IsobaricIsotopeCorrector.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:
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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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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/Matrix.h>
 
// forward decl
namespace Eigen
{
    template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
    class Matrix;
    using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
    using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
}
 
namespace OpenMS
{
  class IsobaricQuantitationMethod;
  class IsobaricQuantifierStatistics;
  class ConsensusMap;
  class ConsensusFeature;
 
  class OPENMS_DLLAPI IsobaricIsotopeCorrector
  {
public:
    static IsobaricQuantifierStatistics correctIsotopicImpurities(const ConsensusMap& consensus_map_in,
                                                                  ConsensusMap& consensus_map_out,
                                                                  const IsobaricQuantitationMethod* quant_method);
 
private:
    static void fillInputVector_(Eigen::VectorXd& b,
                                 Matrix<double>& m_b,
                                 const ConsensusFeature& cf,
                                 const ConsensusMap& cm);
 
    static void solveNNLS_(const Matrix<double>& correction_matrix,
                           const Matrix<double>& m_b, Matrix<double>& m_x);
 
    static void computeStats_(const Matrix<double>& m_x,
                              const Eigen::MatrixXd& x,
                              const float cf_intensity,
                              const IsobaricQuantitationMethod* quant_method,
                              IsobaricQuantifierStatistics& stats);
 
    static float updateOutpuMap_(const ConsensusMap& consensus_map_in,
                                 ConsensusMap& consensus_map_out,
                                 Size current_cf,
                                 const Matrix<double>& m_x);
  };
} // namespace