RealTime.proto

// 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.

syntax = "proto3";

option java_multiple_files = true;
option java_package = "edu.umich.andykong.msfragger.realtimesearch";
option csharp_namespace = "edu.umich.andykong.msfragger.realtimesearch";

package edu.umich.andykong.msfragger.realtimesearch;

service RealTimeServer {
	rpc RealTimeSearcherAsync (stream ScanRequest) returns (stream ResultReply) {}
	rpc RealTimeSearcherSync (ScanRequest) returns (ResultReply) {}
}

message ResultReply {
  int32 status = 1; // 0 = finished without any error, 1 = finished with error, 2 = finished without any error but no good result.
  int32 scanNum = 2;
  repeated Hit hits = 3;
}

message Hit {
  int32 rank = 1;
  float hyperscore = 2;
  float expect = 3;
  string peptideSequence = 4;
  float massDiff = 5;
  repeated float modMasses = 6 [packed=true];
  float nTermMass = 7;
  float cTermMass = 8;
  int32 charge = 18;
  float theoreticalMZ = 19;
  bool isDecoy = 9;
  string proteins = 10;

  optional float nextscore = 11;
  optional int32 numMatchedIons = 12;
  optional int32 numTotalIons = 13;
  repeated Fragment matchedFragments = 14;

  optional string glycanComposition = 15;
  optional float glycanMass = 16;
  optional float glycanScore = 17;
}

message Fragment {
  float mz = 1; // observed m/z
  float intensity = 2;
  int32 ionType = 3; // 0 = unspecified, 1 = N-term, 2 = C-term, 3 = N-term-H2O, 4 = C-term-H2O, 5 = Y, 6 = diagnostic ions
  int32 position = 4;	// e.g. 1 for N-term 1, 0 for Y or diagnostic ions
  int32 charge = 5;
  bool modified = 6; // including fixed modification
  float modMass = 7; // theoretical mass of the modification including fixed modification
}

message ScanRequest {
	int32 type = 17; // 0 = send a spectrum to search; 1 = request a searching result.
	int32 scanNum = 6;
	float precursorMz = 7;
	int32 charge = 8;
	repeated float mz = 9 [packed=true];
	repeated float intensity = 10 [packed=true];
	float isolationWindowLowerMz = 11;
	float isolationWindowUpperMz = 12;
}