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

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Stephan Aiche $
// $Authors: 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
{
  /**
    @brief XTandem input file.

    This class is able to create a X!Tandem configuration files to be used with Xtandem.

    @ingroup FileIO
  */
  class OPENMS_DLLAPI XTandemInfile :
    public Internal::XMLFile
  {
public:

    /// error unit, either Da or ppm
    enum ErrorUnit
    {
      DALTONS = 0,
      PPM
    };

    /// Mass type of the precursor, either monoisotopic or average
    enum MassType
    {
      MONOISOTOPIC = 0,
      AVERAGE
    };

    /// constructor
    XTandemInfile();

    /// constructor
    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>

    /// setter for the fragment mass tolerance
    void setFragmentMassTolerance(double tolerance);

    /// returns the fragment mass tolerance
    double getFragmentMassTolerance() const;

    /// sets the precursor mass tolerance (plus only)
    void setPrecursorMassTolerancePlus(double tol);

    /// returns the precursor mass tolerance (plus only)
    double getPrecursorMassTolerancePlus() const;

    /// set the precursor mass tolerance (minus only)
    void setPrecursorMassToleranceMinus(double tol);

    /// returns the precursor mass tolerance (minus only)
    double getPrecursorMassToleranceMinus() const;

    /// sets the precursor mass type
    void setPrecursorErrorType(MassType mono_isotopic);

    /// returns the precursor mass type
    MassType getPrecursorErrorType() const;

    /// sets the fragment mass error unit (Da, ppm)
    void setFragmentMassErrorUnit(ErrorUnit unit);

    /// returns the fragment mass error unit (Da, ppm)
    ErrorUnit getFragmentMassErrorUnit() const;

    /// sets the precursor mass error unit (Da, ppm)
    void setPrecursorMassErrorUnit(ErrorUnit unit);

    /// returns the precursor mass error unit (Da, ppm)
    ErrorUnit getPrecursorMassErrorUnit() const;

    /// sets the number of threads used during the identifications
    void setNumberOfThreads(UInt threads);

    /// returns the number of threads
    UInt getNumberOfThreads() const;

    /// sets the modifications using a modification definitions set
    void setModifications(const ModificationDefinitionsSet& mods);

    /// returns the modifications set, using a modification definitions set
    const ModificationDefinitionsSet& getModifications() const;

    /// sets the output filename
    void setOutputFilename(const String& output);

    /// returns the output filename
    const String& getOutputFilename() const;

    /// sets the input filename
    void setInputFilename(const String& input_file);

    /// returns the input filename
    const String& getInputFilename() const;

    /// set the filename of the taxonomy file
    void setTaxonomyFilename(const String& filename);

    /// returns the filename of the taxonomy file
    const String& getTaxonomyFilename() const;

    /// sets the default paramters file
    void setDefaultParametersFilename(const String& filename);

    /// returns the default parameters file
    const String& getDefaultParametersFilename() const;

    /// sets the taxon used in the taxonomy file
    void setTaxon(const String& taxon);

    /// returns the taxon used in the taxonomy file
    const String& getTaxon() const;

    /// sets the max precursor charge
    void setMaxPrecursorCharge(Int max_charge);

    /// returns the max precursor charge
    Int getMaxPrecursorCharge() const;

    /// sets the number of missed cleavages allowed
    void setNumberOfMissedCleavages(UInt missed_cleavages);

    /// returns the number of missed cleavages allowed
    UInt getNumberOfMissedCleavages() const;

    /// sets the max valid E-value allowed in the list
    void setMaxValidEValue(double value);

    /// returns the max valid E-value allowed in the list
    double getMaxValidEValue() const;

    /// get state of refine setting
    bool isRefining() const;

    /// set state of semi cleavage
    void setSemiCleavage(const bool semi_cleavage);

    /// set state of refine setting
    void setRefine(const bool refine);

    /** 
      @brief Writes the XTandemInfile to the given file

      @param filename the name of the file which is written
      @throw UnableToCreateFile is thrown if the given file could not be created
    */
    void write(const String& filename);

    /** 
      @brief Reads the information from the given filename

      @param filename the file which should be read from
      @throw FileNotFound is thrown if the given file could not be found
      @throw ParseError is thrown if the given file could not be parsed
    */
    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);

    /**
      @brief Converts the given set of Modifications into a format compatible to X!Tandem.

      @param mods The modifications to convert.
      @return A X!Tandem compatible string representation.
    */
    String convertModificationSet_(const std::set<ModificationDefinition>& mods) const;

    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_;

    /// Enable/disable xtandem refinement
    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_;

    /** 
      Holds additional nodes that were not translated to member variables, but are conserved for storing.
      &ltnote type="input" label="spectrum, fragment monoisotopic mass error"&gt;0.4&lt;/note&gt;
    */
    std::vector<Internal::XTandemInfileNote> notes_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_XTANDEMINFILE_H