MSSim.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_MSSIM_H
#define OPENMS_SIMULATION_MSSIM_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{


  class OPENMS_DLLAPI MSSim :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:

    MSSim();

    virtual ~MSSim();

    void simulate(const SimRandomNumberGenerator & rnd_gen, SampleChannels & peptides);

    MSSimExperiment const & getExperiment() const;

    FeatureMapSim const & getSimulatedFeatures() const;

    ConsensusMap & getChargeConsensus();

    FeatureMapSim const & getContaminants() const;

    ConsensusMap & getLabelingConsensus();

    MSSimExperiment const & getPeakMap() const;

    Param getParameters() const;

protected:
    void syncParams_(Param & p, bool to_outer);

    void createFeatureMap_(const SampleProteins & peptides, FeatureMapSim & features, Size map_index);

private:
    void updateMembers_();

    MSSimExperiment experiment_;

    MSSimExperiment peak_map_;

    FeatureMapSimVector feature_maps_;

    ConsensusMap consensus_map_;

    FeatureMapSim contaminants_map_;

    BaseLabeler * labeler_;
  };

}

#endif