CResults.h

/*
Copyright 2016, Michael R. Hoopmann, Institute for Systems Biology

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.
*/

#ifndef _CRESULTS_H
#define _CRESULTS_H

#include "CTable.h"
#include "MSReader.h"
#include "PepXMLParser3.h"
#include "Structs.h"

using namespace MSToolkit;
using namespace std;

class CResults {
public:

  CResults();
  ~CResults();

  kvPSM& operator[](const int& index);

  int       findSpectrum(int scanNum);
  Spectrum& getSpectrum (const int& index);
  int       readPepXML  (char* fn, CTable* t);
  size_t    size        ();

private:

  int     activeFile;
  int     indexFile(string& s);

  MSReader      msr;
  Spectrum      spec;

  vector<kvPSM>*  psms;
  vector<string>* dataFiles;
  vector<string>* dataFilesActive;
};

#endif