XTandemInfile.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.
//
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
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// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/FORMAT/XMLFile.h>

namespace OpenMS
{
  class OPENMS_DLLAPI XTandemInfile :
    public Internal::XMLFile
  {
public:

    enum ErrorUnit
    {
      DALTONS = 0,
      PPM
    };

    enum MassType
    {
      MONOISOTOPIC = 0,
      AVERAGE
    };

    XTandemInfile();

    ~XTandemInfile() override;

    void setFragmentMassTolerance(double tolerance);

    double getFragmentMassTolerance() const;

    void setPrecursorMassTolerancePlus(double tol);

    double getPrecursorMassTolerancePlus() const;

    void setPrecursorMassToleranceMinus(double tol);

    double getPrecursorMassToleranceMinus() const;

    void setPrecursorErrorType(MassType mono_isotopic);

    MassType getPrecursorErrorType() const;

    void setFragmentMassErrorUnit(ErrorUnit unit);

    ErrorUnit getFragmentMassErrorUnit() const;

    void setPrecursorMassErrorUnit(ErrorUnit unit);

    ErrorUnit getPrecursorMassErrorUnit() const;

    void setNumberOfThreads(UInt threads);

    UInt getNumberOfThreads() const;

    void setModifications(const ModificationDefinitionsSet& mods);

    const ModificationDefinitionsSet& getModifications() const;

    void setOutputFilename(const String& output);

    const String& getOutputFilename() const;

    void setInputFilename(const String& input_file);

    const String& getInputFilename() const;

    void setTaxonomyFilename(const String& filename);

    const String& getTaxonomyFilename() const;

    void setDefaultParametersFilename(const String& filename);

    const String& getDefaultParametersFilename() const;

    void setTaxon(const String& taxon);

    const String& getTaxon() const;

    void setMaxPrecursorCharge(Int max_charge);

    Int getMaxPrecursorCharge() const;

    void setNumberOfMissedCleavages(UInt missed_cleavages);

    UInt getNumberOfMissedCleavages() const;

    void setOutputResults(String result);

    String getOutputResults() const;

    void setMaxValidEValue(double value);

    double getMaxValidEValue() const;

    void setSemiCleavage(const bool semi_cleavage);

    void setAllowIsotopeError(const bool allow_isotope_error);

    bool getNoiseSuppression() const;

    void setNoiseSuppression(const bool noise_suppression);

    void setCleavageSite(const String& cleavage_site);
    
    const String& getCleavageSite() const;

    void write(const String& filename, bool ignore_member_parameters = false,
               bool force_default_mods = false);

protected:

    XTandemInfile(const XTandemInfile& rhs);

    XTandemInfile& operator=(const XTandemInfile& rhs);

    void writeTo_(std::ostream& os, bool ignore_member_parameters);

    void writeNote_(std::ostream& os, const String& label, const String& value);

    void writeNote_(std::ostream& os, const String& label, const char* value);

    void writeNote_(std::ostream& os, const String& label, bool value);

    String convertModificationSet_(const std::set<ModificationDefinition>& mods, std::map<String, double>& affected_origins) const;

    double fragment_mass_tolerance_;

    double precursor_mass_tolerance_plus_;

    double precursor_mass_tolerance_minus_;

    ErrorUnit fragment_mass_error_unit_;

    ErrorUnit precursor_mass_error_unit_;

    MassType fragment_mass_type_;

    MassType precursor_mass_type_;

    UInt max_precursor_charge_;

    double precursor_lower_mz_;

    double fragment_lower_mz_;

    UInt number_of_threads_;

    UInt batch_size_;

    ModificationDefinitionsSet modifications_;

    String input_filename_;

    String output_filename_;

    String taxonomy_file_;

    String taxon_;

    String cleavage_site_;

    bool semi_cleavage_;

    bool allow_isotope_error_;

    // scoring
    UInt number_of_missed_cleavages_;

    String default_parameters_file_;

    // output parameters
    String output_results_;

    double max_valid_evalue_;

    // force writing of mods covered by special parameters?
    bool force_default_mods_;

  };

} // namespace OpenMS