Scaler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_FILTERING_TRANSFORMERS_SCALER_H
#define OPENMS_FILTERING_TRANSFORMERS_SCALER_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <map>

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

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

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

    // @}

    // @name Accessors
    // @{

    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      if (spectrum.empty()) return;

      spectrum.sortByIntensity();
      typename SpectrumType::size_type count = spectrum.size();
      ++count;
      typename SpectrumType::PeakType::IntensityType last_int = 0.0;
      typename SpectrumType::Iterator it = spectrum.end();
      do
      {
        --it;
        if (it->getIntensity() != last_int)
        {
          --count;
        }
        last_int = it->getIntensity();
        it->setIntensity(count);
      }
      while (it != spectrum.begin());
    }

    void filterPeakSpectrum(PeakSpectrum & spectrum);

    void filterPeakMap(PeakMap & exp);

    //TODO reimplement DefaultParamHandler::updateMembers_() when introducing member variables

    // @}

  };

}
#endif //OPENMS_FILTERING_TRANSFORMERS_SCALER_H