PILISIdentification.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 2002-2012.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H
#define OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H

#include <OpenMS/ANALYSIS/ID/PILISModel.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <vector>
#include <map>

namespace OpenMS
{
  // forward declarations
  class PeakSpectrumCompareFunctor;

  class OPENMS_DLLAPI PILISIdentification :
    public DefaultParamHandler
  {

public:


    PILISIdentification();

    PILISIdentification(const PILISIdentification & source);

    virtual ~PILISIdentification();

    PILISIdentification & operator=(const PILISIdentification & source);


    //void setSequenceDB(const SuffixArrayPeptideFinder& sapf);

    void setModel(PILISModel * hmm_model);

    void getIdentifications(const std::vector<std::map<String, UInt> > & candidates, std::vector<PeptideIdentification> & ids, const RichPeakMap & exp);

    void getIdentification(const std::map<String, UInt> & candidates, PeptideIdentification & id, const RichPeakSpectrum & spectrum);

protected:

    void getSpectrum_(RichPeakSpectrum & spec, const String & sequence, int charge);

    void getPreIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const std::map<String, UInt> & cand_peptides);

    void getFinalIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const PeptideIdentification & pre_id);

    PILISModel * getPILISModel_();

    //PILISSequenceDB* getSequenceDB_();
    //SuffixArrayPeptideFinder* getSequenceDB_();

    //PILISSequenceDB* sequence_db_;
    //SuffixArrayPeptideFinder sapf_;

    PILISModel * hmm_model_;

    Map<char, double> aa_weight_;

    PeakSpectrumCompareFunctor * pre_scorer_;

    PeakSpectrumCompareFunctor * scorer_;

    RichPeak1D p_;

    std::vector<RichPeakSpectrum> sim_specs_;

    bool own_sequence_db_;

    bool own_model_;

    void updateMembers_();
  };
}

#endif