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 2002-2020.
//
// 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.
//  * Neither the name of any author or any participating institution
//    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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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_;
  };
 
}