MascotInfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------

#pragma once

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

#include <vector>
#include <fstream>

namespace OpenMS
{
  class OPENMS_DLLAPI MascotInfile :
    public ProgressLogger
  {
public:

    MascotInfile();

    virtual ~MascotInfile();

    void store(const String & filename, const PeakSpectrum & spec, double mz, double retention_time, String search_title);

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

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

      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;
      while (getNextSpectrum_(is, spec, charge, pre_mz, pre_int, rt, title))
      {
        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 = "";
        }

        exp.addSpectrum(spectrum);

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

    const String & getBoundary();
    void setBoundary(const String & boundary);

    const String & getDB();
    void setDB(const String & db);

    const String & getSearchType();
    void setSearchType(const String & search_type);

    const String & getHits();
    void setHits(const String & hits);

    const String & getCleavage();
    void setCleavage(const String & cleavage);

    const String & getMassType();
    void setMassType(const String & mass_type);

    const std::vector<String> & getModifications();
    void setModifications(const std::vector<String> & mods);

    const std::vector<String> & getVariableModifications();
    void setVariableModifications(const std::vector<String> & mods);

    const String & getInstrument();
    void setInstrument(const String & instrument);

    UInt getMissedCleavages();
    void setMissedCleavages(UInt missed_cleavages);

    float getPrecursorMassTolerance();
    void setPrecursorMassTolerance(float precursor_mass_tolerance);

    float getPeakMassTolerance();
    void setPeakMassTolerance(float ion_mass_tolerance);

    const String & getTaxonomy();
    void setTaxonomy(const String & taxonomy);

    const String & getFormVersion();
    void setFormVersion(const String & form_version);

    const String & getCharges();
    void setCharges(std::vector<Int> & charges);

protected:
    double mz_;

    String charges_;

    String search_title_;

    String db_;

    String search_type_;

    String hits_;

    String cleavage_;

    String mass_type_;

    std::vector<String> mods_;

    std::vector<String> variable_mods_;

    String instrument_;

    UInt missed_cleavages_;

    float precursor_mass_tolerance_;

    float ion_mass_tolerance_;

    String taxonomy_;

    String form_version_;

    String boundary_;

    double retention_time_;

    void writeParameterHeader_(const String & name, FILE * fp, bool line_break = true);

    void writeHeader_(FILE * fp);

    void writeSpectrum_(FILE * fp,
                        const String & filename,
                        const PeakSpectrum & peaks);

    void writeMSExperiment_(FILE * fp,
                            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);
  };

} // namespace OpenMS