RNaseDigestion.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Samuel Wein $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/NASequence.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
 
#include <boost/regex.hpp>
 
namespace OpenMS
{
  class OPENMS_DLLAPI RNaseDigestion: public EnzymaticDigestion
  {
  public:
    void setEnzyme(const DigestionEnzyme* enzyme) override;
 
    void setEnzyme(const String& name);
 
    void digest(const NASequence& rna, std::vector<NASequence>& output,
                Size min_length = 0, Size max_length = 0) const;
 
    void digest(IdentificationData& id_data, Size min_length = 0,
                Size max_length = 0) const;
 
  protected:
    const Ribonucleotide* five_prime_gain_; 
    const Ribonucleotide* three_prime_gain_; 
    std::vector<boost::regex> cuts_after_regexes_; 
    std::vector<boost::regex> cuts_before_regexes_; 
 
    std::vector<std::pair<Size, Size>> getFragmentPositions_(
      const NASequence& rna, Size min_length, Size max_length)
      const;
  };
 
} // namespace OpenMS