IDMergerAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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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 IDMergerAlgorithm:
    public DefaultParamHandler,
    public ProgressLogger
  {
  public:
    explicit IDMergerAlgorithm (const String& runIdentifier = "merged");

    void insertRun(std::vector<ProteinIdentification>& prots,
        std::vector<PeptideIdentification>& peps);

    void returnResultsAndClear(ProteinIdentification& prots,
                   std::vector<PeptideIdentification>& peps);

  private:
    String getNewIdentifier_() const;
    void copySearchParams_(ProteinIdentification& from, ProteinIdentification& to);

    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;


    void movePepIDsAndRefProteinsToResult_(
        std::vector<PeptideIdentification>& pepIDs,
        std::vector<ProteinIdentification>& oldProtRuns
    );

    ProteinIdentification protResult;
    std::vector<PeptideIdentification> pepResult;
    std::unordered_set<std::string> proteinsCollected;
    bool filled = false;
    std::map<String, Size> fileOriginToIdx;
    String id;
  };
} // namespace OpenMS