EnzymaticDigestion.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow $
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#ifndef OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
#define OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/AASequence.h>

#include <string>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI EnzymaticDigestion
  {
public:
    enum Enzyme
    {
      TRYPSIN,
      SIZE_OF_ENZYMES
    };

    static const std::string NamesOfEnzymes[SIZE_OF_ENZYMES];

    EnzymaticDigestion();

    SignedSize getMissedCleavages() const;

    void setMissedCleavages(SignedSize missed_cleavages);

    Enzyme getEnzyme() const;

    void setEnzyme(Enzyme enzyme);

    Enzyme getEnzymeByName(const String & name);

    void digest(const AASequence & protein, std::vector<AASequence> & output);

    Size peptideCount(const AASequence & protein);

    bool isLogModelEnabled() const;

    void setLogModelEnabled(bool enabled);

    DoubleReal getLogThreshold() const;

    void setLogThreshold(DoubleReal threshold);

protected:
    SignedSize missed_cleavages_;
    Enzyme enzyme_;
    bool use_log_model_;
    DoubleReal log_model_threshold_;

    // define a binding site by position and AA
    struct BindingSite
    {
      Size position;
      String AAname;

      BindingSite() :
        position(), AAname() {}

      BindingSite(const Size & p, const String & name) :
        position(p), AAname(name) {}

      bool operator<(const BindingSite & rhs) const
      {
        return (position < rhs.position) || ((position == rhs.position) && (AAname < rhs.AAname));
      }

      bool operator==(const BindingSite & rhs) const
      {
        return position == rhs.position && AAname == rhs.AAname;
      }

    };

    // define the log likelihood for missed and cleavage model
    struct CleavageModel
    {
      DoubleReal p_cleave;
      DoubleReal p_miss;

      CleavageModel() :
        p_cleave(0), p_miss(0) {}
      CleavageModel(const DoubleReal & p_c, const DoubleReal & p_m) :
        p_cleave(p_c), p_miss(p_m) {}
    };

    Map<BindingSite, CleavageModel> model_data_;

    void nextCleavageSite_(const AASequence & sequence, AASequence::ConstIterator & iterator);
  };

} // namespace OpenMS

#endif // OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H