MissedCleavages.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 $
// $Authors: Swenja Wagner, Patricia Scheil $
// --------------------------------------------------------------------------


#pragma once

#include <OpenMS/QC/QCBase.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>

#include <vector>
#include <map>
namespace OpenMS
{
  class FeatureMap;
  class OPENMS_DLLAPI MissedCleavages : public QCBase
  {
  private:
    typedef std::map<UInt32, UInt32> MapU32;
    void get_missed_cleavages_from_peptide_identification_(const ProteaseDigestion& digestor, MapU32& result, const UInt32& max_mc, PeptideIdentification& pep_id);
  public:
    MissedCleavages() = default;

    virtual ~MissedCleavages() = default;

    void compute(FeatureMap& fmap);
    void compute(std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids);

    const String& getName() const override;
    
    const std::vector<std::map<UInt32, UInt32>>& getResults() const;

    QCBase::Status requires() const override;

  private:
    std::vector<std::map<UInt32, UInt32>> mc_result_;
  };
} // namespace OpenMS