ThresholdMower.h

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

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

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

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

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

    // @name Accessors
    // @{

    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      threshold_ = ((double)param_.getValue("threshold"));
      std::vector<Size> indices;
      for (Size i = 0; i != spectrum.size(); ++i)
      {
        if (spectrum[i].getIntensity() >= threshold_)
        {
          indices.push_back(i);
        } 
      }
      spectrum.select(indices);
    }

    void filterPeakSpectrum(PeakSpectrum & spectrum);

    void filterPeakMap(PeakMap & exp);

    //TODO reimplement DefaultParamHandler::updateMembers_()

private:
    double threshold_;

    // @}
  };

}

#endif //OPENMS_FILTERING_TRANSFORMERS_THRESHOLDMOWER_H