CompNovoIonScoringBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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.
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// 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,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
 
#pragma once
 
// OpenMS includes
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
// stl includes
#include <vector>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI CompNovoIonScoringBase :
    public DefaultParamHandler
  {
 
public:
 
    enum IsotopeType
    {
      PARENT = 0,
      CHILD = 1,
      LONE = 2
    };
 
    struct OPENMS_DLLAPI IonScore
    {
      IonScore();
 
      IonScore(const IonScore & rhs);
 
      virtual ~IonScore();
 
      IonScore & operator=(const IonScore & rhs);
 
 
      double score;
      double s_bion;
      double s_yion;
      double s_witness;
      double position;
      double s_isotope_pattern_1;   
      Int is_isotope_1_mono;   
      double s_isotope_pattern_2;   
    };
 
 
    CompNovoIonScoringBase();
 
    CompNovoIonScoringBase(const CompNovoIonScoringBase & source);
 
    ~CompNovoIonScoringBase() override;
 
    CompNovoIonScoringBase & operator=(const CompNovoIonScoringBase & source);
 
    double scoreIsotopes(const PeakSpectrum & CID_spec, PeakSpectrum::ConstIterator it, Size charge);
 
protected:
 
    void updateMembers_() override;
 
 
    IsotopeType classifyIsotopes_(const PeakSpectrum & spec, PeakSpectrum::ConstIterator it) const;
 
    double scoreIsotopes_(const PeakSpectrum & spec, PeakSpectrum::ConstIterator it, std::map<double, IonScore> & CID_nodes, Size charge = 1);
 
    virtual void scoreWitnessSet_(Size charge, double precursor_weight, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec) = 0;
 
    void addSingleChargedIons_(std::map<double, IonScore> & ion_scores, PeakSpectrum & CID_spec);
 
    void initIsotopeDistributions_();
 
    std::map<Size, std::vector<double> > isotope_distributions_;
 
    double fragment_mass_tolerance_;
 
public:
 
  };
 
}