ConsensusIDAlgorithm.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/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <map>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusIDAlgorithm : public DefaultParamHandler
  {
  public:
    void apply(PeptideIdentificationList& ids, const std::map<std::string, std::string>& se_info, Size number_of_runs = 0);
 
    void apply(PeptideIdentificationList& ids, Size number_of_runs = 0);
 
    ~ConsensusIDAlgorithm() override;
 
  protected:
    struct HitInfo {
      Int charge;
      std::vector<double> scores;
      std::vector<std::string> types;
      // in case too much information is stored, TD and evidence
      // could be re-annotated with PeptideIndexer later
      std::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_(PeptideIdentificationList& ids, const std::map<std::string, std::string>& se_info, SequenceGrouping& results) = 0;
 
    void updateMembers_() override;
 
    void compareChargeStates_(Int& recorded_charge, Int new_charge, const AASequence& peptide);
 
  private:
    ConsensusIDAlgorithm(const ConsensusIDAlgorithm&) = delete;
 
    ConsensusIDAlgorithm& operator=(const ConsensusIDAlgorithm&) = delete;
  };
 
} // namespace OpenMS