ConsensusMapMergerAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
 
#include <unordered_set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusMapMergerAlgorithm:
    public DefaultParamHandler,
    public ProgressLogger
  {
  public:
    ConsensusMapMergerAlgorithm ();
 
    void mergeProteinsAcrossFractionsAndReplicates(ConsensusMap& cmap, const ExperimentalDesign& exp_design) const;
 
    void mergeAllIDRuns(ConsensusMap& cmap) const;
 
    void mergeProteinIDRuns(ConsensusMap &cmap,
                            const std::map<unsigned, unsigned>& mapIdx_to_new_protIDRun) const;
 
  private:
 
    bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const String& experiment_type) const;
    bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const ProteinIdentification& ref, const String& experiment_type) const;
    bool checkRunSettings_(const ProteinIdentification& idRun, const ProteinIdentification& ref, const String& experiment_type) const;
 
 
    static size_t accessionHash_(const ProteinHit& p)
    {
      return std::hash<String>()(p.getAccession());
    }
    static bool accessionEqual_(const ProteinHit& p1, const ProteinHit& p2)
    {
      return p1.getAccession() == p2.getAccession();
    }
    using hash_type = std::size_t (*)(const ProteinHit&);
    using equal_type = bool (*)(const ProteinHit&, const ProteinHit&);
 
  };
} // namespace OpenMS