1;
+ * @param value The readId to set.
+ * @return This builder for chaining.
+ */
+ public Builder setReadId(
+ java.lang.String value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+
+ readId_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * string read_id = 1;
+ * @return This builder for chaining.
+ */
+ public Builder clearReadId() {
+
+ readId_ = getDefaultInstance().getReadId();
+ onChanged();
+ return this;
+ }
+ /**
+ * string read_id = 1;
+ * @param value The bytes for readId to set.
+ * @return This builder for chaining.
+ */
+ public Builder setReadIdBytes(
+ com.google.protobuf.ByteString value) {
+ if (value == null) {
+ throw new NullPointerException();
+ }
+ checkByteStringIsUtf8(value);
+
+ readId_ = value;
+ onChanged();
+ return this;
+ }
+
+ private boolean usefulness_ ;
+ /**
+ * bool usefulness = 2;
+ * @return The usefulness.
+ */
+ public boolean getUsefulness() {
+ return usefulness_;
+ }
+ /**
+ * bool usefulness = 2;
+ * @param value The usefulness to set.
+ * @return This builder for chaining.
+ */
+ public Builder setUsefulness(boolean value) {
+
+ usefulness_ = value;
+ onChanged();
+ return this;
+ }
+ /**
+ * bool usefulness = 2;
+ * @return This builder for chaining.
+ */
+ public Builder clearUsefulness() {
+
+ usefulness_ = false;
+ onChanged();
+ return this;
+ }
+ @java.lang.Override
+ public final Builder setUnknownFields(
+ final com.google.protobuf.UnknownFieldSet unknownFields) {
+ return super.setUnknownFields(unknownFields);
+ }
+
+ @java.lang.Override
+ public final Builder mergeUnknownFields(
+ final com.google.protobuf.UnknownFieldSet unknownFields) {
+ return super.mergeUnknownFields(unknownFields);
+ }
+
+
+ // @@protoc_insertion_point(builder_scope:assembly.ResponseAssembly)
+ }
+
+ // @@protoc_insertion_point(class_scope:assembly.ResponseAssembly)
+ private static final org.rtassembly.npgraph.grpc.ResponseAssembly DEFAULT_INSTANCE;
+ static {
+ DEFAULT_INSTANCE = new org.rtassembly.npgraph.grpc.ResponseAssembly();
+ }
+
+ public static org.rtassembly.npgraph.grpc.ResponseAssembly getDefaultInstance() {
+ return DEFAULT_INSTANCE;
+ }
+
+ private static final com.google.protobuf.Parserstring read_id = 1;
+ * @return The readId.
+ */
+ java.lang.String getReadId();
+ /**
+ * string read_id = 1;
+ * @return The bytes for readId.
+ */
+ com.google.protobuf.ByteString
+ getReadIdBytes();
+
+ /**
+ * bool usefulness = 2;
+ * @return The usefulness.
+ */
+ boolean getUsefulness();
+}
diff --git a/src/main/java/org/rtassembly/npgraph/grpc/package-info.java b/src/main/java/org/rtassembly/npgraph/grpc/package-info.java
new file mode 100644
index 0000000..a8306a2
--- /dev/null
+++ b/src/main/java/org/rtassembly/npgraph/grpc/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author sonnguyen
+ *
+ */
+package org.rtassembly.npgraph.grpc;
\ No newline at end of file
diff --git a/src/main/java/org/rtassembly/npscarf/RealtimeScaffolding.java b/src/main/java/org/rtassembly/npscarf/RealtimeScaffolding.java
index d1b48e4..9bee231 100644
--- a/src/main/java/org/rtassembly/npscarf/RealtimeScaffolding.java
+++ b/src/main/java/org/rtassembly/npscarf/RealtimeScaffolding.java
@@ -209,7 +209,7 @@ protected void analysis() {
sg.connectBridges();
try {
- // This function is for the sake of real-time annotation experiments being more readable
+ // This function make real-time annotation experiments more readable
scaffolding.graph.printRT(scaffolding.currentBaseCount);
sg.printSequences(ScaffoldGraph.updateGenome,false);
outOS.print("Time |\tStep |\tRead count |\tBase count|\tNumber of scaffolds|\tCircular scaffolds |\tN50 | \tBreaks (maxlen)\n");
diff --git a/src/main/proto/npgraph_service.proto b/src/main/proto/npgraph_service.proto
new file mode 100644
index 0000000..51006c4
--- /dev/null
+++ b/src/main/proto/npgraph_service.proto
@@ -0,0 +1,38 @@
+syntax = "proto3";
+
+option java_multiple_files = true;
+option java_package = "org.rtassembly.npgraph.grpc";
+option java_outer_classname = "AssemblyGuideProto";
+option objc_class_prefix = "AGP";
+
+package assembly;
+
+// Interface exported by the server.
+service AssemblyGuide {
+ rpc GetAssemblyContribution(RequestAssembly) returns (ResponseAssembly) {}
+}
+
+// An alignment from minimap2 sent to the server
+message AlignmentMsg {
+ string query_name = 1;
+ int32 query_length = 2;
+ int32 query_start = 3;
+ int32 query_end = 4;
+ bool strand = 5;
+ string target_name = 6;
+ int32 target_length = 7;
+ int32 target_start = 8;
+ int32 target_end = 9;
+ int32 quality = 10;
+ int32 score = 11;
+}
+// Client sent all hits from a chunk simultaneously
+message RequestAssembly {
+ string read_id = 1;
+ repeated AlignmentMsg hits_list = 2;
+}
+// Response from the assembly guide service: useful or not
+message ResponseAssembly {
+ string read_id = 1;
+ bool usefulness = 2;
+}
\ No newline at end of file