CompNovoIonScoring.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:
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
 
#pragma once
 
// OpenMS includes
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringBase.h>
 
// stl includes
#include <vector>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI CompNovoIonScoring :
    public CompNovoIonScoringBase
  {
 
public:
 
    typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
    typedef CompNovoIonScoringBase::IonScore IonScore;
 
 
    CompNovoIonScoring();
 
    CompNovoIonScoring(const CompNovoIonScoring & source);
 
    ~CompNovoIonScoring() override;
 
    CompNovoIonScoring & operator=(const CompNovoIonScoring & source);
 
    void scoreSpectra(std::map<double, IonScore> & CID_ion_scores, PeakSpectrum & CID_spec, PeakSpectrum & ETD_spec, double precursor_weight, Size charge);
 
protected:
 
    void scoreETDFeatures_(Size charge, double precursor_weight, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec);
 
    void scoreWitnessSet_(Size charge, double precursor_weight, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec) override;
 
  };
 
}