MascotXMLHandler.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, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
 
#include <vector>
 
namespace OpenMS
{
  namespace Internal
  {
    class OPENMS_DLLAPI MascotXMLHandler :
      public XMLHandler
    {
public:
      MascotXMLHandler(ProteinIdentification& protein_identification,
                       PeptideIdentificationList& identifications,
                       const std::string& filename,
                       std::map<std::string, std::vector<AASequence> >& peptides,
                       const SpectrumMetaDataLookup& lookup);
 
      ~MascotXMLHandler() override;
 
      // 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;
 
      // Docu in base class
      void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
      
      static std::vector<std::string> splitModificationBySpecifiedAA(const std::string& mod);
 
private:
 
      ProteinIdentification& protein_identification_; 
      PeptideIdentificationList& id_data_; 
      ProteinHit actual_protein_hit_;
      PeptideHit actual_peptide_hit_;
      PeptideEvidence actual_peptide_evidence_;
      UInt peptide_identification_index_;
      std::string tag_;
      DateTime date_;
      std::string date_time_string_;
      UInt actual_query_;
      ProteinIdentification::SearchParameters search_parameters_;
      std::string identifier_;
      std::string actual_title_;
      std::map<std::string, std::vector<AASequence> >& modified_peptides_;
 
      StringList tags_open_; 
      std::string character_buffer_; 
      std::string major_version_;
      std::string minor_version_;
      
      // list of modifications, which cannot be set as fixed and needs
      // to be removed, because added from mascot as variable modification
      std::vector<std::string> remove_fixed_mods_;
 
      const SpectrumMetaDataLookup& lookup_;
 
      bool no_rt_error_;
    };
 
  } // namespace Internal
} // namespace OpenMS