ITRAQLabeler.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
#define OPENMS_SIMULATION_LABELING_ITRAQLABELER_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();

    virtual ~ITRAQLabeler();

    static BaseLabeler * create()
    {
      return new ITRAQLabeler();
    }

    static const String getProductName()
    {
      return "itraq";
    }

    // redeclaration of virtual methods
    void preCheck(Param & param) const;

    void setUpHook(FeatureMapSimVector & /* channels */);

    void postDigestHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRTHook(FeatureMapSimVector & /* features_to_simulate */);

    void postDetectabilityHook(FeatureMapSimVector & /* features_to_simulate */);

    void postIonizationHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRawMSHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRawTandemMSHook(FeatureMapSimVector & /* features_to_simulate */, MSSimExperiment & /* simulated map */);

protected:

    void addModificationToPeptideHit_(Feature & feature, const String & modification, const Size & pos) const;

    void labelPeptide_(const Feature & feature, FeatureMapSim & result) const;

    Feature mergeFeatures_(Feature & labeled_channel_feature, const AASequence & unmodified_sequence, std::map<AASequence, Feature> & unlabeled_features_index) const;

    void updateMembers_();

    // get the closest RT profile factor of a feature for a given RT
    DoubleReal getRTProfileIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;

    Matrix<SimIntensityType> getItraqIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;


    // Members:

    Int itraq_type_;

    ChannelMapType channel_map_;

    IsotopeMatrices isotope_corrections_;

    DoubleReal y_labeling_efficiency_;

  };
} // namespace OpenMS

#endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H