Normalizer.h

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// $Maintainer: Mathias Walzer $
// $Authors: $
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//
#ifndef OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H
#define OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H

#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI Normalizer :
    public DefaultParamHandler
  {
public:

    // @name Constructors and Destructors
    // @{
    Normalizer();
    virtual ~Normalizer();

    Normalizer & operator=(const Normalizer & source);
    Normalizer(const Normalizer & source);

    // @}

    // @name Accessors
    // @{

    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      typedef typename SpectrumType::Iterator Iterator;
      typedef typename SpectrumType::ConstIterator ConstIterator;

      method_ = param_.getValue("method");

      // normalizes the max peak to 1 and the rest of the peaks to values relative to max
      if (method_ == "to_one")
      {
        double max(0);
        for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
        {
          if (max < it->getIntensity())
          {
            max = it->getIntensity();
          }
        }
        for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
        {
          it->setIntensity(it->getIntensity() / max);
        }
      }
      // normalizes the peak intensities to the TIC
      else if (method_ == "to_TIC")
      {
        double sum(0);
        for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
        {
          sum += it->getIntensity();
        }

        for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
        {
          it->setIntensity(it->getIntensity() / sum);
        }
      }
      // method unknown
      else
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Method not known", method_);
      }
      return;

    }

    void filterPeakSpectrum(PeakSpectrum & spectrum);
    void filterPeakMap(PeakMap & exp);

    //TODO reimplement DefaultParamHandler::updateMembers_()

    // @}

private:
    String method_;

  };


}
#endif //OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H