/usr/include/OpenMS/ANALYSIS/ID/IDRipper.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:
// * 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;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Immanuel Luhn $
// $Authors: Immanuel Luhn $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_ID_IDRIPPER_H
#define OPENMS_ANALYSIS_ID_IDRIPPER_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
namespace OpenMS
{
/**
@brief Ripping protein/peptide identification according their file origin.
Helper class, which is used by @ref TOPP_ProteinQuantifier. See there for further documentation.
@htmlinclude OpenMS_IDRipper.parameters
@ingroup Analysis_ID
*/
class OPENMS_DLLAPI IDRipper :
public DefaultParamHandler
{
public:
/// Default constructor
IDRipper();
/// Desctructor
virtual ~IDRipper();
/**
@brief Ripping protein/peptide identification according their file origin
Iteration over all @p PeptideIdentification. For each annotated file origin create a map entry and store the
respective @p PeptideIdentification and @p ProteinIdentification.
@param ripped Contains the protein identification and peptide identification for each file origin annotated in proteins and peptides
@param proteins Peptide identification annotated with file origin
@param peptides Protein identification
*/
void rip(std::map<String, std::pair<std::vector<ProteinIdentification>, std::vector<PeptideIdentification> > > & ripped, std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides);
private:
//Not implemented
/// Copy constructor
IDRipper(const IDRipper & rhs);
// Not implemented
/// Assignment
IDRipper & operator=(const IDRipper & rhs);
/// helper function, extracts all protein hits that match the protein accession
void getProteinHits_(std::vector<ProteinHit> & result, const std::vector<ProteinHit> & protein_hits, const std::vector<String> & protein_accessions);
/// helper function, returns the string representation of the peptide hit accession
void getProteinAccessions_(std::vector<String> & result, const std::vector<PeptideHit> & peptide_hits);
/// helper function, returns the protein identification for the given peptide identification based on the same identifier
void getProteinIdentification_(ProteinIdentification & result, PeptideIdentification pep_ident, std::vector<ProteinIdentification> & prot_idents);
};
} // namespace OpenMS
#endif // OPENMS_ANALYSIS_ID_IDRIPPER_H
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