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OpenMS
2.6.0
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45 class ControlledVocabulary;
98 bool locateTerm(
const String & path,
const CVTerm & parsed_term)
const;
101 void setTag(
const String & tag);
104 void setAccessionAttribute(
const String & accession);
107 void setNameAttribute(
const String & name);
110 void setValueAttribute(
const String & value);
120 void setCheckTermValueTypes(
bool check);
129 void setCheckUnits(
bool check);
132 void setUnitAccessionAttribute(
const String & accession);
135 void setUnitNameAttribute(
const String & name);
140 void startElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname,
const xercesc::Attributes & attributes)
override;
143 void endElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname)
override;
146 void characters(
const XMLCh *
const chars,
const XMLSize_t )
override;
149 virtual String getPath_(
UInt remove_from_end = 0)
const;
152 virtual void getCVTerm_(
const xercesc::Attributes & attributes,
CVTerm & parsed_term);
159 virtual void handleTerm_(
const String & path,
const CVTerm & parsed_term);
StringList warnings_
Validation warnings.
Definition: SemanticValidator.h:171
Base class for TOPP applications.
Definition: TOPPBase.h:144
bool has_unit_accession
Definition: SemanticValidator.h:79
Used to load CvMapping files.
Definition: CVMappingFile.h:58
bool validate(const std::vector< std::string > &file_names)
Validates the given files against the XML schema (if available)
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
Base class for XML handlers.
Definition: XMLHandler.h:151
String name
Definition: SemanticValidator.h:75
StringList errors_
Validation errors.
Definition: SemanticValidator.h:168
Map< String, Map< String, Map< String, UInt > > > fulfilled_
Definition: SemanticValidator.h:182
String cv_tag_
Definition: SemanticValidator.h:187
void load(const String &filename, CVMappings &cv_mappings, bool strip_namespaces=false)
loads CvMappings from the given file
bool check_term_value_types_
Definition: SemanticValidator.h:193
A more convenient string class.
Definition: String.h:59
bool has_unit_name
Definition: SemanticValidator.h:81
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
String name_att_
Definition: SemanticValidator.h:189
String value
Definition: SemanticValidator.h:76
Representation of controlled vocabulary mapping rules (for PSI formats)
Definition: CVMappings.h:56
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
void loadFromOBO(const String &name, const String &filename)
Loads the CV from an OBO file.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Map< String, std::vector< CVMappingRule > > rules_
Rules (location => rule)
Definition: SemanticValidator.h:177
Semantically validates XML files using CVMappings and a ControlledVocabulary.
Definition: SemanticValidator.h:55
String unit_name_att_
Definition: SemanticValidator.h:192
bool has_value
Definition: SemanticValidator.h:77
bool check_units_
Definition: SemanticValidator.h:194
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Representation of a parsed CV term.
Definition: SemanticValidator.h:72
const ControlledVocabulary & cv_
Reference to the CVs.
Definition: SemanticValidator.h:165
const CVMappings & mapping_
Reference to the mappings.
Definition: SemanticValidator.h:162
String value_att_
Definition: SemanticValidator.h:190
String accession
Definition: SemanticValidator.h:74
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
String unit_accession_att_
Definition: SemanticValidator.h:191
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
String unit_accession
Definition: SemanticValidator.h:78
StringList open_tags_
List of open tags.
Definition: SemanticValidator.h:174
String unit_name
Definition: SemanticValidator.h:80
String accession_att_
Definition: SemanticValidator.h:188