text: // --------------------------------------------------------------------------
  //                   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:
  //  * 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 $
  // $Authors: Sandro Andreotti, Andreas Bertsch$
  // --------------------------------------------------------------------------
  
  #ifndef OPENMS_ANALYSIS_DENOVO_DENOVOIONSCORING_H
  #define OPENMS_ANALYSIS_DENOVO_DENOVOIONSCORING_H
  
  #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
  #include <OpenMS/KERNEL/StandardTypes.h>
  #include <vector>
  
  namespace OpenMS
  {
    /**
      @brief Base class for ion scoring implementation for de novo algorithms
  
  
  
          @ingroup Analysis_DeNovo
    */
    class OPENMS_DLLAPI DeNovoIonScoring :
      public DefaultParamHandler
    {
  public:
      /** @brief IonScore
  
                    IonScore describes the likelihood of position to be prefix residue masses (in case of
                    an b-ion centric algorithm).
            */
      class IonScore
      {
  public:
        /// score
        double score;
  
        /// position of the ion
        double position;
  
        /// index of peak in the spectrum, -1 if not in spectrum
        SignedSize index;
  
  
        IonScore() :
          score(0),
          position(0.0),
          index(-1)
        {
        }
  
        IonScore(const IonScore & rhs) :
          score(rhs.score),
          position(rhs.score),
          index(rhs.index)
        {
        }
  
        virtual ~IonScore()
        {
        }
  
        IonScore & operator=(const IonScore & rhs)
        {
          if (this != &rhs)
          {
            score = rhs.score;
            position = rhs.position;
            index = rhs.index;
          }
          return *this;
        }
  
      };
  
  
      /** @name Constructors and destructors
      */
      //@{
      /// default constructor
      DeNovoIonScoring();
  
      /// destructor
      ~DeNovoIonScoring() override;
  
      /// copy constructor
      DeNovoIonScoring(const DeNovoIonScoring & rhs);
      //@}
  
      /// assignment operator
      DeNovoIonScoring & operator=(const DeNovoIonScoring & rhs);
  
      virtual void getIonScores(std::vector<IonScore> & ion_scores, const PeakSpectrum & spec) = 0;
  
      virtual void getIonScores(std::vector<std::vector<IonScore> > & ion_scores, const PeakMap & exp) = 0;
    };
  
  } // namespace OpenMS
  
  #endif // OPENMS_ANALYSIS_DENOVO_DENOVOIONSCORING_H
  