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 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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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/DATASTRUCTURES/Map.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>

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(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, Map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec);

    void scoreWitnessSet_(Size charge, double precursor_weight, Map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec) override;

  };

}