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 2002-2020.
//
// 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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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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_;
  };
 
}