PepXMLFileMascot.h

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// $Maintainer: Nico Pfeifer $
// $Authors: Nico Pfeifer $
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#ifndef OPENMS_FORMAT_PEPXMLFILEMASCOT_H
#define OPENMS_FORMAT_PEPXMLFILEMASCOT_H

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

    // Docu in base class
    virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);

    void matchModification_(DoubleReal 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, DoubleReal> > variable_modifications_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_PEPXMLFILEMASCOT_H