libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / MascotInfile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Nico Pfeifer $
// $Authors: $
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#ifndef OPENMS_FORMAT_MASCOTINFILE_H
#define OPENMS_FORMAT_MASCOTINFILE_H

#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
{
  /**
      @brief Mascot input file adapter.

  @deprecated Use MascotGenericFile.h instead, which uses DefaultParamHandler, is more up to date and avoids weird behaviors of this class (especially in terms of
              MIME boundaries when writing MGF....

      Creates a file that can be used for Mascot search from a peak list or a whole experiment.

  @ingroup FileIO
  */
  class OPENMS_DLLAPI MascotInfile :
    public ProgressLogger
  {
public:

    /// constructor
    MascotInfile();

    /// constructor
    virtual ~MascotInfile();

    /// stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution
    void store(const String & filename, const PeakSpectrum & spec, DoubleReal mz, DoubleReal retention_time, String search_title);

    /// stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution
    void store(const String & filename, const MSExperiment<> & experiment, String search_title);

    /** loads a Mascot Generic File into a PeakMap

            @param filename file name which the map should be read from
            @param exp the map which is filled with the data from the given file
            @throw FileNotFound is thrown if the given file could not be found
    */
    template <typename MapType>
    void load(const String & filename, MapType & exp)
    {
      exp.reset();
      if (!File::exists(filename))
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, __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;
      }
    }

    /// returns the boundary used for the MIME format
    const String & getBoundary();
    /// sets the boundary used for the MIME format.<br>By default a 22 character random string is used
    void setBoundary(const String & boundary);

    /// returns the DB to use
    const String & getDB();
    /// sets the DB to use (default: MSDB). See &lt;mascot path&gt;/config/mascot.dat in "Databases" section for possible settings
    void setDB(const String & db);

    /// returns the search type
    const String & getSearchType();
    /// sets the seach type (default: MIS). So far only MIS is supported!<br>Valid types are "MIS" (MS/MS Ion Search), "PMF" (Peptide Mass Fingerprint) , "SQ" (Sequence Query)
    void setSearchType(const String & search_type);

    /// returns the number of hits to report back
    const String & getHits();
    /// sets the number of hits to report back (default: 20)
    void setHits(const String & hits);

    /// returns the enzyme used for cleavage
    const String & getCleavage();
    /// sets the enzyme used for cleavage (default: Trypsin). <BR>See &lt;mascot path&gt;/config/enzymes for possible settings.
    void setCleavage(const String & cleavage);

    /// returns the used mass type ("Monoisotopic" or "Average")
    const String & getMassType();
    /// sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)
    void setMassType(const String & mass_type);

    /// returns a vector containing the fixed modifications (default: none)
    const std::vector<String> & getModifications();
    /// sets the fixed modifications (default: none). <BR>See &lt;mascot path&gt;/config/mod_file for possible settings.
    void setModifications(const std::vector<String> & mods);

    /// returns a vector containing the variable modifications (default: none)
    const std::vector<String> & getVariableModifications();
    /// sets the fixed modifications (default: none). <BR>See &lt;mascot path&gt;/config/mod_file for possible settings.
    void setVariableModifications(const std::vector<String> & mods);

    /// returns the instrument type
    const String & getInstrument();
    /// sets the instrument type (Default: Default). <BR>Possible instruments: ESI-QUAD-TOF, MALDI-TOF-PSD, ESI-TRAP, ESI-QUAD, ESI-FTICR, MALDI-TOF-TOF, ESI-4SECTOR, FTMS-ECD, MALDI-QUAD-TOF, MALDI-QIT-TOF
    void setInstrument(const String & instrument);

    /// returns the number of allowed missed cleavages
    UInt getMissedCleavages();
    /// sets the number of allowed missed cleavages (default: 1)
    void setMissedCleavages(UInt missed_cleavages);

    /// returns the precursor mass tolerance
    Real getPrecursorMassTolerance();
    /// sets the precursor mass tolerance in Da (default: 2.0)
    void setPrecursorMassTolerance(Real precursor_mass_tolerance);

    /// returns the peak mass tolerance in Da
    Real getPeakMassTolerance();
    /// sets the peak mass tolerance in Da (default: 1.0)
    void setPeakMassTolerance(Real ion_mass_tolerance);

    /// returns the taxonomy
    const String & getTaxonomy();
    /// sets the taxonomy (default: All entries). <BR>See &lt;mascot path&gt;/config/taxonomy for possible settings.
    void setTaxonomy(const String & taxonomy);

    /// returns the Mascot form version
    const String & getFormVersion();
    /// sets the Mascot form version (default: 1.01)
    void setFormVersion(const String & form_version);

    /// returns the charges
    const String & getCharges();
    /// sets the charges (default: 1+, 2+ and 3+)
    void setCharges(std::vector<Int> & charges);

protected:
    /// parent mass
    DoubleReal mz_;

    /// charge states to use
    String charges_;

    /// the search title of the mascot search
    String search_title_;

    /// the DB to search in
    String db_;

    /// search type: MIS, SQ or PMF
    String search_type_;

    /// number of hits to report
    String hits_;

    /// Enzyme used for cleavage
    String cleavage_;

    /// Monoisotopic/average mass
    String mass_type_;

    /// fixed Modifications
    std::vector<String> mods_;

    /// variable Modifications
    std::vector<String> variable_mods_;

    /// the used instument
    String instrument_;

    /// number of missed cleavages
    UInt missed_cleavages_;

    /// precursor mass toerance in Da
    Real precursor_mass_tolerance_;

    /// m/z tolerance of ions  in Da
    Real ion_mass_tolerance_;

    /// taxonomy
    String taxonomy_;

    /// form version
    String form_version_;

    /// the boundary used for the MIME format
    String boundary_;

    /// the retention time
    DoubleReal retention_time_;

    /// writes a parameter header
    void writeParameterHeader_(const String & name, FILE * fp, bool line_break = true);

    /// writes the full header
    void writeHeader_(FILE * fp);

    /// writes the spectrum
    void writeSpectrum_(FILE * fp,
                        const String & filename,
                        const PeakSpectrum & peaks);

    /// writes the MSExperiment
    void writeMSExperiment_(FILE * fp,
                            const String & filename,
                            const MSExperiment<> & 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

#endif // OPENMS_FORMAT_MASCOTINFILE_H