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PepXMLFileMascot.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/ProteinIdentification.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
40 #include <OpenMS/FORMAT/XMLFile.h>
41 #include <OpenMS/CHEMISTRY/AASequence.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
61 PepXMLFileMascot();
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
86 String actual_title_;
87
89 String actual_sequence_;
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
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
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PepXMLFileMascot::fixed_modifications_
std::vector< String > fixed_modifications_
stores the fixed residue modifications
Definition: PepXMLFileMascot.h:101
XMLFile.h
XMLHandler.h
AASequence.h
OpenMS::PepXMLFileMascot::actual_title_
String actual_title_
Pointer to fill in protein identifications.
Definition: PepXMLFileMascot.h:86
OpenMS::PepXMLFileMascot::peptides_
std::map< String, std::vector< AASequence > > * peptides_
The peptides together with the spectrum title.
Definition: PepXMLFileMascot.h:95
OpenMS::PepXMLFileMascot::actual_sequence_
String actual_sequence_
The sequence of the actual peptide hit.
Definition: PepXMLFileMascot.h:89
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PepXMLFileMascot
Used to load Mascot PepXML files.
Definition: PepXMLFileMascot.h:54
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:151
OpenMS::PepXMLFileMascot::actual_aa_sequences_
std::vector< AASequence > actual_aa_sequences_
stores the actual peptide sequences
Definition: PepXMLFileMascot.h:98