OMSSAXMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
 
#include <vector>
 
namespace OpenMS
{
  class String;
  class ModificationsDB;
 
  class OPENMS_DLLAPI OMSSAXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:
 
    OMSSAXMLFile();
 
    ~OMSSAXMLFile() override;
    void load(const String& filename,
              ProteinIdentification& protein_identification,
              std::vector<PeptideIdentification>& id_data,
              bool load_proteins = true,
              bool load_empty_hits = true);
 
    void setModificationDefinitionsSet(const ModificationDefinitionsSet& rhs);
 
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;
 
    // Docu in base class
    void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
 
private:
 
    OMSSAXMLFile(const OMSSAXMLFile& rhs);
 
    OMSSAXMLFile& operator=(const OMSSAXMLFile& rhs);
 
    void readMappingFile_();
 
    std::vector<PeptideIdentification>* peptide_identifications_;
 
    ProteinHit actual_protein_hit_;
 
    PeptideHit actual_peptide_hit_;
 
    PeptideEvidence actual_peptide_evidence_;
 
    std::vector<PeptideEvidence> actual_peptide_evidences_;
 
    PeptideIdentification actual_peptide_id_;
 
    ProteinIdentification actual_protein_id_;
 
    String tag_;
 
    UInt actual_mod_site_;
 
    String actual_mod_type_;
 
    std::vector<std::pair<UInt, String> > modifications_;
 
    bool load_proteins_;
 
    bool load_empty_hits_;
 
    Map<UInt, std::vector<const ResidueModification*> > mods_map_;
 
    Map<String, UInt> mods_to_num_;
 
    ModificationDefinitionsSet mod_def_set_;
  };
 
} // namespace OpenMS