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 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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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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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{

  class BaseLabeler;

  class OPENMS_DLLAPI MSSim :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:
    MSSim();

    ~MSSim() override;

    void simulate(SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels& peptides);

    const SimTypes::MSSimExperiment& getExperiment() const;

    const SimTypes::FeatureMapSim& getSimulatedFeatures() const;

    ConsensusMap& getChargeConsensus();

    const SimTypes::FeatureMapSim& getContaminants() const;

    ConsensusMap& getLabelingConsensus();

    const SimTypes::MSSimExperiment& getPeakMap() const;

    void getIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    void getMS2Identifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    void getFeatureIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    Param getParameters() const;

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

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

    void updateMembers_() override;

private:
    SimTypes::MSSimExperiment experiment_;

    SimTypes::MSSimExperiment peak_map_;

    SimTypes::FeatureMapSimVector feature_maps_;

    ConsensusMap consensus_map_;

    SimTypes::FeatureMapSim contaminants_map_;

    BaseLabeler* labeler_;
  };

}