ProteaseDigestion.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Chris Bielow, Xiao Liang $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

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

#include <string>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
  {
  public:
    using EnzymaticDigestion::setEnzyme;

    void setEnzyme(const String& name);

    Size digest(const AASequence& protein, std::vector<AASequence>& output, Size min_length = 1, Size max_length = 0) const;

    Size peptideCount(const AASequence& protein);

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

    bool isValidProduct(const AASequence& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true, bool allow_nterm_protein_cleavage = false, bool allow_random_asp_pro_cleavage = false) const;

  };

} // namespace OpenMS