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 2002-2020.
//
// 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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// --------------------------------------------------------------------------
// $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