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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. More...
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virtual | ~NUMLDocument () |
| Destroys this NUMLDocument. More...
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| NUMLDocument (const NUMLDocument &rhs) |
| Copy constructor; creates a copy of this NUMLDocument. More...
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virtual bool | accept (NUMLVisitor &v) const |
| Accepts the given NUMLVisitor for this instance of NUMLDocument. More...
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virtual NUMLDocument * | clone () const |
| Creates and returns a deep copy of this NUMLDocument. More...
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unsigned int | getNumOntologyTerms () const |
| Get a the number of ontologyTerm objects in this NUMLDocument. More...
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OntologyTerms * | getOntologyTerms () |
| Returns the OntologyTerms object stored in this NUMLDocument. More...
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const OntologyTerms * | getOntologyTerms () const |
| Returns the OntologyTerms object stored in this NUMLDocument. More...
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ResultComponents * | getResultComponents () |
| Returns the ResultComponents object stored in this NUMLDocument. More...
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const ResultComponents * | getResultComponents () const |
| Returns the ResultComponents object stored in this NUMLDocument. More...
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unsigned int | getNumResultComponents () const |
| Get a the number of resultComponent objects in this NUMLDocument. More...
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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. More...
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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. More...
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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. More...
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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. More...
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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. More...
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virtual NUMLTypeCode_t | getTypeCode () const |
| Returns the libNUML type code for this NUML object. More...
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virtual const std::string & | getElementName () const |
| Returns the XML element name of this object, which for NUMLDocument, is always "numl" . More...
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NUMLErrorLog * | getErrorLog () |
| Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model. More...
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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. More...
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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. More...
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virtual | ~NMBase () |
| Destroy this object. More...
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NMBase & | operator= (const NMBase &orig) |
| Assignment operator for NMBase. More...
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virtual bool | accept (NUMLVisitor &v) const =0 |
| Accepts the given NUMLVisitor for this instance of NMBase. More...
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virtual NMBase * | clone () const =0 |
| Creates and returns a deep copy of this NMBase object. More...
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const std::string & | getMetaId () const |
| Returns the value of the "metaid" attribute of this object. More...
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std::string & | getMetaId () |
| Returns the value of the "metaid" attribute of this object. More...
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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. More...
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const NUMLDocument * | getNUMLDocument () const |
| Returns the parent NUMLDocument object. More...
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NUMLDocument * | getNUMLDocument () |
| Returns the parent NUMLDocument object. More...
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NMBase * | getParentNUMLObject () |
| Returns the parent NUML object. More...
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NMBase * | getAncestorOfType (NUMLTypeCode_t type) |
| Returns the ancestor NUML object that corresponds to the given NUMLTypeCode_t. More...
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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. More...
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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. More...
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bool | isSetMetaId () const |
| Predicate returning true or false depending on whether this object's "metaid" attribute has been set. More...
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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. More...
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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. More...
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virtual void | setParentNUMLObject (NMBase *sb) |
| Sets the parent NUML object of this NUML object. More...
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int | setNamespaces (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns) |
| Sets the namespaces relevant of this NUML object. More...
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int | unsetMetaId () |
| Unsets the value of the "metaid" attribute of this NUML object. More...
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unsigned int | getLevel () const |
| Returns the NUML Level of the overall NUML document. More...
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unsigned int | getVersion () const |
| Returns the Version within the NUML Level of the overall NUML document. More...
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virtual NUMLTypeCode_t | getTypeCode () const |
| Returns the libnuml type code for this object. More...
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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. More...
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virtual const std::string & | getElementName () const =0 |
| Returns the XML element name of this object. More...
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char * | toNUML () |
| Returns a string that consists of the partial NUML describing this object. More...
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void | read (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
| Reads (initializes) this NUML object by reading from XMLInputStream. More...
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void | write (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
| Writes (serializes) this NUML object by writing it to XMLOutputStream. More...
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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. More...
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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. More...
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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. More...
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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. More...
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| NMBase (const std::string &id="", const std::string &name="") |
| Only subclasses may create NMBase objects. More...
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| NMBase (unsigned int level, unsigned int version) |
| Creates a new NMBase object with the given sboTerm. More...
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| NMBase (NUMLNamespaces *numlns) |
| Creates a new NMBase object with the given NUMLNamespaces. More...
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| NMBase (const NMBase &orig) |
| Copy constructor. More...
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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. More...
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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. More...
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virtual int | getElementPosition () const |
| The NUML XML Schema is written such that the order of child elements is significant. More...
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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. More...
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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. More...
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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. More...
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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. More...
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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. More...
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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. More...
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void | checkOrderAndLogError (NMBase *object, int expected) |
| Checks that NUML element has been read in the proper order. More...
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void | checkNUMLListPopulated (NMBase *object) |
| Checks that an NUML NUMLList element has been populated. More...
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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. More...
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void | checkXHTML (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *) |
| Checks that the XHTML is valid. More...
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void | checkAnnotation () |
| Checks the annotation does not declare an numl namespace. More...
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This represents the numl document that contains all information.