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hub / github.com/OpenMS/OpenMS / startElement

Method startElement

src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp:94–237  ·  view source on GitHub ↗

Source from the content-addressed store, hash-verified

92 = default;
93
94 void MzIdentMLHandler::startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes)
95 {
96 tag_ = sm_.convert(qname);
97 open_tags_.push_back(tag_);
98
99 static set<String> to_ignore;
100 if (to_ignore.empty())
101 {
102 to_ignore.insert("peptideSequence");
103 }
104
105 if (to_ignore.find(tag_) != to_ignore.end())
106 {
107 return;
108 }
109
110 //determine parent tag
111 String parent_tag;
112 if (open_tags_.size() > 1)
113 {
114 parent_tag = *(open_tags_.end() - 2);
115 }
116 String parent_parent_tag;
117 if (open_tags_.size() > 2)
118 {
119 parent_parent_tag = *(open_tags_.end() - 3);
120 }
121
122 if (tag_ == "cvParam")
123 {
124 static const XMLCh* s_value = xercesc::XMLString::transcode("value");
125 static const XMLCh* s_unit_accession = xercesc::XMLString::transcode("unitAccession");
126 static const XMLCh* s_cv_ref = xercesc::XMLString::transcode("cvRef");
127 //~ static const XMLCh* s_name = xercesc::XMLString::transcode("name");
128 static const XMLCh* s_accession = xercesc::XMLString::transcode("accession");
129
130 String value, unit_accession, cv_ref;
131 optionalAttributeAsString_(value, attributes, s_value);
132 optionalAttributeAsString_(unit_accession, attributes, s_unit_accession);
133 optionalAttributeAsString_(cv_ref, attributes, s_cv_ref);
134 handleCVParam_(parent_parent_tag, parent_tag, attributeAsString_(attributes, s_accession), /* attributeAsString_(attributes, s_name), value, */ attributes, cv_ref /*, unit_accession */);
135 return;
136 }
137
138 if (tag_ == "MzIdentML")
139 {
140 // TODO handle version with mzid 1.2 release
141 return;
142 }
143
144 if (tag_ == "Peptide")
145 {
146 // start new peptide
147 actual_peptide_ = AASequence();
148
149 // name attribute (opt)
150 String name;
151 if (optionalAttributeAsString_(name, attributes, "name"))

Callers

nothing calls this directly

Calls 15

attributeAsString_Function · 0.85
optionalAttributeAsInt_Function · 0.85
asBool_Function · 0.85
attributeAsInt_Function · 0.85
setPassThresholdMethod · 0.80
AASequenceClass · 0.50
convertMethod · 0.45
push_backMethod · 0.45

Tested by

no test coverage detected