BaseLabeler.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, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/KERNEL/ConsensusMap.h>

#include <OpenMS/SIMULATION/SimTypes.h>

namespace OpenMS
{

  class OPENMS_DLLAPI BaseLabeler :
    public DefaultParamHandler
  {
public:

    BaseLabeler();

    ~BaseLabeler() override;

    static void registerChildren();

    virtual Param getDefaultParameters() const;

    virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng);

    virtual void preCheck(Param& param) const = 0;


    virtual void setUpHook(SimTypes::FeatureMapSimVector& /* features */) = 0;

    virtual void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;

    virtual void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;

    virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;

    virtual void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;

    virtual void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;

    virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) = 0;


    ConsensusMap& getConsensus();

    const String& getDescription() const;

    String getChannelIntensityName(const Size channel_index) const;


protected:
    SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector& maps);

    void mergeProteinAccessions_(Feature& target, const Feature& source) const;

    void recomputeConsensus_(const SimTypes::FeatureMapSim& simulated_features);


    ConsensusMap consensus_;

    SimTypes::MutableSimRandomNumberGeneratorPtr rng_;

    String channel_description_;

  };
} // namespace OpenMS