Contaminants.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Chris Bielow $
// $Authors:  Dominik Schmitz, Chris Bielow$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/QC/QCBase.h>

#include <unordered_set>


namespace OpenMS
{
  class OPENMS_DLLAPI Contaminants: public QCBase
  {
  public:
    struct ContaminantsSummary
    {
      double assigned_contaminants_ratio;
      
      double unassigned_contaminants_ratio;
      
      double all_contaminants_ratio;
      
      double assigned_contaminants_intensity_ratio;
      
      std::pair<Int64, Int64> empty_features;
    };
    
    Contaminants() = default;
    
    virtual ~Contaminants() = default;
    
    void compute(FeatureMap& features, const std::vector<FASTAFile::FASTAEntry>& contaminants);
    
    const String& getName() const override;
    
    const std::vector<Contaminants::ContaminantsSummary>& getResults();
    
    Status requires() const override;
    
  private:
    const String name_ = "Contaminants";
    
    std::vector<Contaminants::ContaminantsSummary> results_;
    
    std::unordered_set<String> digested_db_;
    
    void compare_(const String& key, PeptideHit& pep_hit, Int64& total, Int64& cont, double& sum_total, double& sum_cont, double intensity);
  };
} // namespace OpenMS