BaseModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Clemens Groepl $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/DPeak.h>

namespace OpenMS
{

  template <UInt D>
  class BaseModel :
    public DefaultParamHandler
  {

public:

    typedef DoubleReal IntensityType;
    typedef DoubleReal CoordinateType;
    typedef DPosition<D> PositionType;
    typedef typename DPeak<D>::Type PeakType;
    typedef std::vector<PeakType> SamplesType;


    BaseModel() :
      DefaultParamHandler("BaseModel")
    {
      defaults_.setValue("cutoff", 0.0, "Low intensity cutoff of the model.  Peaks below this intensity are not considered part of the model.");
    }

    BaseModel(const BaseModel & source) :
      DefaultParamHandler(source),
      cut_off_(source.cut_off_)
    {
    }

    virtual ~BaseModel()
    {
    }

    virtual BaseModel & operator=(const BaseModel & source)
    {
      if (&source == this) return *this;

      DefaultParamHandler::operator=(source);
      cut_off_ = source.cut_off_;

      return *this;
    }

    static void registerChildren();

    virtual IntensityType getIntensity(const PositionType & pos) const = 0;

    virtual bool isContained(const PositionType & pos) const
    {
      return getIntensity(pos) >= cut_off_;
    }

    template <typename PeakType>
    void fillIntensity(PeakType & peak) const
    {
      peak.setIntensity(getIntensity(peak.getPosition()));
    }

    template <class PeakIterator>
    void fillIntensities(PeakIterator begin, PeakIterator end) const
    {
      for (PeakIterator it = begin; it != end; ++it)
      {
        fillIntensity(*it);
      }
    }

    virtual IntensityType getCutOff() const
    {
      return cut_off_;
    }

    virtual void setCutOff(IntensityType cut_off)
    {
      cut_off_ = cut_off;
      param_.setValue("cutoff", cut_off_);
    }

    virtual void getSamples(SamplesType & cont) const = 0;

    virtual void getSamples(std::ostream & os)
    {
      SamplesType samples;
      getSamples(samples);
      for (typename SamplesType::const_iterator it = samples.begin(); it != samples.end(); ++it)
      {
        os << *it << std::endl;
      }
    }

protected:
    IntensityType cut_off_;

    virtual void updateMembers_()
    {
      cut_off_ = (double)param_.getValue("cutoff");
    }

  };
}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H