libNuML 1.1.1
Library for reading / writing NuML documents
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ontology terms store information about what individual elements represents More...
#include <OntologyTerm.h>
Public Member Functions | |
OntologyTerm (unsigned int level, unsigned int version) | |
Creates an new OntologyTerm using the given NUML level and version values. More... | |
OntologyTerm (NUMLNamespaces *numlns) | |
Creates a new OntologyTerm using the given NUMLNamespaces object numlns . More... | |
virtual bool | accept (NUMLVisitor &v) const |
Accepts the given NUMLVisitor for this instance of OntologyTerm. More... | |
virtual OntologyTerm * | clone () const |
Creates and returns a deep copy of this OntologyTerm. More... | |
const std::string & | getId () const |
Returns the value of the "id" attribute of this OntologyTerm. More... | |
const std::string & | getTerm () const |
Returns the value of the "term" attribute of this OntologyTerm. More... | |
const std::string & | getSourceTermId () const |
Returns the value of the "sourceTermId" attribute of this OntologyTerm. More... | |
const std::string & | getOntologyURI () const |
Returns the value of the "ontologyURI" attribute of this OntologyTerm. More... | |
virtual | ~OntologyTerm () |
int | setId (const std::string &sid) |
int | setTerm (const std::string &term) |
Sets the value of the "term" attribute of this NUML object. More... | |
int | setSourceTermId (const std::string &sourceTermId) |
Sets the value of the "sourceTermId" attribute of this NUML object. More... | |
int | setOntologyURI (const std::string &ontologyURI) |
Sets the value of the "ontologyURI" attribute of this NUML object. More... | |
virtual NUMLTypeCode_t | getTypeCode () const |
Returns the libNUML type code for this NUML object. More... | |
virtual const std::string & | getElementName () const |
Returns the XML element name of this object, which for OntologyTerm, is always "ontologyTerm" . More... | |
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... | |
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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virtual | ~NMBase () |
Destroy this object. More... | |
NMBase & | operator= (const NMBase &orig) |
Assignment operator for NMBase. More... | |
virtual bool | accept (NUMLVisitor &v) const =0 |
Accepts the given NUMLVisitor for this instance of NMBase. More... | |
virtual NMBase * | clone () const =0 |
Creates and returns a deep copy of this NMBase object. More... | |
const std::string & | getMetaId () const |
Returns the value of the "metaid" attribute of this object. More... | |
std::string & | getMetaId () |
Returns the value of the "metaid" attribute of this object. More... | |
virtual const std::string & | getId () const |
virtual const std::string & | getName () const |
virtual LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces * | getNamespaces () const |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
const NUMLDocument * | getNUMLDocument () const |
Returns the parent NUMLDocument object. More... | |
NUMLDocument * | getNUMLDocument () |
Returns the parent NUMLDocument object. More... | |
NMBase * | getParentNUMLObject () |
Returns the parent NUML object. More... | |
NMBase * | getAncestorOfType (NUMLTypeCode_t type) |
Returns the ancestor NUML object that corresponds to the given NUMLTypeCode_t. More... | |
unsigned int | getLine () const |
Returns the line number on which this object first appears in the XML representation of the NUML document. More... | |
unsigned int | getColumn () const |
Returns the column number on which this object first appears in the XML representation of the NUML document. More... | |
bool | isSetMetaId () const |
Predicate returning true or false depending on whether this object's "metaid" attribute has been set. More... | |
bool | isSetName () const |
int | setMetaId (const std::string &metaid) |
Sets the value of the "metaid" attribute of this object. More... | |
virtual int | setId (const std::string &sid) |
virtual void | setNUMLDocument (NUMLDocument *d) |
Sets the parent NUMLDocument of this NUML object. More... | |
virtual void | setParentNUMLObject (NMBase *sb) |
Sets the parent NUML object of this NUML object. More... | |
int | setNamespaces (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns) |
Sets the namespaces relevant of this NUML object. More... | |
int | unsetMetaId () |
Unsets the value of the "metaid" attribute of this NUML object. More... | |
unsigned int | getLevel () const |
Returns the NUML Level of the overall NUML document. More... | |
unsigned int | getVersion () const |
Returns the Version within the NUML Level of the overall NUML document. More... | |
virtual NUMLTypeCode_t | getTypeCode () const |
Returns the libnuml type code for this object. More... | |
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... | |
virtual const std::string & | getElementName () const =0 |
Returns the XML element name of this object. More... | |
char * | toNUML () |
Returns a string that consists of the partial NUML describing this object. More... | |
void | read (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
Reads (initializes) this NUML object by reading from XMLInputStream. More... | |
void | write (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
Writes (serializes) this NUML object by writing it to XMLOutputStream. More... | |
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... | |
virtual bool | hasRequiredAttributes () const |
virtual bool | hasRequiredElements () const |
void | setNUMLNamespaces (NUMLNamespaces *numlns) |
NUMLNamespaces * | getNUMLNamespaces () const |
void | syncAnnotation () |
bool | isSetNotes () const |
bool | isSetAnnotation () const |
virtual int | setAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
virtual int | setAnnotation (const std::string &annotation) |
virtual int | appendAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
virtual int | appendAnnotation (const std::string &annotation) |
int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
int | replaceTopLevelAnnotationElement (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation) |
int | replaceTopLevelAnnotationElement (const std::string &annotation) |
int | setNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes) |
int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
int | appendNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes) |
int | appendNotes (const std::string ¬es) |
int | unsetNotes () |
int | unsetAnnotation () |
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | getNotes () const |
std::string | getNotesString () const |
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | getAnnotation () const |
std::string | getAnnotationString () const |
Protected Member Functions | |
OntologyTerm () | |
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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... | |
