ConsensusIDAlgorithmSimilarity.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithm.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusIDAlgorithmSimilarity :
    public ConsensusIDAlgorithm
  {
  protected:
    ConsensusIDAlgorithmSimilarity();
 
    typedef std::map<std::pair<AASequence, AASequence>, double> SimilarityCache;
 
    SimilarityCache similarities_;
 
    virtual double getSimilarity_(AASequence seq1, AASequence seq2) = 0;
 
  private:
    ConsensusIDAlgorithmSimilarity(const ConsensusIDAlgorithmSimilarity&);
 
    ConsensusIDAlgorithmSimilarity& operator=(const ConsensusIDAlgorithmSimilarity&);
 
    void apply_(PeptideIdentificationList& ids,
        const std::map<String, String>& se_info,
        SequenceGrouping& results) override;
  };
 
} // namespace OpenMS