| OpenMS 2.5.0

UnimodXMLHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
38 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
39 #include <OpenMS/CHEMISTRY/ResidueModification.h>
40
41 #include <vector>
42
43 namespace OpenMS
44 {
45 namespace Internal
46 {
51 class OPENMS_DLLAPI UnimodXMLHandler :
52 public XMLHandler
53 {
54 public:
56 UnimodXMLHandler(std::vector<ResidueModification*>& mods, const String& filename);
57
59 ~UnimodXMLHandler() override;
60
61 // Docu in base class
62 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
63
64 // Docu in base class
65 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
66
67 // Docu in base class
68 void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
69
70 private:
71
72 String tag_;
73
74 double avge_mass_;
75
76 double mono_mass_;
77
78 EmpiricalFormula diff_formula_;
79
80 EmpiricalFormula neutral_loss_diff_formula_;
81
82 bool was_valid_peptide_modification_;
83 std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;
84
85 ResidueModification* modification_;
86
87 std::vector<ResidueModification*>& modifications_;
88
89 std::vector<char> sites_;
90
91 std::vector<ResidueModification::TermSpecificity> term_specs_;
92 };
93
94 } // namespace Internal
95 } // namespace OpenMS
96
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::UnimodXMLHandler::tag_
String tag_
Definition: UnimodXMLHandler.h:72
XMLHandler.h
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::Internal::UnimodXMLHandler::avge_mass_
double avge_mass_
Definition: UnimodXMLHandler.h:74
OpenMS::Internal::UnimodXMLHandler::diff_formula_
EmpiricalFormula diff_formula_
Definition: UnimodXMLHandler.h:78
OpenMS::Internal::UnimodXMLHandler::sites_
std::vector< char > sites_
Definition: UnimodXMLHandler.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Internal::UnimodXMLHandler::was_valid_peptide_modification_
bool was_valid_peptide_modification_
Definition: UnimodXMLHandler.h:82
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
EmpiricalFormula.h
OpenMS::Internal::UnimodXMLHandler::modification_
ResidueModification * modification_
Definition: UnimodXMLHandler.h:85
OpenMS::Internal::UnimodXMLHandler
Handler that is used for parsing XTandemXML data.
Definition: UnimodXMLHandler.h:51
OpenMS::Internal::UnimodXMLHandler::mono_mass_
double mono_mass_
Definition: UnimodXMLHandler.h:76
OpenMS::Internal::UnimodXMLHandler::neutral_loss_diff_formula_
EmpiricalFormula neutral_loss_diff_formula_
Definition: UnimodXMLHandler.h:80
OpenMS::Internal::UnimodXMLHandler::term_specs_
std::vector< ResidueModification::TermSpecificity > term_specs_
Definition: UnimodXMLHandler.h:91
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::Internal::UnimodXMLHandler::neutral_loss_diff_formulas_
std::vector< EmpiricalFormula > neutral_loss_diff_formulas_
Definition: UnimodXMLHandler.h:83
ResidueModification.h
OpenMS::Internal::UnimodXMLHandler::modifications_
std::vector< ResidueModification * > & modifications_
Definition: UnimodXMLHandler.h:87