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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 
46 
47 #include <vector>
48 
49 namespace OpenMS
50 {
51  namespace Internal
52  {
56  class OPENMS_DLLAPI MascotXMLHandler :
57  public XMLHandler
58  {
59 public:
61  MascotXMLHandler(ProteinIdentification& protein_identification,
62  std::vector<PeptideIdentification>& identifications,
63  const String& filename,
64  std::map<String, std::vector<AASequence> >& peptides,
65  const SpectrumMetaDataLookup& lookup);
66 
68  virtual ~MascotXMLHandler();
69 
70  // Docu in base class
71  virtual void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname);
72 
73  // Docu in base class
74  virtual void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes);
75 
76  // Docu in base class
77  virtual void characters(const XMLCh* const chars, const XMLSize_t /*length*/);
78 
80  static std::vector<String> splitModificationBySpecifiedAA(String mod);
81 
82 private:
83 
85  std::vector<PeptideIdentification>& id_data_;
97  std::map<String, std::vector<AASequence> >& modified_peptides_;
98 
103 
104  // list of modifications, which cannot be set as fixed and needs
105  // to be removed, because added from mascot as variable modification
106  std::vector<String> remove_fixed_mods_;
107 
110 
113  };
114 
115  } // namespace Internal
116 } // namespace OpenMS
117 
118 #endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:62
A more convenient string class.
Definition: String.h:57
String date_time_string_
Definition: MascotXMLHandler.h:92
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
StringList tags_open_
tracking the current XML tree
Definition: MascotXMLHandler.h:99
String minor_version_
Definition: MascotXMLHandler.h:102
String actual_title_
Definition: MascotXMLHandler.h:96
Base class for XML handlers.
Definition: XMLHandler.h:110
ProteinIdentification & protein_identification_
the protein identifications
Definition: MascotXMLHandler.h:84
ProteinHit actual_protein_hit_
Definition: MascotXMLHandler.h:86
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Handler that is used for parsing MascotXML data.
Definition: MascotXMLHandler.h:56
Search parameters of the DB search.
Definition: ProteinIdentification.h:104
bool no_rt_error_
Error for missing RT information already reported?
Definition: MascotXMLHandler.h:112
String tag_
Definition: MascotXMLHandler.h:90
String major_version_
Definition: MascotXMLHandler.h:101
DateTime date_
Definition: MascotXMLHandler.h:91
PeptideEvidence actual_peptide_evidence_
Definition: MascotXMLHandler.h:88
Representation of a peptide hit.
Definition: PeptideHit.h:55
Representation of a peptide evidence.
Definition: PeptideEvidence.h:51
UInt actual_query_
Definition: MascotXMLHandler.h:93
std::vector< PeptideIdentification > & id_data_
the identifications (storing the peptide hits)
Definition: MascotXMLHandler.h:85
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
Representation of a protein hit.
Definition: ProteinHit.h:54
UInt peptide_identification_index_
Definition: MascotXMLHandler.h:89
DateTime Class.
Definition: DateTime.h:55
const SpectrumMetaDataLookup & lookup_
Helper object for looking up RT information.
Definition: MascotXMLHandler.h:109
String identifier_
Definition: MascotXMLHandler.h:95
PeptideHit actual_peptide_hit_
Definition: MascotXMLHandler.h:87
ProteinIdentification::SearchParameters search_parameters_
Definition: MascotXMLHandler.h:94
String character_buffer_
filled by MascotXMLHandler::characters
Definition: MascotXMLHandler.h:100
std::vector< String > remove_fixed_mods_
Definition: MascotXMLHandler.h:106
std::map< String, std::vector< AASequence > > & modified_peptides_
Definition: MascotXMLHandler.h:97

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:01 using doxygen 1.8.13