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Viewing changes to include/OpenMS/ANALYSIS/QUANTITATION/ItraqChannelExtractor.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/QUANTITATION/ItraqChannelExtractor.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: Chris Bielow $
 
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// $Authors: $
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_ANALYSIS_QUANTITATION_ITRAQCHANNELEXTRACTOR_H
 
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#define OPENMS_ANALYSIS_QUANTITATION_ITRAQCHANNELEXTRACTOR_H
 
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#include <vector>
 
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#include <OpenMS/KERNEL/ConsensusMap.h>
 
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#include <OpenMS/KERNEL/MSExperiment.h>
 
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#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
 
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namespace OpenMS
 
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{
 
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        /**
 
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                @brief [experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map
 
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                [experimental class]
 
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                This class supports 4 and 8 channel iTRAQ and will optionally do peak picking before the quantitation step.
 
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                Quantitation is done by adding all signals within a small delta around the expected m/z of each channel.
 
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                When all channels are found to be empty, the ConsensusFeature is not created.
 
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                No postprocessing is done here. Use ItraqQuantifier for that!
 
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                @htmlinclude OpenMS_ItraqChannelExtractor.parameters    
 
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        */
 
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        class OPENMS_DLLAPI ItraqChannelExtractor
 
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                : public DefaultParamHandler,
 
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                        public ItraqConstants
 
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        {
 
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        public:
 
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                typedef ItraqConstants::ChannelMapType ChannelMapType;
 
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                /// Constructor (assuming 4plex)
 
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                ItraqChannelExtractor();
 
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                /// Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES)
 
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                ItraqChannelExtractor(Int itraq_type);
 
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                /// Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param
 
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                ItraqChannelExtractor(Int itraq_type, const Param& param);
 
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                /// copy constructor
 
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                ItraqChannelExtractor(const ItraqChannelExtractor& cp);
 
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                /// assignment operator
 
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                ItraqChannelExtractor& operator = (const ItraqChannelExtractor& rhs);
 
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                /// @brief extracts the iTRAQ channels from the tandem MS data and stores intensity values in a consensus map
 
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                ///
 
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                /// @param ms_exp_data Raw data to read
 
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                /// @param consensus_map 
 
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                void run(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map);
 
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        protected:
 
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                void setDefaultParams_();
 
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                /// implemented for DefaultParamHandler
 
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                void updateMembers_();
 
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        private:
 
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                /// initialize
 
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                void init_();
 
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                /// set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
 
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                Int itraq_type_;
 
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                /// map the channel-name (eg 114) onto its description and the centroid mass
 
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                /// the channel-name is also the id-string in the mapList section of the ConsensusMap
 
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                ChannelMapType channel_map_;    
 
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        }; // !class
 
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} // !namespace
 
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#endif // OPENMS_ANALYSIS_QUANTITATION_ITRAQCHANNELEXTRACTOR_H
 
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