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 $
// --------------------------------------------------------------------------

#ifndef OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
#define OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H

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

#include <string>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI EnzymaticDigestion
  {
public:
    enum Specificity
    {
      SPEC_FULL, //< fully enzyme specific, e.g., tryptic (ends with KR, AA-before is KR), or peptide is at protein terminal ends
      SPEC_SEMI, //< semi specific, i.e., one of the two cleavage sites must fulfill requirements
      SPEC_NONE, //< no requirements on start / end
      SIZE_OF_SPECIFICITY
    };
    static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
    
    static const std::string UnspecificCleavage;

    EnzymaticDigestion();

    EnzymaticDigestion(const EnzymaticDigestion& rhs);

    EnzymaticDigestion& operator=(const EnzymaticDigestion& rhs);

    Size getMissedCleavages() const;

    void setMissedCleavages(Size missed_cleavages);

    String getEnzymeName() const;

    void setEnzyme(const String name);

    Specificity getSpecificity() const;

    void setSpecificity(Specificity spec);

    static Specificity getSpecificityByName(const String& name);

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

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

    Size peptideCount(const AASequence& protein);

    bool isValidProduct(const AASequence& protein, Size pep_pos, Size pep_length, bool methionine_cleavage = false, bool ignore_missed_cleavages = true) const;

    bool isValidProduct(const String& protein, Size pep_pos, Size pep_length, bool methionine_cleavage = false, bool ignore_missed_cleavages = true) const;

protected:
    std::vector<Size> tokenize_(const String& protein) const;

    inline Size countMissedCleavages_(const std::vector<Size>& cleavage_positions, Size pep_start, Size pep_end) const;

    Size missed_cleavages_;

    Enzyme enzyme_;

    Specificity specificity_;
  };

} // namespace OpenMS

#endif // OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H