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 2002-2020.
//
// 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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//    documentation and/or other materials provided with the distribution.
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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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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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