RawMSSignalSimulation.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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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

#include <OpenMS/SIMULATION/SimTypes.h>
#include <OpenMS/SIMULATION/EGHModel.h>

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ProductModel.h>

namespace OpenMS
{

  class IsotopeModel;

  class OPENMS_DLLAPI RawMSSignalSimulation :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:
    RawMSSignalSimulation();

    explicit RawMSSignalSimulation(SimTypes::MutableSimRandomNumberGeneratorPtr rng);

    RawMSSignalSimulation(const RawMSSignalSimulation& source);

    ~RawMSSignalSimulation() override;

    RawMSSignalSimulation& operator=(const RawMSSignalSimulation& source);

    void loadContaminants();

    void generateRawSignals(SimTypes::FeatureMapSim& features,
                            SimTypes::MSSimExperiment& experiment,
                            SimTypes::MSSimExperiment& experiment_ct,
                            SimTypes::FeatureMapSim& contaminants);

protected:

    enum IONIZATIONMETHOD {IM_ESI = 0, IM_MALDI = 1, IM_ALL = 2};
    enum PROFILESHAPE {RT_RECTANGULAR, RT_GAUSSIAN};
    enum RESOLUTIONMODEL {RES_CONSTANT, RES_LINEAR, RES_SQRT};

    void updateMembers_() override;

    void setDefaultParams_();

    void add1DSignal_(Feature& feature, SimTypes::MSSimExperiment& experiment, SimTypes::MSSimExperiment& experiment_ct);

    void add2DSignal_(Feature& feature, SimTypes::MSSimExperiment& experiment, SimTypes::MSSimExperiment& experiment_ct);

    void samplePeptideModel1D_(const IsotopeModel& iso,
                               const SimTypes::SimCoordinateType mz_start,
                               const SimTypes::SimCoordinateType mz_end,
                               SimTypes::MSSimExperiment& experiment,
                               SimTypes::MSSimExperiment& experiment_ct,
                               Feature& activeFeature);

    void samplePeptideModel2D_(const ProductModel<2>& pm,
                               const SimTypes::SimCoordinateType mz_start,
                               const SimTypes::SimCoordinateType mz_end,
                               SimTypes::SimCoordinateType rt_start,
                               SimTypes::SimCoordinateType rt_end,
                               SimTypes::MSSimExperiment& experiment,
                               SimTypes::MSSimExperiment& experiment_ct,
                               Feature& activeFeature);

    void chooseElutionProfile_(EGHModel* const elutionmodel,
                               Feature& feature,
                               const double scale,
                               const double rt_sampling_rate,
                               const SimTypes::MSSimExperiment& experiment);

    void createContaminants_(SimTypes::FeatureMapSim& contaminants, SimTypes::MSSimExperiment& exp, SimTypes::MSSimExperiment& exp_ct);

    void addShotNoise_(SimTypes::MSSimExperiment& experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit, SimTypes::SimCoordinateType maximal_mz_measurement_limit);

    void addWhiteNoise_(SimTypes::MSSimExperiment& experiment);

    void addDetectorNoise_(SimTypes::MSSimExperiment& experiment);

    void addBaseLine_(SimTypes::MSSimExperiment& experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit);

    void getSamplingGrid_(std::vector<SimTypes::SimCoordinateType>& grid,
                          const SimTypes::SimCoordinateType mz_min,
                          const SimTypes::SimCoordinateType mz_max,
                          const Int step_Da);

    void compressSignals_(SimTypes::MSSimExperiment& experiment);

    Int sampling_points_per_FWHM_;

    SimTypes::SimCoordinateType mz_error_mean_;
    SimTypes::SimCoordinateType mz_error_stddev_;

    SimTypes::SimIntensityType getFeatureScaledIntensity_(const SimTypes::SimIntensityType feature_intensity,
                                                          const SimTypes::SimIntensityType natural_scaling_factor);


    double getResolution_(const double query_mz, const double resolution, const RESOLUTIONMODEL model) const;

    double getPeakWidth_(const double mz, const bool is_gaussian) const;

    SimTypes::SimIntensityType intensity_scale_;
    SimTypes::SimIntensityType intensity_scale_stddev_;


    RESOLUTIONMODEL res_model_;
    double res_base_;
    std::vector<SimTypes::SimCoordinateType> grid_;

    SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_;

    struct ContaminantInfo
    {
      String name;
      EmpiricalFormula sf;
      double rt_start, rt_end, intensity;
      Int q;
      PROFILESHAPE shape;
      IONIZATIONMETHOD im;
    };

    std::vector<ContaminantInfo> contaminants_;

    std::vector<std::vector<double> > threaded_random_numbers_;

    std::vector<Size> threaded_random_numbers_index_;

    static const Size THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500;

    bool contaminants_loaded_;
  };

}