NMBase (const std::string &id="", const std::string &name="") | |
Only subclasses may create NMBase objects. More... | |
NMBase (unsigned int level, unsigned int version) | |
Creates a new NMBase object with the given sboTerm. More... | |
NMBase (NUMLNamespaces *numlns) | |
Creates a new NMBase object with the given NUMLNamespaces. More... | |
NMBase (const NMBase &orig) | |
Copy constructor. More... | |
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... | |
virtual bool | readOtherXML (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream) |
Subclasses should override this method to read (and store) XHTML, MathML, etc. More... | |
virtual int | getElementPosition () const |
The NUML XML Schema is written such that the order of child elements is significant. More... | |
NUMLErrorLog * | getErrorLog () |
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... | |
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... | |
void | logUnknownElement (const std::string element, const unsigned int level, const unsigned int version) |
Helper to log a common type of error. More... | |
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... | |
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... | |
virtual void | writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const |
Subclasses should override this method to write their XML attributes to the XMLOutputStream. More... | |
void | checkOrderAndLogError (NMBase *object, int expected) |
Checks that NUML element has been read in the proper order. More... | |
void | checkNUMLListPopulated (NMBase *object) |
Checks that an NUML NUMLList element has been populated. More... | |
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... | |
void | checkXHTML (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *) |
Checks that the XHTML is valid. More... | |
void | checkAnnotation () |
Checks the annotation does not declare an numl namespace. More... | |
Protected Attributes | |
std::string | mId |
std::string | mTerm |
std::string | mSourceTermId |
std::string | mOntologyURI |
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std::string | mMetaId |
std::string | mId |
std::string | mName |
NUMLDocument * | mNUML |
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | mNotes |
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * | mAnnotation |
NUMLNamespaces * | mNUMLNamespaces |
unsigned int | mLine |
unsigned int | mColumn |
int | mDept |
NMBase * | mParentNUMLObject |
bool | mHasBeenDeleted |
std::string | mEmptyString |
Friends | |
class | Validator |
class | ConsistencyValidator |
class | IdentifierConsistencyValidator |
class | InternalConsistencyValidator |
ontology terms store information about what individual elements represents
LIBNUML_CPP_NAMESPACE_BEGIN OntologyTerm::OntologyTerm | ( | unsigned int | level, |
unsigned int | version | ||
) |
Creates an new OntologyTerm using the given NUML level
and version
values.
level | an unsigned int, the NUML Level to assign to thisOntologyTerm |
version | an unsigned int, the NUML Version to assign to this OntologyTerm |
level
, version
for the document override those used to create the OntologyTerm. Despite this, the ability to supply the values at creation time is an important aid to creating valid NUML. Knowledge of the intented NUML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing NUMLDocument. OntologyTerm::OntologyTerm | ( | NUMLNamespaces * | numlns | ) |
Creates a new OntologyTerm using the given NUMLNamespaces object numlns
.
The NUMLNamespaces object encapsulates NUML Level/Version/namespaces information. It is used to communicate the NUML Level, Version, and (in Level 3) packages used in addition to NUML Level Core. A common approach to using this class constructor is to create an NUMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.
It is worth emphasizing that although this constructor does not take an identifier argument, in NUML Level 2 and beyond, the "id" (identifier) attribute of an OntologyTerm is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method
numlns | an NUMLNamespaces object. |
level
, version
and xmlns
namespaces for the document override those used to create the OntologyTerm. Despite this, the ability to supply the values at creation time is an important aid to creating valid NUML. Knowledge of the intented NUML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing NUMLDocument.
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Accepts the given NUMLVisitor for this instance of OntologyTerm.
v | the NUMLVisitor instance to be used. |
v.visit()
. Implements NMBase.
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Creates and returns a deep copy of this OntologyTerm.
Implements NMBase.
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Returns the XML element name of this object, which for OntologyTerm, is always "ontologyTerm"
.
"ontologyTerm"
. Implements NMBase.
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Returns the value of the "id" attribute of this OntologyTerm.
Reimplemented from NMBase.
const string & OntologyTerm::getOntologyURI | ( | ) | const |
Returns the value of the "ontologyURI" attribute of this OntologyTerm.
const string & OntologyTerm::getSourceTermId | ( | ) | const |
Returns the value of the "sourceTermId" attribute of this OntologyTerm.
const string & OntologyTerm::getTerm | ( | ) | const |
Returns the value of the "term" attribute of this OntologyTerm.
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Returns the libNUML type code for this NUML object.
NUML_UNKNOWN
(default).Reimplemented from NMBase.
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Subclasses should override this method to read values from the given XMLAttributes set into their specific fields.
Be sure to call your parents implementation of this method as well.
Reimplemented from NMBase.
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Reimplemented from NMBase.
int OntologyTerm::setOntologyURI | ( | const std::string & | ontologyURI | ) |
Sets the value of the "ontologyURI" attribute of this NUML object.
The string in ontologyURI
is copied.
ontologyURI | the new ontologyURI for the object |
int OntologyTerm::setSourceTermId | ( | const std::string & | sourceTermId | ) |
Sets the value of the "sourceTermId" attribute of this NUML object.
The string in sourceTermId
is copied.
sourceTermId | the new sourceTermId for the object |
int OntologyTerm::setTerm | ( | const std::string & | term | ) |
Sets the value of the "term" attribute of this NUML object.
The string in term
is copied.
term | the new term for the object |
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Subclasses should override this method to write their XML attributes to the XMLOutputStream.
Be sure to call your parents implementation of this method as well.
Reimplemented from NMBase.
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