ITRAQLabeler.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 2002-2023.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once
 
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
#include <OpenMS/SIMULATION/SimTypes.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>;
}
typedef boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr;
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI ITRAQLabeler :
    public BaseLabeler
  {
public:
 
    typedef ItraqConstants::ChannelInfo ChannelInfo;
    typedef ItraqConstants::ChannelMapType ChannelMapType;
    typedef ItraqConstants::IsotopeMatrices IsotopeMatrices;
 
    ITRAQLabeler();
 
    ~ITRAQLabeler() override;
 
    static BaseLabeler* create()
    {
      return new ITRAQLabeler();
    }
 
    static const String getProductName()
    {
      return "itraq";
    }
 
    // redeclaration of virtual methods
    void preCheck(Param& param) const override;
 
    void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
 
    void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
 
    void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
 
    void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
 
    void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
 
    void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
 
    void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
 
protected:
 
    void addModificationToPeptideHit_(Feature& feature, const String& modification, const Size& pos) const;
 
    void labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const;
 
    Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
 
    void updateMembers_() override;
 
    // get the closest RT profile factor of a feature for a given RT
    double getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const;
 
    EigenMatrixXdPtr getItraqIntensity_(const Feature& f, const double MS2_RT_time) const;
 
 
    // Members:
 
    Int itraq_type_;
 
    ChannelMapType channel_map_;
 
    IsotopeMatrices isotope_corrections_;
 
    double y_labeling_efficiency_;
 
  };
} // namespace OpenMS