MarkerMower.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.
//
// This software is released under a three-clause BSD license:
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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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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_FILTERING_TRANSFORMERS_MARKERMOWER_H
#define OPENMS_FILTERING_TRANSFORMERS_MARKERMOWER_H

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

#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <vector>
#include <map>

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

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

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

    // @name Accessors
    // @{
    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      typedef typename SpectrumType::Iterator Iterator;

      std::map<double, int> marks;
      for (std::vector<PeakMarker *>::const_iterator cvit = markers_.begin(); cvit != markers_.end(); ++cvit)
      {
        std::map<double, bool> marked;
        (*cvit)->apply(marked, spectrum);
        for (std::map<double, bool>::const_iterator cmit = marked.begin(); cmit != marked.end(); ++cmit)
        {
          if (cmit->second)
          {
            marks[cmit->first]++;
          }
        }
      }

      for (Iterator it = spectrum.begin(); it != spectrum.end(); )
      {
        if (marks[it->getMZ()] > 0)
        {
          ++it;
        }
        else
        {
          it = spectrum.erase(it);
        }
      }
    }

    void filterPeakSpectrum(PeakSpectrum & spectrum);

    void filterPeakMap(PeakMap & exp);

    static const String getProductName()
    {
      return "MarkerMower";
    }

    void insertmarker(PeakMarker * peak_marker);

    //TODO reimplement DefaultParamHandler::updateMembers_()

    // @}

private:
    std::vector<PeakMarker *> markers_;

  };
}
#endif // OPENMS_COMPARISON_CLUSTERING_MARKERMOWER_H