/usr/include/OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifier.h is in libopenms-dev 1.11.1-3.
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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.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_H
#define OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h>
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifierStatistics.h>
namespace OpenMS
{
/**
@brief Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes
the intensities for further processing.
@htmlinclude OpenMS_IsobaricQuantifier.parameters
*/
class OPENMS_DLLAPI IsobaricQuantifier :
public DefaultParamHandler
{
public:
/**
@brief Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).
@param quant_method The quantification method used for the data set to analyze.
*/
IsobaricQuantifier(const IsobaricQuantitationMethod* const quant_method);
/// Copy c'tor
IsobaricQuantifier(const IsobaricQuantifier& other);
/// Assignment operator
IsobaricQuantifier& operator=(const IsobaricQuantifier& rhs);
/**
@brief Using the raw isobaric intensities we apply isotope correction, normalization (using median).
@param consensus_map_in Raw isobaric channel intensities from channel extraction.
@param consensus_map_out Corrected and normalized isobaric channel ratios for peptides.
@throws Exception::FailedAPICall is least-squares fit fails
@throws Exception::InvalidParameter if parameter is invalid (e.g. reference_channel)
*/
void quantify(const ConsensusMap& consensus_map_in, ConsensusMap& consensus_map_out);
protected:
/// implemented for DefaultParamHandler
void setDefaultParams_();
/// implemented for DefaultParamHandler
void updateMembers_();
private:
/// Stats of current quantitation run.
IsobaricQuantifierStatistics stats_;
/// The quantification method used for the dataset to be analyzed.
const IsobaricQuantitationMethod* quant_method_;
/// Is true if isotope correction is enabled, false otherwise.
bool isotope_correction_enabled_;
/// Is true if normalization is enabled, false otherwise.
bool normalization_enabled_;
/// Computes labeling statistics (efficiency, number of empty scans,...)
void computeLabelingStatistics_(ConsensusMap& consensus_map_out);
};
} // namespace
#endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_H
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