// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------


#ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H
#define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H

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

// stl includes
#include <vector>

namespace OpenMS
{
  /**
    @brief  run with CompNovoIdentification

      @htmlinclude OpenMS_CompNovoIdentification.parameters

      @ingroup Analysis_ID
  */
  class OPENMS_DLLAPI CompNovoIdentification :
    public CompNovoIdentificationBase
  {

public:

    /** @name constructors and destructors
     */
    //@{
    /// default constructor
    CompNovoIdentification();

    /// copy constructor
    CompNovoIdentification(const CompNovoIdentification & source);

    /// destructor
    virtual ~CompNovoIdentification();
    //@}

    ///
    CompNovoIdentification & operator=(const CompNovoIdentification & source);

    /** @name Accessors
     */
    //@{
    /// performs an ProteinIdentification run on a PeakMap
    void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp);

    /// performs an ProteinIdentification run on a PeakSpectrum
    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:

    /// call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences
    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);

    /// reduces the given number of permuts by scoring the permutations to the CID and ETD spec
    void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, double prefix, double suffix);

    /// fills the spectrum with c and z type ions
    void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);

    /// estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec
    double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);

  };
}

#endif
