RankScaler.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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 <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI RankScaler :
    public DefaultParamHandler
  {
public:
 
    // @name Constructors and Destructors
    // @{
    RankScaler();
    ~RankScaler() override;
 
    RankScaler(const RankScaler & source);
    RankScaler & operator=(const RankScaler & 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
 
    // @}
 
  };
 
}