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 2002-2020.
//
// 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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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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: $
// --------------------------------------------------------------------------
//
#pragma once
 
#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();
    ~MarkerMower() override;
 
    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_;
 
  };
}