ConsensusIDAlgorithm.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: 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,
               const std::map<String, String>& se_info,
               Size number_of_runs = 0);

    void apply(std::vector<PeptideIdentification>& ids,
               Size number_of_runs = 0);

    ~ConsensusIDAlgorithm() override;

  protected:
    struct HitInfo
    {
      Int charge;
      std::vector<double> scores;
      std::vector<String> types;
      // in case too much information is stored, TD and evidence
      // could be re-annotated with PeptideIndexer later
      String target_decoy;
      std::set<PeptideEvidence> evidence;
      double final_score;
      double support;
      //TODO: we could gather spectrum_refs here as well,
      // to support passing of spectrum_ref if ALL refs of a group are the same
      // For now, we do it in the ConsensusID TOPP tool class in cases where we
      // know that refs will be the same.
    };

    typedef std::map<AASequence, HitInfo>
      SequenceGrouping;

    Size considered_hits_;

    Size number_of_runs_;

    double min_support_;

    bool count_empty_;

    bool keep_old_scores_;
   
    ConsensusIDAlgorithm();

    virtual void apply_(std::vector<PeptideIdentification>& ids,
                        const std::map<String, String>& se_info,
                        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