PepXMLFileMascot.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
 
#pragma once
 
#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
{
  class OPENMS_DLLAPI PepXMLFileMascot :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:
 
    PepXMLFileMascot();
 
    void load(const String & filename, std::map<String, std::vector<AASequence> > & peptides);
 
protected:
 
    // Docu in base class
    void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
 
    // Docu in base class
    void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
 
    void matchModification_(double mass, String & modification_description);
 
 
 
    String actual_title_;
 
    String actual_sequence_;
 
    std::vector<std::pair<String, UInt> > actual_modifications_;
 
    std::map<String, std::vector<AASequence> > * peptides_;
 
    std::vector<AASequence> actual_aa_sequences_;
 
    std::vector<String> fixed_modifications_;
 
    std::vector<std::pair<String, double> > variable_modifications_;
  };
 
} // namespace OpenMS