SILACLabeler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
 
namespace OpenMS
{
 
 
  class OPENMS_DLLAPI SILACLabeler :
    public BaseLabeler
  {
public:
 
    SILACLabeler();
 
    ~SILACLabeler() override;
 
    static BaseLabeler* create()
    {
      return new SILACLabeler();
    }
 
    static const String getProductName()
    {
      return "SILAC";
    }
 
    // 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;
 
    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_(SimTypes::FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;
 
    void updateMembers_() override;
 
    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