XTandemXMLFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_FORMAT_XTANDEMXMLFILE_H
#define OPENMS_FORMAT_XTANDEMXMLFILE_H

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

#include <vector>

namespace OpenMS
{
  class String;
  class ProteinIdentification;

  class OPENMS_DLLAPI XTandemXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    XTandemXMLFile();

    virtual ~XTandemXMLFile();
    void load(const String & filename, ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data);


    void setModificationDefinitionsSet(const ModificationDefinitionsSet & rhs);

protected:

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

    // Docu in base class
    void characters(const XMLCh * const chars, const XMLSize_t /*length*/);

    XTandemXMLFile(const XTandemXMLFile & rhs);

    XTandemXMLFile & operator=(const XTandemXMLFile & rhs);

private:

    ProteinIdentification * protein_identification_;

    // used to indicate that an protein tag is open
    bool protein_open_;

    // true if actual
    bool is_description_;

    // peptide hits of one spectrum
    Map<UInt, std::vector<PeptideHit> > peptide_hits_;

    // protein hits, sorted by the id
    Map<String, ProteinHit> protein_hits_;

    // id of the actual protein
    String actual_protein_id_;

    // charge of actual peptide
    Int actual_charge_;

    // id of actual peptide
    Int actual_id_;

    // tag
    String tag_;

    // actual start position of peptide in protein sequence
    UInt actual_start_;

    // actual stop position of peptide in protein sequence
    UInt actual_stop_;

    // modification definitions
    ModificationDefinitionsSet mod_def_set_;

  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_XTANDEMXMLFILE_H