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MascotXMLHandler.h
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32 // $Authors: Nico Pfeifer, Chris Bielow $
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34 
35 #ifndef OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
36 #define OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
37 
43 
44 #include <vector>
45 #include <boost/regex.hpp>
46 
47 namespace OpenMS
48 {
49  namespace Internal
50  {
54  class OPENMS_DLLAPI MascotXMLHandler :
55  public XMLHandler
56  {
57 public:
58 
60 
62  MascotXMLHandler(ProteinIdentification& protein_identification,
63  std::vector<PeptideIdentification>& identifications,
64  const String& filename,
65  std::map<String, std::vector<AASequence> >& peptides,
66  const RTMapping& rt_mapping = RTMapping(),
67  const String& scan_regex = "");
68 
70  virtual ~MascotXMLHandler();
71 
72  // Docu in base class
73  virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
74 
75  // Docu in base class
76  virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
77 
78  // Docu in base class
79  virtual void characters(const XMLCh * const chars, const XMLSize_t /*length*/);
80 
81  // Primary regex used to extract a scan number (for use by PepXMLFile)
82  static const String primary_scan_regex;
83 
84 private:
85 
87  std::vector<PeptideIdentification> & id_data_;
98  std::map<String, std::vector<AASequence> > & modified_peptides_;
99 
104 
106 
110  std::vector<boost::regex> scan_regex_;
111 
114  };
115 
116  } // namespace Internal
117 } // namespace OpenMS
118 
119 #endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
A more convenient string class.
Definition: String.h:56
String date_time_string_
Definition: MascotXMLHandler.h:93
StringList tags_open_
tracking the current XML tree
Definition: MascotXMLHandler.h:100
String minor_version_
Definition: MascotXMLHandler.h:103
String actual_title_
Definition: MascotXMLHandler.h:97
Base class for XML handlers.
Definition: XMLHandler.h:89
ProteinIdentification & protein_identification_
the protein identifications
Definition: MascotXMLHandler.h:86
ProteinHit actual_protein_hit_
Definition: MascotXMLHandler.h:88
Handler that is used for parsing MascotXML data.
Definition: MascotXMLHandler.h:54
Search parameters of the DB search.
Definition: ProteinIdentification.h:115
bool no_rt_error_
Error for missing RT information already reported?
Definition: MascotXMLHandler.h:113
String tag_
Definition: MascotXMLHandler.h:91
String major_version_
Definition: MascotXMLHandler.h:102
DateTime date_
Definition: MascotXMLHandler.h:92
Representation of a peptide hit.
Definition: PeptideHit.h:54
UInt actual_query_
Definition: MascotXMLHandler.h:94
std::vector< PeptideIdentification > & id_data_
the identifications (storing the peptide hits)
Definition: MascotXMLHandler.h:87
Representation of a protein hit.
Definition: ProteinHit.h:54
UInt peptide_identification_index_
Definition: MascotXMLHandler.h:90
String list.
Definition: StringList.h:56
std::vector< boost::regex > scan_regex_
List of possible Perl-style regular expressions used to extract the scan number (named group &quot;SCAN&quot;) ...
Definition: MascotXMLHandler.h:110
DateTime Class.
Definition: DateTime.h:55
String identifier_
Definition: MascotXMLHandler.h:96
const RTMapping & rt_mapping_
Definition: MascotXMLHandler.h:105
PeptideHit actual_peptide_hit_
Definition: MascotXMLHandler.h:89
ProteinIdentification::SearchParameters search_parameters_
Definition: MascotXMLHandler.h:95
Map< Size, Real > RTMapping
Definition: MascotXMLHandler.h:59
String character_buffer_
filled by MascotXMLHandler::characters
Definition: MascotXMLHandler.h:101
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
static const String primary_scan_regex
Definition: MascotXMLHandler.h:82
std::map< String, std::vector< AASequence > > & modified_peptides_
Definition: MascotXMLHandler.h:98

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:16 using doxygen 1.8.5