SqrtMower.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once

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

#include <cmath>

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

    // @name Constructors and Destructors
    // @{
    SqrtMower();
    ~SqrtMower() override;

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

    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      bool warning = false;
      for (typename SpectrumType::Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
      {
        double intens = it->getIntensity();
        if (intens < 0)
        {
          intens = 0;
          warning = true;
        }
        it->setIntensity(std::sqrt(intens));
      }
      if (warning)
      {
        std::cerr << "Warning negative intensities were set to zero" << std::endl;
      }
      return;
    }

    void filterPeakSpectrum(PeakSpectrum & spectrum);

    void filterPeakMap(PeakMap & exp);

    //TODO reimplement DefaultParamHandler::updateMembers_()

    // @}

  };

}