EnzymaticDigestionLogModel.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Chris Bielow, Xiao Liang $
// $Authors: Marc Sturm, Chris Bielow, Xiao Liang $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>
 
#include <string>
#include <vector>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI EnzymaticDigestionLogModel
  {
public:
    EnzymaticDigestionLogModel();
 
    EnzymaticDigestionLogModel(const EnzymaticDigestionLogModel& rhs);
 
    EnzymaticDigestionLogModel& operator=(const EnzymaticDigestionLogModel& rhs);
 
    String getEnzymeName() const;
 
    void setEnzyme(const String& name);
 
    void digest(const AASequence& protein, std::vector<AASequence>& output) const;
 
    Size peptideCount(const AASequence& protein);
 
    double getLogThreshold() const;
 
    void setLogThreshold(double threshold);
 
protected:
    // 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_
    {
      double p_cleave;
      double p_miss;
 
      CleavageModel_() :
        p_cleave(0), p_miss(0) {}
      CleavageModel_(const double& p_c, const double& p_m) :
        p_cleave(p_c), p_miss(p_m) {}
    };
 
    void nextCleavageSite_(const AASequence& sequence, AASequence::ConstIterator& p) const;
 
    bool isCleavageSite_(const AASequence& sequence, const AASequence::ConstIterator& p) const;
 
    const DigestionEnzyme* enzyme_;
 
    double log_model_threshold_;
    std::map<BindingSite_, CleavageModel_> model_data_;
  };
 
} // namespace OpenMS