IsobaricIsotopeCorrector.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/Matrix.h>
#include <memory>
 
// 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);
 
    static void
    correctIsotopicImpurities(std::vector<double> & intensities,
                              const IsobaricQuantitationMethod* quant_method);
                               
    // No instance methods as this is a purely static class
 
private:
    static void fillInputVector_(Eigen::VectorXd& b,
                                 Matrix<double>& m_b,
                                 const ConsensusFeature& cf,
                                 const ConsensusMap& cm);
 
    static std::vector<double> getIntensities_(const IsobaricQuantitationMethod* quant_method, 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 solveNNLS_(Matrix<double>::EigenMatrixType& correction_matrix, std::vector<double>& b, std::vector<double>& x);
 
    static void computeStats_(const std::vector<double>& m_x,
                              const Eigen::MatrixXd& x, const float cf_intensity,
                               const IsobaricQuantitationMethod* quant_method, IsobaricQuantifierStatistics& stats);
 
    
    static void computeStats_(const Matrix<double>& m_x,
                              const Eigen::MatrixXd& x, const float cf_intensity,
                              const IsobaricQuantitationMethod* quant_method, IsobaricQuantifierStatistics& stats);
 
    static float updateOutputMap_(const ConsensusMap& consensus_map_in,
                                 ConsensusMap& consensus_map_out,
                                 Size current_cf,
                                 const std::vector<double>& m_x);
 
    static float updateOutputMap_(const ConsensusMap& consensus_map_in,
                                 ConsensusMap& consensus_map_out,
                                 Size current_cf,
                                 const Matrix<double>& m_x);
  };
} // namespace