ProtXMLFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Chris Bielow $
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#pragma once

#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>

#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI ProtXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    typedef ProteinIdentification::ProteinGroup ProteinGroup;

    ProtXMLFile();

    void load(const String & filename, ProteinIdentification & protein_ids, PeptideIdentification & peptide_ids);

    void store(const String & filename, const ProteinIdentification & protein_ids, const PeptideIdentification & peptide_ids, const String & document_id = "");

protected:

    void resetMembers_();

    void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;

    void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;

    void registerProtein_(const String & protein_name);

    void matchModification_(const double mass, const String & origin, String & modification_description);


    ProteinIdentification * prot_id_;
    PeptideIdentification * pep_id_;
    PeptideHit * pep_hit_;
    ProteinGroup protein_group_;


  };

} // namespace OpenMS