SILACLabeler.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 2002-2012.
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// $Maintainer: Stephan Aiche $
// $Authors: Stephan Aiche$
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#ifndef OPENMS_SIMULATION_LABELING_SILACLABELER_H
#define OPENMS_SIMULATION_LABELING_SILACLABELER_H

#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>

namespace OpenMS
{


  class OPENMS_DLLAPI SILACLabeler :
    public BaseLabeler
  {
public:

    SILACLabeler();

    virtual ~SILACLabeler();

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

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

    // 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;

    Feature mergeFeatures_(Feature& labeled_channel_feature, const String& unmodified_sequence, Map<String, Feature>& unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const;

    Feature mergeAllChannelFeatures_(Feature& heavy_channel_feature, const String& unmodified_feature_sequence, Map<String, Feature>& light_channel_feature_index, Map<String, Feature>& medium_channel_feature_index) const;

    String medium_channel_lysine_label_;
    String medium_channel_arginine_label_;

    String heavy_channel_lysine_label_;
    String heavy_channel_arginine_label_;

    bool canModificationBeApplied_(const String& modification_id, const String& aa) const;

    void applyLabelToProteinHit_(FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;

    void updateMembers_();

    String getUnmodifiedSequence_(const Feature& feature, const String& arginine_label, const String& lysine_label) const;

private:
    static const int LIGHT_FEATURE_MAPID_;
    static const int MEDIUM_FEATURE_MAPID_;
    static const int HEAVY_FEATURE_MAPID_;
  };

} // namespace OpenMS

#endif //#ifndef OPENMS_SIMULATION_LABELING_SILACLABELER_H