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Viewing changes to include/OpenMS/ANALYSIS/DENOVO/CompNovoIdentification.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/DENOVO/CompNovoIdentification.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: Sandro Andreotti $
 
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// $Authors: Andreas Bertsch $
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H
 
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#define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H
 
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// OpenMS includes
 
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#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>
 
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// stl includes
 
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#include <vector>
 
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namespace OpenMS
 
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{
 
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        /**
 
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          @brief  run with CompNovoIdentification
 
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                @htmlinclude OpenMS_CompNovoIdentification.parameters
 
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                @ingroup Analysis_ID
 
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        */
 
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        class OPENMS_DLLAPI CompNovoIdentification : public CompNovoIdentificationBase
 
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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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                        CompNovoIdentification();
 
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                        /// copy constructor
 
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                        CompNovoIdentification(const CompNovoIdentification& source);
 
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                        /// destructor
 
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                        virtual ~CompNovoIdentification();
 
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                        //@}
 
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                        ///
 
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                        CompNovoIdentification& operator = (const CompNovoIdentification& source);
 
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                        /** @name Accessors
 
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                         */
 
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                        //@{
 
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                        /// performs an ProteinIdentification run on a PeakMap
 
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                        void getIdentifications(std::vector<PeptideIdentification>& ids, const PeakMap& exp);
 
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                        /// performs an ProteinIdentification run on a PeakSpectrum
 
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                        void getIdentification(PeptideIdentification& id, const PeakSpectrum& CID_spec, const PeakSpectrum& ETD_spec);
 
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                        //@}
 
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                        typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
 
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                        typedef CompNovoIonScoringBase::IonScore IonScore;
 
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                        typedef CompNovoIdentificationBase::Permut Permut;
 
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                protected:
 
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                        /// call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences
 
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                        void getDecompositionsDAC_(std::set<String>& sequences, Size left, Size right, DoubleReal peptide_weight, const PeakSpectrum& CID_orig_spec, const PeakSpectrum& ETD_orig_spec, Map<DoubleReal, IonScore>& CID_nodes);
 
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                        /// reduces the given number of permuts by scoring the perumtations to the CID and ETD spec
 
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                        void reducePermuts_(std::set<String>& permuts, const PeakSpectrum& CID_orig_spec, const PeakSpectrum& ETD_orig_spec, DoubleReal prefix, DoubleReal suffix);
 
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                        /// fills the spectrum with c and z type ions
 
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                        void getETDSpectrum_(PeakSpectrum& spec, const String& sequence, Size /* charge */, DoubleReal prefix = 0.0, DoubleReal suffix = 0.0);
 
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                        /// estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec
 
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                        DoubleReal estimatePrecursorWeight_(const PeakSpectrum& ETD_spec, Size& charge);
 
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        };
 
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}
 
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#endif