libopenms-dev 1.11.1-3 / usr / include / OpenMS / ANALYSIS / ID / PILISIdentification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------


#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;

  /**
    @brief This class actually implements a complete ProteinIdentification run with PILIS

      The PILISIdentification class needs a PILISModel and a PILISSequenceDB to generate
      identifications. Simply call getIdentifications with a RichPeakMap.

      @htmlinclude OpenMS_PILISIdentification.parameters

      @ingroup Analysis_ID
  */
  class OPENMS_DLLAPI PILISIdentification :
    public DefaultParamHandler
  {

public:

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

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

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

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

    /** @name Accessors
     */
    //@{
    /// sets the sequence DB to be used for the ProteinIdentification runs
    //void setSequenceDB(const SuffixArrayPeptideFinder& sapf);

    /// sets the model to be used for the ProteinIdentification run
    void setModel(PILISModel * hmm_model);

    /// performs an ProteinIdentification run on a RichPeakMap
    void getIdentifications(const std::vector<std::map<String, UInt> > & candidates, std::vector<PeptideIdentification> & ids, const RichPeakMap & exp);

    /// performs an ProteinIdentification run on a PeakSpectrum
    void getIdentification(const std::map<String, UInt> & candidates, PeptideIdentification & id, const RichPeakSpectrum & spectrum);
    //@}

protected:

    /// fast method to create spectra for pre-scoring
    void getSpectrum_(RichPeakSpectrum & spec, const String & sequence, int charge);

    /// performs a pre-scoring of the given spec with very simple spectra from the candidate peptides
    void getPreIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const std::map<String, UInt> & cand_peptides);

    /// performs a ProteinIdentification via spectra comparison with the PILISModel spectrum generator
    void getFinalIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const PeptideIdentification & pre_id);

    /// returns the model pointer
    PILISModel * getPILISModel_();

    /// returns the sequence database pointer
    //PILISSequenceDB* getSequenceDB_();
    //SuffixArrayPeptideFinder* getSequenceDB_();

    /// the sequence database for the candidate peptides
    //PILISSequenceDB* sequence_db_;
    //SuffixArrayPeptideFinder sapf_;

    /// the model for spectra simulation
    PILISModel * hmm_model_;

    /// amino acids weights for the simple spectra generator
    Map<char, double> aa_weight_;

    /// scorer for pre comparison
    PeakSpectrumCompareFunctor * pre_scorer_;

    /// scorer for spectra comparison
    PeakSpectrumCompareFunctor * scorer_;

    /// a peaks, just to not instantiate it over and over again
    RichPeak1D p_;

    ///
    std::vector<RichPeakSpectrum> sim_specs_;

    /// flag whether the istance has a internal sequence db
    bool own_sequence_db_;

    /// flag whether the istance has a internal model
    bool own_model_;

    /// update members method from DefaultParamHandler to update the members
    void updateMembers_();
  };
}

#endif