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 2002-2018.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once

#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
#include <OpenMS/DATASTRUCTURES/Utils/MatrixUtils.h>
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
#include <OpenMS/SIMULATION/SimTypes.h>

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