OpenMS  3.0.0
PepXMLFileMascot.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer $
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34 
35 #pragma once
36 
40 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
54  class OPENMS_DLLAPI PepXMLFileMascot :
55  protected Internal::XMLHandler,
56  public Internal::XMLFile
57  {
58 public:
59 
62 
69  void load(const String & filename, std::map<String, std::vector<AASequence> > & peptides);
70 
71 protected:
72 
73  // Docu in base class
74  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
75 
76  // Docu in base class
77  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
78 
79  void matchModification_(double mass, String & modification_description);
80 
82 
83 
87 
90 
92  std::vector<std::pair<String, UInt> > actual_modifications_;
93 
95  std::map<String, std::vector<AASequence> > * peptides_;
96 
98  std::vector<AASequence> actual_aa_sequences_;
99 
101  std::vector<String> fixed_modifications_;
102 
104  std::vector<std::pair<String, double> > variable_modifications_;
106  };
107 
108 } // namespace OpenMS
109 
XMLFile.h
OpenMS::PepXMLFileMascot::variable_modifications_
std::vector< std::pair< String, double > > variable_modifications_
stores the variable residue modifications
Definition: PepXMLFileMascot.h:104
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::PepXMLFileMascot::actual_aa_sequences_
std::vector< AASequence > actual_aa_sequences_
stores the actual peptide sequences
Definition: PepXMLFileMascot.h:98
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PepXMLFileMascot
Used to load Mascot PepXML files.
Definition: PepXMLFileMascot.h:54
XMLHandler.h
OpenMS::PepXMLFileMascot::actual_title_
String actual_title_
Pointer to fill in protein identifications.
Definition: PepXMLFileMascot.h:86
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
ProteinIdentification.h
OpenMS::PepXMLFileMascot::peptides_
std::map< String, std::vector< AASequence > > * peptides_
The peptides together with the spectrum title.
Definition: PepXMLFileMascot.h:95
AASequence.h
OpenMS::PepXMLFileMascot::actual_modifications_
std::vector< std::pair< String, UInt > > actual_modifications_
The modifications of the actual peptide hit (position is 1-based)
Definition: PepXMLFileMascot.h:92
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::PepXMLFileMascot::actual_sequence_
String actual_sequence_
The sequence of the actual peptide hit.
Definition: PepXMLFileMascot.h:89
OpenMS::PepXMLFileMascot::fixed_modifications_
std::vector< String > fixed_modifications_
stores the fixed residue modifications
Definition: PepXMLFileMascot.h:101
PeptideIdentification.h