IsobaricIsotopeCorrector.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/Matrix.h>
#include <Eigen/Core>

namespace OpenMS
{
  class IsobaricQuantitationMethod;
  struct 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