ConsensusIDAlgorithmPEPMatrix.h

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// $Maintainer: Hendrik Weisser $
// $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
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#pragma once

#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmSimilarity.h>
#include <OpenMS/ANALYSIS/SEQUENCE/NeedlemanWunsch.h>

namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusIDAlgorithmPEPMatrix :
    public ConsensusIDAlgorithmSimilarity
  {
  public:
    ConsensusIDAlgorithmPEPMatrix();


  private:

    NeedlemanWunsch alignment_;

    ConsensusIDAlgorithmPEPMatrix(const ConsensusIDAlgorithmPEPMatrix&);

    ConsensusIDAlgorithmPEPMatrix& operator=(const ConsensusIDAlgorithmPEPMatrix&);

    double getSimilarity_(AASequence seq1, AASequence seq2) override;

    // Docu in base class
    void updateMembers_() override;
  };

} // namespace OpenMS