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 2002-2018.
//
// 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
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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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// $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;
  };
}