text: // --------------------------------------------------------------------------
  //                   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:
  //  * 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
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Timo Sachsenberg $
  // $Authors: $
  // --------------------------------------------------------------------------
  //
  
  #pragma once
  
  #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
  
  #include <map>
  #include <string>
  #include <cmath>
  
  namespace OpenMS
  {
    /**
      @brief GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss
  
          @htmlinclude OpenMS_GoodDiffFilter.parameters
  
          @ingroup SpectraFilter
    */
    class OPENMS_DLLAPI GoodDiffFilter :
      public FilterFunctor
    {
  public:
  
      // @name Constructors and Destructors
      // @{
      /// default constructor
      GoodDiffFilter();
  
      /// copy constructor
      GoodDiffFilter(const GoodDiffFilter & source);
  
      /// destructor
      ~GoodDiffFilter() override;
      // @}
  
      // @name Operators
      // @{
      /// assignment operator
      GoodDiffFilter & operator=(const GoodDiffFilter & source);
      // @}
  
      // @name Accessors
      // @{
      ///
      static FilterFunctor * create() { return new GoodDiffFilter(); }
  
      ///
      template <typename SpectrumType>
      double apply(SpectrumType & spectrum)
      {
        double tolerance = (double)param_.getValue("tolerance");
        double gooddiff = 0;
        //iterate over all peaks
        double totaldiff = 0;
        for (Size i = 0; i < spectrum.size(); ++i)
        {
          //look for each peakdifference that is in range of aa residuemasses (56/187), if it could be a aa (aamass)
          for (Size j = i; i + j < spectrum.size(); ++j)
          {
            double diff =  spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0];
            if (diff < 56)
            {
              continue;
            }
  
            if (diff > 187)
            {
              j = spectrum.size();
            }
            else
            {
              totaldiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
              std::map<double, char>::const_iterator aait = aamass_.lower_bound(diff);
              if (aait == aamass_.end())
              {
                continue;
              }
              //look for aamasses that fit diff
              if (fabs(aait->first - diff) <= tolerance)
              {
                gooddiff += spectrum[i + j].getIntensity()  + spectrum[i].getIntensity();
              }
              else
              {
                ++aait;
                if ((aait) != aamass_.end() && fabs((aait)->first - diff) <= tolerance)
                {
                  gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
                }
              }
            }
          }
        }
  
        return gooddiff / totaldiff;
      }
  
      ///
      static const String getProductName()
      {
        return "GoodDiffFilter";
      }
  
      // @}
  
  
  private:
  
      /// list of unique amino acid masses
      std::map<double, char> aamass_;
    };
  }
  
  