IDMergerAlgorithm.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: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
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#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
{

  //TODO add params for checking consistency (i.e. how strict to check)
  //TODO add another subclass that does score-aware merging? (i.e. only keep best per peptide[sequence])

  class OPENMS_DLLAPI IDMergerAlgorithm:
    public DefaultParamHandler,
    public ProgressLogger
  {
  public:
    explicit IDMergerAlgorithm (const String& runIdentifier = "merged");

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

    //TODO add methods to just insert prots or just peps. Especially makes sense if you do re-indexing anyway,
    // then you do not need the proteins. But then we need origin information. Either externally in form of a
    // String or StringList (like the one from ProteinID.getPrimaryMSRunPath). Or by having the file annotated
    // at the PeptideID (with getBasename maybe?)
    // Current solution would be to clear the ProteinIdentification if you do not need the proteins and add all the
    // necessary information about origin(s) to this ProteinIdentification.

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

  private:

    String getNewIdentifier_() const;

    static void copySearchParams_(const 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 insertProteinIDs_(
        std::vector<ProteinIdentification>&& old_protRuns
    );

    void updateAndMovePepIDs_(
        std::vector<PeptideIdentification>&& pepIDs,
        const std::map<String, Size>& runID_to_runIdx,
        const std::vector<StringList>& originFiles,
        bool annotate_origin
    );


    void movePepIDsAndRefProteinsToResultFaster_(
        std::vector<PeptideIdentification>&& pepIDs,
        std::vector<ProteinIdentification>&& old_protRuns
    );

    ProteinIdentification prot_result_;

    std::vector<PeptideIdentification> pep_result_;

    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&);
    std::unordered_set<ProteinHit, hash_type, equal_type> collected_protein_hits_;

    bool filled_ = false;

    std::map<String, Size> file_origin_to_idx_;

    String id_;
  };
} // namespace OpenMS