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 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
//
#pragma once
 
#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();
    ~ThresholdMower() override;
 
    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_;
 
    // @}
  };
 
}