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 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------


#pragma once

// OpenMS includes
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>

// stl includes
#include <vector>

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, 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);

    void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);

    double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);

  };
}