RTSimulation.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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// 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/Map.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>

namespace OpenMS
{
  class OPENMS_DLLAPI RTSimulation :
    public DefaultParamHandler
  {


public:

    RTSimulation();

    explicit RTSimulation(SimTypes::MutableSimRandomNumberGeneratorPtr random_generator);

    RTSimulation(const RTSimulation& source);

    ~RTSimulation() override;

    RTSimulation& operator=(const RTSimulation& source);

    void predictRT(SimTypes::FeatureMapSim& features);

    void predictContaminantsRT(SimTypes::FeatureMapSim&);

    bool isRTColumnOn() const;

    void wrapSVM(std::vector<AASequence>& peptide_sequences, std::vector<double>& predicted_retention_times);

    SimTypes::SimCoordinateType getGradientTime() const;

    void createExperiment(SimTypes::MSSimExperiment& experiment);

private:
    void setDefaultParams_();

    void noRTColumn_(SimTypes::FeatureMapSim&);

    void smoothRTDistortion_(SimTypes::MSSimExperiment& experiment);

    void calculateMT_(SimTypes::FeatureMapSim& features, std::vector<double>& predicted_retention_times);

    void getChargeContribution_(Map<String, double>& q_cterm,
                                Map<String, double>& q_nterm,
                                Map<String, double>& q_aa_basic,
                                Map<String, double>& q_aa_acidic);

    // MEMBERS:

    // Name of the svm model file
    OpenMS::String rt_model_file_;

    SimTypes::SimCoordinateType total_gradient_time_;


    SimTypes::SimCoordinateType gradient_min_;
    SimTypes::SimCoordinateType gradient_max_;

    SimTypes::SimCoordinateType rt_sampling_rate_;

    double egh_tau_location_;
    double egh_tau_scale_;

    double egh_variance_location_;
    double egh_variance_scale_;

protected:
    SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_;

    void updateMembers_() override;

  };

}