AbsoluteQuantitationStandards.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    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
//    without specific prior written permission.
// 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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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/KERNEL/FeatureMap.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI AbsoluteQuantitationStandards
  {
 
public:
    AbsoluteQuantitationStandards() = default;
 
    ~AbsoluteQuantitationStandards() = default;
 
    struct runConcentration
    {
      String sample_name;
      String component_name;
      String IS_component_name;
      double actual_concentration;
      double IS_actual_concentration;
      String concentration_units;
      double dilution_factor;
    };
 
    struct featureConcentration
    {
      Feature feature;
      Feature IS_feature;
      double actual_concentration;
      double IS_actual_concentration;
      String concentration_units;
      double dilution_factor;
    };
 
    void mapComponentsToConcentrations(
      const std::vector<AbsoluteQuantitationStandards::runConcentration>& run_concentrations,
      const std::vector<FeatureMap>& feature_maps,
      std::map<String, std::vector<AbsoluteQuantitationStandards::featureConcentration>>& components_to_concentrations
    ) const;
 
    void getComponentFeatureConcentrations(
      const std::vector<AbsoluteQuantitationStandards::runConcentration>& run_concentrations,
      const std::vector<FeatureMap>& feature_maps,
      const String& component_name,
      std::vector<AbsoluteQuantitationStandards::featureConcentration>& feature_concentrations
    ) const;
 
private:
    bool findComponentFeature_(
      const FeatureMap& feature_map,
      const String& component_name,
      Feature& feature_found
    ) const;
  };
}