EnzymaticDigestion.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Chris Bielow, Xiao Liang $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>
#include <OpenMS/CONCEPT/Types.h>
#include <boost/regex_fwd.hpp> // forward declaration of boost::regex
#include <functional>          // for std::function
#include <memory>              // unique_ptr
#include <string>
#include <vector>

namespace OpenMS
{
  class StringView;

  class OPENMS_DLLAPI EnzymaticDigestion
  {
  public:
    enum Specificity
    { // note: the value of the first three items is important, since some engines just report the number of required termini (0, 1, 2)
      SPEC_NONE = 0, 
      SPEC_SEMI = 1, 
      SPEC_FULL = 2, 
      SPEC_UNKNOWN = 3,
      SPEC_NOCTERM = 8, 
      SPEC_NONTERM = 9, 
      SIZE_OF_SPECIFICITY = 10
    };
    static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];

    static const std::string NoCleavage;

    static const std::string UnspecificCleavage;

    EnzymaticDigestion();

    EnzymaticDigestion(const EnzymaticDigestion& rhs);

    EnzymaticDigestion& operator=(const EnzymaticDigestion& rhs);

    virtual ~EnzymaticDigestion();

    Size getMissedCleavages() const;

    void setMissedCleavages(Size missed_cleavages);

    String getEnzymeName() const;

    virtual void setEnzyme(const DigestionEnzyme* enzyme);

    Specificity getSpecificity() const;

    void setSpecificity(Specificity spec);

    static Specificity getSpecificityByName(const String& name);

    Size digestUnmodified(const StringView& sequence, std::vector<StringView>& output, Size min_length = 1, Size max_length = 0) const;

    Size digestUnmodified(const StringView& sequence, std::vector<std::pair<Size, Size>>& output, Size min_length = 1, Size max_length = 0) const;

    bool isValidProduct(const String& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true) const;

    Size countInternalCleavageSites(const String& sequence) const;

    bool filterByMissedCleavages(const String& sequence, const std::function<bool(const Int)>& filter) const;


  protected:
    bool isValidProduct_(const String& sequence,
                         int pos,
                         int length,
                         bool ignore_missed_cleavages,
                         bool allow_nterm_protein_cleavage,
                         bool allow_random_asp_pro_cleavage) const;
    std::vector<int> tokenize_(const String& sequence, int start = 0, int end = -1) const;

    Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<StringView>& output, Size min_length = 0, Size max_length = -1) const;
    Size digestAfterTokenize_(const std::vector<int>& fragment_positions, const StringView& sequence, std::vector<std::pair<Size, Size>>& output, Size min_length = 0, Size max_length = -1) const;

    Size countMissedCleavages_(const std::vector<int>& cleavage_positions, Size seq_start, Size seq_end) const;

    Size missed_cleavages_;

    const DigestionEnzyme* enzyme_;
    std::unique_ptr<boost::regex> re_; // use PImpl, since #include cost is huge

    Specificity specificity_;
  };

} // namespace OpenMS