BaseModel.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/DPeak.h>
 
namespace OpenMS
{
 
  template<UInt D>
  class BaseModel : public DefaultParamHandler
  {
  public:
    typedef double IntensityType;
    typedef double 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_)
    {
    }
 
    ~BaseModel() override
    {
    }
 
    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_;
 
    void updateMembers_() override
    {
      cut_off_ = (double)param_.getValue("cutoff");
    }
  };
} // namespace OpenMS