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| | NUMLDocument (unsigned int level=0, unsigned int version=0) |
| | Creates a new NUMLDocument, optionally with given values for the NUML Level and Version.
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| virtual | ~NUMLDocument () |
| | Destroys this NUMLDocument.
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| | NUMLDocument (const NUMLDocument &rhs) |
| | Copy constructor; creates a copy of this NUMLDocument.
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| virtual bool | accept (NUMLVisitor &v) const |
| | Accepts the given NUMLVisitor for this instance of NUMLDocument.
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| virtual NUMLDocument * | clone () const |
| | Creates and returns a deep copy of this NUMLDocument.
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| unsigned int | getNumOntologyTerms () const |
| | Get a the number of ontologyTerm objects in this NUMLDocument.
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| OntologyTerms * | getOntologyTerms () |
| | Returns the OntologyTerms object stored in this NUMLDocument.
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| const OntologyTerms * | getOntologyTerms () const |
| | Returns the OntologyTerms object stored in this NUMLDocument.
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| ResultComponents * | getResultComponents () |
| | Returns the ResultComponents object stored in this NUMLDocument.
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| const ResultComponents * | getResultComponents () const |
| | Returns the ResultComponents object stored in this NUMLDocument.
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| unsigned int | getNumResultComponents () const |
| | Get a the number of resultComponent objects in this NUMLDocument.
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| ResultComponent * | getResultComponent (unsigned int index) |
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| bool | setLevelAndVersion (unsigned int level, unsigned int version, bool strict=true) |
| | Sets the NUML Level and Version of this NUMLDocument instance, attempting to convert the model as needed.
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| OntologyTerm * | createOntologyTerm () |
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| ResultComponent * | createResultComponent () |
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| const NUMLError * | getError (unsigned int n) const |
| | Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model.
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| unsigned int | getNumErrors () const |
| | Returns the number of errors or warnings mencountered during parsing, consistency checking, or attempted translation of this model.
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| void | printErrors (std::ostream &stream=std::cerr) const |
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| virtual void | setParentNUMLObject (NMBase *sb) |
| | Sets the parent NUML object of this NUML object.
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| virtual void | setNUMLDocument (NUMLDocument *d) |
| | No-op; it is provided for consistency with the method available on other libNUML object classes but has no effect on NUMLDocument.
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| virtual NUMLTypeCode_t | getTypeCode () const |
| | Returns the libNUML type code for this NUML object.
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| virtual const std::string & | getElementName () const |
| | Returns the XML element name of this object, which for NUMLDocument, is always "numl".
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| NUMLErrorLog * | getErrorLog () |
| | Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
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| virtual LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces * | getNamespaces () const |
| | Returns a list of XML Namespaces associated with the XML content of this NUML document.
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| int | getElementPosition () const |
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| virtual void | writeElements (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Subclasses should override this method to write out their contained NUML objects as XML elements.
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| virtual | ~NMBase () |
| | Destroy this object.
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| NMBase & | operator= (const NMBase &orig) |
| | Assignment operator for NMBase.
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| virtual bool | accept (NUMLVisitor &v) const =0 |
| | Accepts the given NUMLVisitor for this instance of NMBase.
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| virtual NMBase * | clone () const =0 |
| | Creates and returns a deep copy of this NMBase object.
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| const std::string & | getMetaId () const |
| | Returns the value of the "metaid" attribute of this object.
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| std::string & | getMetaId () |
| | Returns the value of the "metaid" attribute of this object.
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| virtual const std::string & | getId () const |
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| virtual const std::string & | getName () const |
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| virtual LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces * | getNamespaces () const |
| | Returns the content of the "annotation" subelement of this object as a character string.
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| const NUMLDocument * | getNUMLDocument () const |
| | Returns the parent NUMLDocument object.
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| NUMLDocument * | getNUMLDocument () |
| | Returns the parent NUMLDocument object.
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| NMBase * | getParentNUMLObject () |
| | Returns the parent NUML object.
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| NMBase * | getAncestorOfType (NUMLTypeCode_t type) |
| | Returns the ancestor NUML object that corresponds to the given NUMLTypeCode_t.
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| unsigned int | getLine () const |
| | Returns the line number on which this object first appears in the XML representation of the NUML document.
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| unsigned int | getColumn () const |
| | Returns the column number on which this object first appears in the XML representation of the NUML document.
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| bool | isSetMetaId () const |
| | Predicate returning true or false depending on whether this object's "metaid" attribute has been set.
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| bool | isSetName () const |
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| int | setMetaId (const std::string &metaid) |
| | Sets the value of the "metaid" attribute of this object.
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| virtual int | setId (const std::string &sid) |
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| virtual void | setNUMLDocument (NUMLDocument *d) |
| | Sets the parent NUMLDocument of this NUML object.
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| virtual void | setParentNUMLObject (NMBase *sb) |
| | Sets the parent NUML object of this NUML object.
