XTandemInfile.h

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// $Maintainer: Andreas Bertsch $
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#ifndef OPENMS_FORMAT_XTANDEMINFILE_H
#define OPENMS_FORMAT_XTANDEMINFILE_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/HANDLERS/XTandemInfileXMLHandler.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();

    virtual ~XTandemInfile();

    //<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
    //<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
    //<note type="input" label="spectrum, parent monoisotopic mass error plus">100</note>
    //<note type="input" label="spectrum, parent monoisotopic mass error minus">100</note>
    //<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
    //<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
    //<note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
    //<note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
    //<note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
    //<note type="input" label="spectrum, fragment mass type">monoisotopic</note>
    //<note>values are monoisotopic|average </note>

    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 setMaxValidEValue(double value);

    double getMaxValidEValue() const;

    bool isRefining() const;

    void setSemiCleavage(const bool semi_cleavage);

    void setRefine(const bool refine);

    void write(const String & filename);

    void load(const String & filename);

protected:

    XTandemInfile(const XTandemInfile & rhs);

    XTandemInfile & operator=(const XTandemInfile & rhs);

    void writeTo_(std::ostream & os);

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

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

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

    double fragment_mass_tolerance_;

    double precursor_mass_tolerance_plus_;

    double precursor_mass_tolerance_minus_;

    MassType precursor_mass_type_;

    ErrorUnit precursor_mass_error_unit_;

    ErrorUnit fragment_mass_error_unit_;

    MassType fragment_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_;

    // Sment
    bool refine_;

    //semi cleavage
    bool semi_cleavage_;

    double refine_max_valid_evalue_;

    // scoring
    UInt number_of_missed_cleavages_;

    String default_parameters_file_;

    // output parameters
    double max_valid_evalue_;

    //<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
    std::vector<Internal::XTandemInfileNote> notes_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_XTANDEMINFILE_H