/usr/include/OpenMS/ANALYSIS/QUANTITATION/ProteinInference.h is in libopenms-dev 1.11.1-5.
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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:
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// 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"
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_QUANTITATION_PROTEININFERENCE_H
#define OPENMS_ANALYSIS_QUANTITATION_PROTEININFERENCE_H
#include <vector>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/Peak2D.h>
namespace OpenMS
{
/**
@brief [experimental class] given a peptide quantitation, infer corresponding protein quantities
Infers protein ratios from peptide ratios (currently using unique peptides only).
Use the IDMapper class to add protein and peptide information to a
quantitative ConsensusMap prior to this step.
*/
class OPENMS_DLLAPI ProteinInference
{
public:
typedef Peak2D::IntensityType IntensityType;
/// Constructor
ProteinInference();
/// copy constructor
ProteinInference(const ProteinInference & cp);
/// assignment operator
ProteinInference & operator=(const ProteinInference & rhs);
/**
@brief given a peptide quantitation, infer corresponding protein quantities
Infers protein ratios from peptide ratios (currently using unique peptides only).
Use the IDMapper class to add protein and peptide information to a
quantitative ConsensusMap prior to this step.
@param consensus_map Peptide quantitation with ProteinIdentifications attached, where
Protein quantitation will be attached
@param reference_map Index of (iTRAQ) reference channel within the consensus map
@throws Exception::MissingInformation if Protein/PeptideIdentifications are missing
*/
void infer(ConsensusMap & consensus_map,
const UInt reference_map);
protected:
void infer_(ConsensusMap & consensus_map,
const size_t protein_idenfication_index,
const UInt reference_map);
bool sortByUnique_(std::vector<PeptideHit> & peptide_hits_local, const bool is_higher_score_better);
}; // !class
} // !namespace
#endif // OPENMS_ANALYSIS_QUANTITATION_PROTEININFERENCE_H
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