libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / HANDLERS / MascotXMLHandler.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Nico Pfeifer $
// $Authors: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
#define OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/Map.h>

#include <vector>
#include <boost/regex.hpp>

namespace OpenMS
{
  namespace Internal
  {
    /**
      @brief Handler that is used for parsing MascotXML data
    */
    class OPENMS_DLLAPI MascotXMLHandler :
      public XMLHandler
    {
public:

      typedef Map<Size, Real> RTMapping;

      /// Constructor
      MascotXMLHandler(ProteinIdentification& protein_identification,
                       std::vector<PeptideIdentification>& identifications,
                       const String& filename,
                       std::map<String, std::vector<AASequence> >& peptides,
                       const RTMapping& rt_mapping = RTMapping(),
                       const String& scan_regex = "");

      /// Destructor
      virtual ~MascotXMLHandler();

      // 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);

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

      // Primary regex used to extract a scan number (for use by PepXMLFile)
      static const String primary_scan_regex;

private:

      ProteinIdentification & protein_identification_; ///< the protein identifications
      std::vector<PeptideIdentification> & id_data_; ///< the identifications (storing the peptide hits)
      ProteinHit actual_protein_hit_;
      PeptideHit actual_peptide_hit_;
      UInt peptide_identification_index_;
      String tag_;
      DateTime date_;
      String date_time_string_;
      UInt actual_query_;
      ProteinIdentification::SearchParameters search_parameters_;
      String identifier_;
      String actual_title_;
      std::map<String, std::vector<AASequence> > & modified_peptides_;

      StringList tags_open_; ///< tracking the current XML tree
      String character_buffer_; ///< filled by MascotXMLHandler::characters
      String major_version_;
      String minor_version_;

      const RTMapping & rt_mapping_; ///< optional mapping of scan indices to RTs if scan numbers are given;
                                     ///< without this mapping, other sources of RT information are used (if available);
                                     ///< if all fails, there will be no RT information for peptide hits

      /// List of possible Perl-style regular expressions used to extract the scan number (named group "SCAN") or retention time (named group "RT"), and possibly precursor m/z (named group "MZ") from the "pep_scan_title" element
      std::vector<boost::regex> scan_regex_;

      /// Error for missing RT information already reported?
      bool no_rt_error_;
    };

  }   // namespace Internal
} // namespace OpenMS

#endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H