/usr/include/OpenMS/FORMAT/HANDLERS/UnimodXMLHandler.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;
// 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: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_HANDLERS_UNIMODXMLHANDLER_H
#define OPENMS_FORMAT_HANDLERS_UNIMODXMLHANDLER_H
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <vector>
namespace OpenMS
{
namespace Internal
{
/**
@brief Handler that is used for parsing XTandemXML data
*/
class OPENMS_DLLAPI UnimodXMLHandler :
public XMLHandler
{
public:
/// Default constructor
UnimodXMLHandler(std::vector<ResidueModification *> & mods, const String & filename);
/// Destructor
virtual ~UnimodXMLHandler();
// Docu in base class
void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
// Docu in base class
void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
// Docu in base class
void characters(const XMLCh * const chars, const XMLSize_t /*length*/);
private:
String tag_;
DoubleReal avge_mass_;
DoubleReal mono_mass_;
EmpiricalFormula diff_formula_;
EmpiricalFormula neutral_loss_diff_formula_;
bool was_valid_peptide_modification_;
std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;
ResidueModification * modification_;
std::vector<ResidueModification *> & modifications_;
std::vector<String> sites_;
std::vector<ResidueModification::Term_Specificity> term_specs_;
};
} // namespace Internal
} // namespace OpenMS
#endif // OPENMS_FORMAT_HANDLERS_XTANDEMXMLHANDLER_H
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