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 2002-2012.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_RAWMSSIGNALSIMULATION_H
#define OPENMS_SIMULATION_RAWMSSIGNALSIMULATION_H

#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(const SimRandomNumberGenerator & rng);

    RawMSSignalSimulation(const RawMSSignalSimulation & source);

    virtual ~RawMSSignalSimulation();

    RawMSSignalSimulation & operator=(const RawMSSignalSimulation & source);

    void loadContaminants();

    void generateRawSignals(FeatureMapSim & features, MSSimExperiment & experiment, MSSimExperiment & experiment_ct, 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};


    RawMSSignalSimulation();

    void updateMembers_();

    void setDefaultParams_();

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

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

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

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

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

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

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

    void addWhiteNoise_(MSSimExperiment & experiment);

    void addDetectorNoise_(MSSimExperiment & experiment);

    void addBaseLine_(MSSimExperiment & experiment, SimCoordinateType minimal_mz_measurement_limit);

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

    void compressSignals_(MSSimExperiment & experiment);

    Int sampling_points_per_FWHM_;

    SimCoordinateType mz_error_mean_;
    SimCoordinateType mz_error_stddev_;

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


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

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

    SimIntensityType intensity_scale_;
    SimIntensityType intensity_scale_stddev_;


    RESOLUTIONMODEL res_model_;
    DoubleReal res_base_;
    std::vector<SimCoordinateType> grid_;

    SimRandomNumberGenerator const * rnd_gen_;

    struct ContaminantInfo
    {
      String name;
      EmpiricalFormula sf;
      DoubleReal 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_;
  };

}

#endif