ConsensusIDAlgorithm.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: Hendrik Weisser $
// $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

#include <map>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusIDAlgorithm :
    public DefaultParamHandler
  {
  public:
    void apply(std::vector<PeptideIdentification>& ids, 
               Size number_of_runs = 0);

    ~ConsensusIDAlgorithm() override;

  protected:
    typedef std::map<AASequence, std::pair<Int, std::vector<double> > > 
      SequenceGrouping;

    Size considered_hits_;

    Size number_of_runs_;

    double min_support_;

    bool count_empty_;
   
    ConsensusIDAlgorithm();

    virtual void apply_(std::vector<PeptideIdentification>& ids,
                        SequenceGrouping& results) = 0;

    void updateMembers_() override;

    void compareChargeStates_(Int& recorded_charge, Int new_charge, 
                              const AASequence& peptide);

  private:
    ConsensusIDAlgorithm(const ConsensusIDAlgorithm&);

    ConsensusIDAlgorithm& operator=(const ConsensusIDAlgorithm&);

  };

} // namespace OpenMS