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 2002-2020.
//
// 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.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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() = default;
 
    ~MRMFeatureQC() = default;
 
    // Members
    //
    struct ComponentQCs
    {
      bool operator==(const ComponentQCs& other) const {
        bool members_eq = 
          std::tie(
            component_name,
            retention_time_l,
            retention_time_u,
            intensity_l,
            intensity_u,
            overall_quality_l,
            overall_quality_u
          ) == std::tie(
            other.component_name,
            other.retention_time_l,
            other.retention_time_u,
            other.intensity_l,
            other.intensity_u,
            other.overall_quality_l,
            other.overall_quality_u
          );
        auto compare_maps = [](std::pair<String, std::pair<double, double>> lhs, std::pair<String, std::pair<double, double>> rhs) {return (lhs.first == rhs.first && lhs.second.first == rhs.second.first && lhs.second.second == rhs.second.second); };
        bool meta_values_eq = std::equal(meta_value_qc.begin(), meta_value_qc.end(), other.meta_value_qc.begin(), compare_maps);
        return members_eq && meta_values_eq;
      }
      bool operator!=(const ComponentQCs& other) const
      {
        return !(*this == other);
      }
 
      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
    {
      bool operator==(const ComponentGroupQCs& other) const {
        bool members_eq =
          std::tie(
            component_group_name,
            retention_time_l,
            retention_time_u,
            intensity_l,
            intensity_u,
            overall_quality_l,
            overall_quality_u,
            n_heavy_l,
            n_heavy_u,
            n_light_l,
            n_light_u,
            n_detecting_l,
            n_detecting_u,
            n_quantifying_l,
            n_quantifying_u,
            n_identifying_l,
            n_identifying_u,
            n_transitions_l,
            n_transitions_u,
            ion_ratio_pair_name_1,
            ion_ratio_pair_name_2,
            ion_ratio_l,
            ion_ratio_u,
            ion_ratio_feature_name
          ) == std::tie(
            other.component_group_name,
            other.retention_time_l,
            other.retention_time_u,
            other.intensity_l,
            other.intensity_u,
            other.overall_quality_l,
            other.overall_quality_u,
            other.n_heavy_l,
            other.n_heavy_u,
            other.n_light_l,
            other.n_light_u,
            other.n_detecting_l,
            other.n_detecting_u,
            other.n_quantifying_l,
            other.n_quantifying_u,
            other.n_identifying_l,
            other.n_identifying_u,
            other.n_transitions_l,
            other.n_transitions_u,
            other.ion_ratio_pair_name_1,
            other.ion_ratio_pair_name_2,
            other.ion_ratio_l,
            other.ion_ratio_u,
            other.ion_ratio_feature_name
          );
        auto compare_maps = [](std::pair<String, std::pair<double, double>> lhs, std::pair<String, std::pair<double, double>> rhs) {return (lhs.first == rhs.first && lhs.second.first == rhs.second.first && lhs.second.second == rhs.second.second); };
        bool meta_values_eq = std::equal(meta_value_qc.begin(), meta_value_qc.end(), other.meta_value_qc.begin(), compare_maps);
        return members_eq && meta_values_eq;
      }
      bool operator!=(const ComponentGroupQCs& other) const
      {
        return !(*this == other);
      }
      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;
  };
}