IsotopeLabelingMDVs.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
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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: Ahmed Khalil $
// $Authors: Ahmed Khalil $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
 
//Kernal classes
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/Utils/MatrixUtils.h>
#include <OpenMS/DATASTRUCTURES/Matrix.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/Feature.h>
 
//Standard library
#include <cstddef> // for size_t & ptrdiff_t
#include <vector>
#include <string>
#include <cmath>
#include <numeric>
//#include <unordered_map>
#include <algorithm>
#include <Eigen/Dense>
 
namespace OpenMS
{
  class OPENMS_DLLAPI IsotopeLabelingMDVs :
    public DefaultParamHandler
  {
  public:
    IsotopeLabelingMDVs();
 
    ~IsotopeLabelingMDVs();
    
    enum class DerivatizationAgent
    {
      NOT_SELECTED,
      TBDMS,
      SIZE_OF_DERIVATIZATIONAGENT
    };
    
    enum class MassIntensityType
    {
      NORM_MAX,
      NORM_SUM,
      SIZE_OF_MASSINTENSITYTYPE
    };
    
    static const std::string NamesOfDerivatizationAgent[static_cast<int>(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)];
    
    static const std::string NamesOfMassIntensityType[static_cast<int>(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)];
 
    void isotopicCorrection(
      const Feature& normalized_feature, Feature& corrected_feature,
      const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
    
    void isotopicCorrections(
      const FeatureMap& normalized_featureMap, FeatureMap& corrected_featureMap,
      const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
 
    void calculateIsotopicPurity(
      Feature& normalized_feature,
      const std::vector<double>& experiment_data, const std::string& isotopic_purity_name);
    
    void calculateIsotopicPurities(
      FeatureMap& normalized_featureMap,
      const std::vector<std::vector<double>>& experiment_data, const std::vector<std::string>& isotopic_purity_name);
 
    void calculateMDVAccuracy(
      Feature& normalized_feature,
      const std::string& feature_name, const std::string& fragment_isotopomer_theoretical_formula);
    
    void calculateMDVAccuracies(
      FeatureMap& normalized_featureMap,
      const std::string& feature_name,
      const std::map<std::string, std::string>& fragment_isotopomer_theoretical_formulas);
 
    void calculateMDV(
      const Feature& measured_feature, Feature& normalized_feature,
      const MassIntensityType& mass_intensity_type, const std::string& feature_name);
    
    void calculateMDVs(
      const FeatureMap& measured_featureMap, FeatureMap& normalized_featureMap,
      const MassIntensityType& mass_intensity_type, const std::string& feature_name);
    
  protected:
    void updateMembers_() override;
  };
}