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| int | setNamespaces (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns) |
| | Sets the namespaces relevant of this NUML object.
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| int | unsetMetaId () |
| | Unsets the value of the "metaid" attribute of this NUML object.
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| unsigned int | getLevel () const |
| | Returns the NUML Level of the overall NUML document.
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| unsigned int | getVersion () const |
| | Returns the Version within the NUML Level of the overall NUML document.
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| virtual NUMLTypeCode_t | getTypeCode () const |
| | Returns the libnuml type code for this object.
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| bool | hasValidLevelVersionNamespaceCombination () |
| | Predicate returning true or false depending on whether this object's level/version and namespace values correspond to a valid NUML specification.
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| virtual const std::string & | getElementName () const =0 |
| | Returns the XML element name of this object.
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| char * | toNUML () |
| | Returns a string that consists of the partial NUML describing this object.
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| void | read (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
| | Reads (initializes) this NUML object by reading from XMLInputStream.
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| void | write (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Writes (serializes) this NUML object by writing it to XMLOutputStream.
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| virtual void | writeElements (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Subclasses should override this method to write out their contained NUML objects as XML elements.
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| virtual bool | hasRequiredAttributes () const |
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| virtual bool | hasRequiredElements () const |
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| void | setNUMLNamespaces (NUMLNamespaces *numlns) |
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| NUMLNamespaces * | getNUMLNamespaces () const |
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| void | syncAnnotation () |
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| bool | isSetNotes () const |
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| bool | isSetAnnotation () const |
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| virtual int | setAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
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| virtual int | setAnnotation (const std::string &annotation) |
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| virtual int | appendAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
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| virtual int | appendAnnotation (const std::string &annotation) |
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| int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
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| int | replaceTopLevelAnnotationElement (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
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| int | replaceTopLevelAnnotationElement (const std::string &annotation) |
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| int | setNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes) |
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| int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
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| int | appendNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes) |
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| int | appendNotes (const std::string ¬es) |
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| int | unsetNotes () |
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| int | unsetAnnotation () |
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| LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | getNotes () const |
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| std::string | getNotesString () const |
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| LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | getAnnotation () const |
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| std::string | getAnnotationString () const |
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| virtual NMBase * | createObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
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| virtual void | readAttributes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &attributes) |
| | Subclasses should override this method to read values from the given XMLAttributes set into their specific fields.
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| virtual void | writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Subclasses should override this method to write their XML attributes to the XMLOutputStream.
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| bool | conversion_errors (unsigned int errors) |
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| bool | hasStrictUnits () |
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| bool | hasStrictSBO () |
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| virtual void | writeXMLNS (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Subclasses should override this method to write their xmlns attriubutes (if any) to the XMLOutputStream.
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| | NMBase (const std::string &id="", const std::string &name="") |
| | Only subclasses may create NMBase objects.
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| | NMBase (unsigned int level, unsigned int version) |
| | Creates a new NMBase object with the given sboTerm.
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| | NMBase (NUMLNamespaces *numlns) |
| | Creates a new NMBase object with the given NUMLNamespaces.
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| | NMBase (const NMBase &orig) |
| | Copy constructor.
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| virtual NMBase * | createObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
| | Subclasses should override this method to create, store, and then return an NUML object corresponding to the next XMLToken in the XMLInputStream.
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| virtual bool | readOtherXML (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
| | Subclasses should override this method to read (and store) XHTML, MathML, etc.
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| virtual int | getElementPosition () const |
| | The NUML XML Schema is written such that the order of child elements is significant.
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| NUMLErrorLog * | getErrorLog () |
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| void | logError (unsigned int id, const unsigned int level=2, const unsigned int version=3, const std::string &details="") |
| | Convenience method for easily logging problems from within method implementations.
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| void | logUnknownAttribute (std::string attribute, const unsigned int level, const unsigned int version, const std::string element) |
| | Helper to log a common type of error.
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| void | logUnknownElement (const std::string element, const unsigned int level, const unsigned int version) |
| | Helper to log a common type of error.
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| void | logEmptyString (std::string attribute, const unsigned int level, const unsigned int version, std::string element) |
| | Helper to log a common type of error.
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| virtual void | readAttributes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &attributes) |
| | Subclasses should override this method to read values from the given XMLAttributes set into their specific fields.
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| virtual void | writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| | Subclasses should override this method to write their XML attributes to the XMLOutputStream.
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| void | checkOrderAndLogError (NMBase *object, int expected) |
| | Checks that NUML element has been read in the proper order.
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| void | checkNUMLListPopulated (NMBase *object) |
| | Checks that an NUML NUMLList element has been populated.
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| void | checkDefaultNamespace (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns, const std::string &elementName) |
| | Checks that the given default namespace in the given element is valid.
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| void | checkXHTML (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *) |
| | Checks that the XHTML is valid.
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| void | checkAnnotation () |
| | Checks the annotation does not declare an numl namespace.
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This represents the numl document that contains all information.