BaseLabeler.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: Stephan Aiche $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H
#define OPENMS_SIMULATION_LABELING_BASELABELER_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/KERNEL/ConsensusMap.h>

#include <OpenMS/SIMULATION/SimTypes.h>

// GSL includes (random number generation)
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>

namespace OpenMS
{

  class OPENMS_DLLAPI BaseLabeler :
    public DefaultParamHandler
  {
public:

    BaseLabeler();

    virtual ~BaseLabeler();

    static void registerChildren();

    virtual Param getDefaultParameters() const;

    virtual void setRnd(const SimRandomNumberGenerator & rng);

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


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

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

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

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

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

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

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


    ConsensusMap & getConsensus();

    const String & getDescription() const;

    String getChannelIntensityName(const Size channel_index) const;


protected:
    FeatureMapSim mergeProteinIdentificationsMaps_(const FeatureMapSimVector & maps);

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

    void recomputeConsensus_(const FeatureMapSim & simulated_features);


    ConsensusMap consensus_;

    SimRandomNumberGenerator const * rng_;

    String channel_description_;

  };
} // namespace OpenMS

#endif //#ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H