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Viewing changes to include/OpenMS/ANALYSIS/ID/PILISIdentification.h

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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include/OpenMS/ANALYSIS/ID/PILISIdentification.h
 
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// -*- Mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Andreas Bertsch $
 
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// $Authors: Andreas Bertsch $
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H
 
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#define OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H
 
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#include <OpenMS/ANALYSIS/ID/PILISModel.h>
 
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#include <OpenMS/METADATA/PeptideIdentification.h>
 
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#include <OpenMS/KERNEL/StandardTypes.h>
 
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#include <vector>
 
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#include <map>
 
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namespace OpenMS
 
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{
 
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        // forward declarations
 
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        class PeakSpectrumCompareFunctor;
 
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        /**
 
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          @brief This class actually implements a complete ProteinIdentification run with PILIS
 
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                The PILISIdentification class needs a PILISModel and a PILISSequenceDB to generate
 
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                identifications. Simply call getIdentifications with a RichPeakMap.
 
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                @htmlinclude OpenMS_PILISIdentification.parameters
 
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                @ingroup Analysis_ID
 
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        */
 
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        class OPENMS_DLLAPI PILISIdentification : public DefaultParamHandler
 
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        {
 
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                public:
 
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                        /** @name constructors and destructors
 
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                         */
 
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                        //@{
 
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                        /// default constructor
 
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                        PILISIdentification();
 
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                        /// copy constructor
 
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                        PILISIdentification(const PILISIdentification& source);
 
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                        /// destructor
 
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                        virtual ~PILISIdentification();
 
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                        //@}
 
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                        ///
 
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                        PILISIdentification& operator = (const PILISIdentification& source);
 
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                        /** @name Accessors
 
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                         */
 
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                        //@{
 
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                        /// sets the sequence DB to be used for the ProteinIdentification runs
 
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                        //void setSequenceDB(const SuffixArrayPeptideFinder& sapf);
 
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                        /// sets the model to be used for the ProteinIdentification run
 
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                        void setModel(PILISModel* hmm_model);
 
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                        /// performs an ProteinIdentification run on a RichPeakMap
 
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                        void getIdentifications(const std::vector<std::map<String, UInt> >& candidates, std::vector<PeptideIdentification>& ids, const RichPeakMap& exp);
 
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                        /// performs an ProteinIdentification run on a PeakSpectrum
 
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                        void getIdentification(const std::map<String, UInt>& candidates, PeptideIdentification& id, const RichPeakSpectrum& spectrum);
 
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                        //@}
 
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                protected:
 
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                        /// fast method to create spectra for pre-scoring
 
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                        void getSpectrum_(RichPeakSpectrum& spec, const String& sequence, int charge);
 
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                        /// performs a pre-scoring of the given spec with very simple spectra from the candidate peptides
 
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                        void getPreIdentification_(PeptideIdentification& id, const RichPeakSpectrum& spec, const std::map<String, UInt>& cand_peptides);
 
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                        /// performs a ProteinIdentification via spectra comparison with the PILISModel spectrum generator
 
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                        void getFinalIdentification_(PeptideIdentification& id, const RichPeakSpectrum& spec, const PeptideIdentification& pre_id);
 
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                        /// returns the model pointer
 
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                        PILISModel* getPILISModel_();
 
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                        /// returns the sequence database pointer
 
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                        //PILISSequenceDB* getSequenceDB_();
 
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                        //SuffixArrayPeptideFinder* getSequenceDB_();
 
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                        /// the sequence database for the candidate peptides
 
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                        //PILISSequenceDB* sequence_db_;
 
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                        //SuffixArrayPeptideFinder sapf_;
 
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                        /// the model for spectra simulation
 
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                        PILISModel* hmm_model_;
 
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                        /// amino acids weights for the simple spectra generator
 
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                        Map<char, double> aa_weight_;
 
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                        /// scorer for pre comparison
 
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                        PeakSpectrumCompareFunctor* pre_scorer_;
 
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                        /// scorer for spectra comparison
 
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                        PeakSpectrumCompareFunctor* scorer_;
 
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                        /// a peaks, just to not instantiate it over and over again
 
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                        RichPeak1D p_;
 
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                        ///
 
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                        std::vector<RichPeakSpectrum> sim_specs_;
 
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                        /// flag whether the istance has a internal sequence db
 
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                        bool own_sequence_db_;
 
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                        /// flag whether the istance has a internal model
 
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                        bool own_model_;
 
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                        /// update members method from DefaultParamHandler to update the members 
 
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                        void updateMembers_();
 
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        };
 
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}
 
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#endif