BasicProteinInferenceAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>

namespace OpenMS
{
  class OPENMS_DLLAPI BasicProteinInferenceAlgorithm :
    public DefaultParamHandler,
    public ProgressLogger
  {
    public:

    enum AggregationMethod
    {
      PROD, SUM, MAXIMUM
    };

    BasicProteinInferenceAlgorithm();

    void run(std::vector<PeptideIdentification> &pep_ids, std::vector<ProteinIdentification> &prot_ids) const;
    void run(std::vector<PeptideIdentification> &pep_ids, ProteinIdentification &prot_id) const;

  private:
    void processRun_(
      std::unordered_map<std::string, std::pair<ProteinHit*, Size>>& acc_to_protein_hitP_and_count,
      std::unordered_map<std::string, std::map<Int, PeptideHit*>>& best_pep,
      ProteinIdentification& prot_run,
      std::vector<PeptideIdentification>& pep_ids,
      AggregationMethod aggregation_method,
      String& aggMethodString,
      bool use_shared_peptides,
      bool treat_charge_variants_separately,
      bool treat_modification_variants_separately,
      bool skip_count_annotation) const;
  };
} //namespace OpenMS