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 2002-2012.
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// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_RTSIMULATION_H
#define OPENMS_SIMULATION_RTSIMULATION_H

#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(const SimRandomNumberGenerator & random_generator);

    RTSimulation(const RTSimulation & source);

    virtual ~RTSimulation();

    RTSimulation & operator=(const RTSimulation & source);

    void predictRT(FeatureMapSim & features);

    void predictContaminantsRT(FeatureMapSim &);

    bool isRTColumnOn() const;

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

    SimCoordinateType getGradientTime() const;

    void createExperiment(MSSimExperiment & experiment);

private:
    RTSimulation();

    void setDefaultParams_();

    void noRTColumn_(FeatureMapSim &);

    void smoothRTDistortion_(MSSimExperiment & experiment);

    void calculateMT_(FeatureMapSim & features, std::vector<DoubleReal> & 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_;

    SimCoordinateType total_gradient_time_;


    SimCoordinateType gradient_min_;
    SimCoordinateType gradient_max_;

    SimCoordinateType rt_sampling_rate_;

    DoubleReal egh_tau_location_;
    DoubleReal egh_tau_scale_;

    DoubleReal egh_variance_location_;
    DoubleReal egh_variance_scale_;

protected:
    SimRandomNumberGenerator const * rnd_gen_;

    void updateMembers_();

  };

}

#endif