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XTandemXMLFile.h
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34 
35 #ifndef OPENMS_FORMAT_XTANDEMXMLFILE_H
36 #define OPENMS_FORMAT_XTANDEMXMLFILE_H
37 
39 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
47  class String;
48  class ProteinIdentification;
49 
58  class OPENMS_DLLAPI XTandemXMLFile :
59  protected Internal::XMLHandler,
60  public Internal::XMLFile
61  {
62 public:
63 
66 
68  virtual ~XTandemXMLFile();
81  void load(const String & filename, ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data);
82 
83 
85  void setModificationDefinitionsSet(const ModificationDefinitionsSet & rhs);
86 
87 protected:
88 
89  // Docu in base class
90  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
91 
92  // Docu in base class
93  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
94 
95  // Docu in base class
96  void characters(const XMLCh * const chars, const XMLSize_t /*length*/);
97 
98  XTandemXMLFile(const XTandemXMLFile & rhs);
99 
100  XTandemXMLFile & operator=(const XTandemXMLFile & rhs);
101 
102 private:
103 
105 
106  // used to indicate that an protein tag is open
108 
109  // true if actual
111 
112  // peptide hits of one spectrum
114 
115  // protein hits, sorted by the id
117 
118  // id of the actual protein
120 
121  // charge of actual peptide
123 
124  // id of actual peptide
126 
127  // tag
129 
130  // actual start position of peptide in protein sequence
132 
133  // actual stop position of peptide in protein sequence
135 
136  // modification definitions
138 
139  };
140 
141 } // namespace OpenMS
142 
143 #endif // OPENMS_FORMAT_XTANDEMXMLFILE_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
String actual_protein_id_
Definition: XTandemXMLFile.h:119
A more convenient string class.
Definition: String.h:57
Map< UInt, std::vector< PeptideHit > > peptide_hits_
Definition: XTandemXMLFile.h:113
bool protein_open_
Definition: XTandemXMLFile.h:107
String tag_
Definition: XTandemXMLFile.h:128
Base class for XML handlers.
Definition: XMLHandler.h:99
ModificationDefinitionsSet mod_def_set_
Definition: XTandemXMLFile.h:137
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Used to load XTandemXML files.
Definition: XTandemXMLFile.h:58
bool is_description_
Definition: XTandemXMLFile.h:110
Int actual_charge_
Definition: XTandemXMLFile.h:122
Int actual_id_
Definition: XTandemXMLFile.h:125
UInt actual_start_
Definition: XTandemXMLFile.h:131
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
UInt actual_stop_
Definition: XTandemXMLFile.h:134
Map< String, ProteinHit > protein_hits_
Definition: XTandemXMLFile.h:116
ProteinIdentification * protein_identification_
Definition: XTandemXMLFile.h:104
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
int Int
Signed integer type.
Definition: Types.h:96
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:32 using doxygen 1.8.9.1