ICPLLabeler.h

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

#pragma once

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

namespace OpenMS
{

  class OPENMS_DLLAPI ICPLLabeler :
    public BaseLabeler
  {
public:

    ICPLLabeler();

    ~ICPLLabeler() override;

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

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

    // 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;

    void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;

    Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, Map<String, Feature>& unlabeled_features_index) const;

    String light_channel_label_;
    String medium_channel_label_;
    String heavy_channel_label_;

    void updateMembers_() override;

    String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;

private:
    static const int LIGHT_FEATURE_MAPID_;
    static const int MEDIUM_FEATURE_MAPID_;
    static const int HEAVY_FEATURE_MAPID_;
  };
} // namespace OpenMS