MRMFeatureQC.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
//    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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// $Maintainer: Douglas McCloskey $
// $Authors: Douglas McCloskey $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/QcMLFile.h>

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/LogStream.h>

namespace OpenMS
{

  class OPENMS_DLLAPI MRMFeatureQC
  {

public:

    MRMFeatureQC();

    ~MRMFeatureQC();

    // Members
    //
    struct ComponentQCs
    {
      String component_name;

      // Feature members
      double retention_time_l { 0.0 };
      double retention_time_u { 1e12 };
      double intensity_l { 0.0 };
      double intensity_u { 1e12 };
      double overall_quality_l { 0.0 };
      double overall_quality_u { 1e12 };

      std::map<String,std::pair<double,double>> meta_value_qc;

    };

    struct ComponentGroupQCs
    {
      String component_group_name;

      double retention_time_l { 0.0 };
      double retention_time_u { 1e12 };
      double intensity_l { 0.0 };
      double intensity_u { 1e12 };
      double overall_quality_l { 0.0 };
      double overall_quality_u { 1e12 };

      // number of transitions and labels
      Int n_heavy_l { 0 };
      Int n_heavy_u { 100 };
      Int n_light_l { 0 };
      Int n_light_u { 100 };
      Int n_detecting_l { 0 };
      Int n_detecting_u { 100 };
      Int n_quantifying_l { 0 };
      Int n_quantifying_u { 100 };
      Int n_identifying_l { 0 };
      Int n_identifying_u { 100 };
      Int n_transitions_l { 0 };
      Int n_transitions_u { 100 };

      // Ion Ratio QCs
      String ion_ratio_pair_name_1;
      String ion_ratio_pair_name_2;
      double ion_ratio_l { 0.0 };
      double ion_ratio_u { 1e12 };
      String ion_ratio_feature_name;
      std::map<String,std::pair<double,double>> meta_value_qc;

    };

    struct ComponentGroupPairQCs
    {

      String component_group_name;
      String resolution_pair_name;
      double resolution_l;
      double resolution_u;
      double rt_diff_l;
      double rt_diff_u;
    };

    //members
    std::vector<ComponentQCs> component_qcs;
    std::vector<ComponentGroupQCs> component_group_qcs;
    std::vector<ComponentGroupPairQCs> component_group_pair_qcs;
  };
}