WindowMower.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: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_FILTERING_TRANSFORMERS_WINDOWMOWER_H
#define OPENMS_FILTERING_TRANSFORMERS_WINDOWMOWER_H

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

#include <set>

namespace OpenMS
{

  class OPENMS_DLLAPI WindowMower :
    public DefaultParamHandler
  {
public:

    // @name Constructors, destructors and assignment operators
    // @{
    WindowMower();
    virtual ~WindowMower();

    WindowMower(const WindowMower& source);
    WindowMower& operator=(const WindowMower& source);
    // @}

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

      windowsize_ = (DoubleReal)param_.getValue("windowsize");
      peakcount_ = (UInt)param_.getValue("peakcount");

      //copy spectrum
      SpectrumType old_spectrum = spectrum;
      old_spectrum.sortByPosition();

      //find high peak positions
      bool end  = false;
      std::set<double> positions;
      for (ConstIterator it = old_spectrum.begin(); it != old_spectrum.end(); ++it)
      {
        // copy the window from the spectrum
        SpectrumType window;
        for (ConstIterator it2 = it; (it2->getPosition() - it->getPosition() < windowsize_); )
        {
          window.push_back(*it2);
          if (++it2 == old_spectrum.end())
          {
            end = true;
            break;
          }
        }

        //extract peakcount most intense peaks
        window.sortByIntensity(true);
        for (Size i = 0; i < peakcount_; ++i)
        {
          if (i < window.size())
          {
            positions.insert(window[i].getMZ());
          }
        }
        //abort at the end of the spectrum
        if (end) break;
      }

      // replace the old peaks by the new ones
      spectrum.clear(false);
      for (ConstIterator it = old_spectrum.begin(); it != old_spectrum.end(); ++it)
      {
        if (positions.find(it->getMZ()) != positions.end())
        {
          spectrum.push_back(*it);
        }
      }
    }

    void filterPeakSpectrum(PeakSpectrum& spectrum);

    void filterPeakMap(PeakMap& exp);

    //TODO reimplement DefaultParamHandler::updateMembers_()

private:
    DoubleReal windowsize_;
    UInt peakcount_;
  };

}

#endif //OPENMS_FILTERING_TRANSFORMERS_WINDOWMOWER_H