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PepXMLFileMascot.h
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34 
35 #ifndef OPENMS_FORMAT_PEPXMLFILEMASCOT_H
36 #define OPENMS_FORMAT_PEPXMLFILEMASCOT_H
37 
41 #include <OpenMS/FORMAT/XMLFile.h>
43 
44 #include <vector>
45 
46 namespace OpenMS
47 {
55  class OPENMS_DLLAPI PepXMLFileMascot :
56  protected Internal::XMLHandler,
57  public Internal::XMLFile
58  {
59 public:
60 
63 
70  void load(const String & filename, std::map<String, std::vector<AASequence> > & peptides);
71 
72 protected:
73 
74  // Docu in base class
75  virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
76 
77  // Docu in base class
78  virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
79 
80  void matchModification_(double mass, String & modification_description);
81 
83 
84 
88 
91 
93  std::vector<std::pair<String, UInt> > actual_modifications_;
94 
96  std::map<String, std::vector<AASequence> > * peptides_;
97 
99  std::vector<AASequence> actual_aa_sequences_;
100 
102  std::vector<String> fixed_modifications_;
103 
105  std::vector<std::pair<String, double> > variable_modifications_;
107  };
108 
109 } // namespace OpenMS
110 
111 #endif // OPENMS_FORMAT_PEPXMLFILEMASCOT_H
String actual_title_
Pointer to fill in protein identifications.
Definition: PepXMLFileMascot.h:87
A more convenient string class.
Definition: String.h:57
std::vector< String > fixed_modifications_
stores the fixed residue modifications
Definition: PepXMLFileMascot.h:102
Base class for XML handlers.
Definition: XMLHandler.h:110
std::vector< std::pair< String, double > > variable_modifications_
stores the variable residue modifications
Definition: PepXMLFileMascot.h:105
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< std::pair< String, UInt > > actual_modifications_
The modifications of the actual peptide hit (position is 1-based)
Definition: PepXMLFileMascot.h:93
std::vector< AASequence > actual_aa_sequences_
stores the actual peptide sequences
Definition: PepXMLFileMascot.h:99
Used to load Mascot PepXML files.
Definition: PepXMLFileMascot.h:55
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
String actual_sequence_
The sequence of the actual peptide hit.
Definition: PepXMLFileMascot.h:90
std::map< String, std::vector< AASequence > > * peptides_
The peptides together with the spectrum title.
Definition: PepXMLFileMascot.h:96

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13