CompNovoIdentification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
 
#pragma once
 
// OpenMS includes
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>
 
// stl includes
#include <vector>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI CompNovoIdentification :
    public CompNovoIdentificationBase
  {
 
public:
 
    CompNovoIdentification();
 
    CompNovoIdentification(const CompNovoIdentification & source);
 
    ~CompNovoIdentification() override;
 
    CompNovoIdentification & operator=(const CompNovoIdentification & source);
 
    void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) override;
 
    void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec, const PeakSpectrum & ETD_spec);
 
 
    typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
    typedef CompNovoIonScoringBase::IonScore IonScore;
    typedef CompNovoIdentificationBase::Permut Permut;
 
protected:
 
    void getDecompositionsDAC_(std::set<String> & sequences, Size left, Size right, double peptide_weight, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, std::map<double, IonScore> & CID_nodes);
 
    void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, double prefix, double suffix);
 
    double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);
 
  };
}