OpenMS  3.0.0
UnimodXMLHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
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 
73 
74  double avge_mass_;
75 
76  double mono_mass_;
77 
79 
80  std::vector<EmpiricalFormula> neutral_loss_diff_formula_;
81 
83  std::vector<std::vector<EmpiricalFormula>> neutral_loss_diff_formulas_;
84  std::vector<double> neutral_loss_mono_masses_;
85  std::vector<double> neutral_loss_avg_masses_;
86 
88 
89  std::vector<ResidueModification*>& modifications_;
90 
91  std::vector<char> sites_;
92 
93  std::vector<ResidueModification::TermSpecificity> term_specs_;
94  };
95 
96  } // namespace Internal
97 } // namespace OpenMS
OpenMS::Internal::UnimodXMLHandler::neutral_loss_mono_masses_
std::vector< double > neutral_loss_mono_masses_
Definition: UnimodXMLHandler.h:84
OpenMS::ResidueModification
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:78
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::Internal::UnimodXMLHandler::mono_mass_
double mono_mass_
Definition: UnimodXMLHandler.h:76
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::UnimodXMLHandler::diff_formula_
EmpiricalFormula diff_formula_
Definition: UnimodXMLHandler.h:78
XMLHandler.h
OpenMS::Internal::UnimodXMLHandler::modification_
ResidueModification * modification_
Definition: UnimodXMLHandler.h:87
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::UnimodXMLHandler::neutral_loss_diff_formula_
std::vector< EmpiricalFormula > neutral_loss_diff_formula_
Definition: UnimodXMLHandler.h:80
OpenMS::Internal::UnimodXMLHandler::sites_
std::vector< char > sites_
Definition: UnimodXMLHandler.h:91
OpenMS::Internal::UnimodXMLHandler::modifications_
std::vector< ResidueModification * > & modifications_
Definition: UnimodXMLHandler.h:89
OpenMS::Internal::UnimodXMLHandler
Handler that is used for parsing XTandemXML data.
Definition: UnimodXMLHandler.h:51
EmpiricalFormula.h
OpenMS::Internal::UnimodXMLHandler::neutral_loss_avg_masses_
std::vector< double > neutral_loss_avg_masses_
Definition: UnimodXMLHandler.h:85
OpenMS::Internal::UnimodXMLHandler::tag_
String tag_
Definition: UnimodXMLHandler.h:72
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
ResidueModification.h
OpenMS::Internal::UnimodXMLHandler::avge_mass_
double avge_mass_
Definition: UnimodXMLHandler.h:74
OpenMS::Internal::UnimodXMLHandler::was_valid_peptide_modification_
bool was_valid_peptide_modification_
Definition: UnimodXMLHandler.h:82
OpenMS::Internal::UnimodXMLHandler::term_specs_
std::vector< ResidueModification::TermSpecificity > term_specs_
Definition: UnimodXMLHandler.h:93
OpenMS::Internal::UnimodXMLHandler::neutral_loss_diff_formulas_
std::vector< std::vector< EmpiricalFormula > > neutral_loss_diff_formulas_
Definition: UnimodXMLHandler.h:83