/usr/include/OpenMS/FORMAT/PepXMLFileMascot.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,
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Nico Pfeifer $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_PEPXMLFILEMASCOT_H
#define OPENMS_FORMAT_PEPXMLFILEMASCOT_H
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <vector>
namespace OpenMS
{
/**
@brief Used to load Mascot PepXML files
A schema for this format can be found at http://www.matrixscience.com/xmlns/schema/pepXML_v18/pepXML_v18.xsd.
@ingroup FileIO
*/
class OPENMS_DLLAPI PepXMLFileMascot :
protected Internal::XMLHandler,
public Internal::XMLFile
{
public:
/// Constructor
PepXMLFileMascot();
/**
@brief Loads peptide sequences with modifications out of a PepXML file
@exception Exception::FileNotFound is thrown if the file could not be opened
@exception Exception::ParseError is thrown if an error occurs during parsing
*/
void load(const String & filename, std::map<String, std::vector<AASequence> > & peptides);
protected:
// Docu in base class
virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
// Docu in base class
virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
void matchModification_(DoubleReal mass, String & modification_description);
/// @name members for loading data
//@{
/// Pointer to fill in protein identifications
/// The title of the actual spectrum
String actual_title_;
/// The sequence of the actual peptide hit
String actual_sequence_;
/// The modifications of the actual peptide hit (position is 1-based)
std::vector<std::pair<String, UInt> > actual_modifications_;
/// The peptides together with the spectrum title
std::map<String, std::vector<AASequence> > * peptides_;
/// stores the actual peptide sequences
std::vector<AASequence> actual_aa_sequences_;
/// stores the fixed residue modifications
std::vector<String> fixed_modifications_;
/// stores the variable residue modifications
std::vector<std::pair<String, DoubleReal> > variable_modifications_;
//@}
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_PEPXMLFILEMASCOT_H
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