EnzymaticDigestion.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow, Xiao Liang $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

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

#include <boost/regex.hpp>

#include <string>
#include <vector>
#include <functional>

namespace OpenMS
{
  class OPENMS_DLLAPI EnzymaticDigestion
  {
public:
    enum Specificity
    {
      SPEC_FULL, 
      SPEC_SEMI, 
      SPEC_NONE, 
      SIZE_OF_SPECIFICITY
    };
    static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];

    static const std::string UnspecificCleavage;

    EnzymaticDigestion();

    virtual ~EnzymaticDigestion();

    Size getMissedCleavages() const;

    void setMissedCleavages(Size missed_cleavages);

    String getEnzymeName() const;

    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;

    bool isValidProduct(const String& sequence, int pos, int length, bool ignore_missed_cleavages = true) const;

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

    Size missed_cleavages_;

    const DigestionEnzyme* enzyme_;
    boost::regex re_;

    Specificity specificity_;
  };

} // namespace OpenMS