MascotGenericFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_MASCOTGENERICFILE_H
#define OPENMS_FORMAT_MASCOTGENERICFILE_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <vector>
#include <fstream>

namespace OpenMS
{
  class OPENMS_DLLAPI MascotGenericFile :
    public ProgressLogger,
    public DefaultParamHandler
  {
public:

    MascotGenericFile();

    virtual ~MascotGenericFile();

    void store(const String & filename, const PeakMap & experiment);

    void store(std::ostream & os, const String & filename, const PeakMap & experiment);

    template <typename MapType>
    void load(const String & filename, MapType & exp)
    {
      if (!File::exists(filename))
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
      }

      exp.reset();

      std::ifstream is(filename.c_str());
      std::vector<std::pair<double, double> > spec;
      UInt charge(0);
      double pre_mz(0), pre_int(0), rt(-1);
      String title;
      UInt spectrum_number = 0;
      Size line_number = 0;
      while (getNextSpectrum_(is, spec, charge, pre_mz, pre_int, rt, title, line_number))
      {
        typename MapType::SpectrumType spectrum;
        for (std::vector<std::pair<double, double> >::const_iterator it = spec.begin(); it != spec.end(); ++it)
        {
          typename MapType::PeakType p;
          p.setPosition(it->first);
          p.setIntensity(it->second);
          spectrum.push_back(p);
        }
        spectrum.setMSLevel(2);
        spectrum.getPrecursors().resize(1);
        spectrum.getPrecursors()[0].setMZ(pre_mz);
        spectrum.getPrecursors()[0].setIntensity(pre_int);
        spectrum.getPrecursors()[0].setCharge(charge);
        spectrum.setRT(rt);
        if (title != "")
        {
          spectrum.setMetaValue("TITLE", title);
          title = "";
        }

        spectrum.setNativeID(String("index=") + (spectrum_number++));
        exp.push_back(spectrum);

        // clean up
        spec.clear();
        charge = 0;
        pre_mz = 0;
        pre_int = 0;
      }
    }

    std::pair<String, String> getHTTPPeakListEnclosure(const String & filename) const;

protected:

    void writeParameterHeader_(const String & name, std::ostream & os);

    void writeHeader_(std::ostream & os);

    void writeSpectrum_(std::ostream & os, const PeakSpectrum & spec, const String & filename);

    void writeMSExperiment_(std::ostream & os, const String & filename, const PeakMap & experiment);

    bool getNextSpectrum_(std::istream & is, std::vector<std::pair<double, double> > & spectrum, UInt & charge, double & precursor_mz, double & precursor_int, double & rt, String & title, Size & line_number);
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_MASCOTGENERICFILE_H