libNuML 1.1.1
Library for reading / writing NuML documents
OntologyTerm Class Reference

ontology terms store information about what individual elements represents More...

#include <OntologyTerm.h>

Inheritance diagram for OntologyTerm:
NMBase

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 OntologyTermclone () 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...
 
- Public Member Functions inherited from NMBase
virtual ~NMBase ()
 Destroy this object. More...
 
NMBaseoperator= (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 NMBaseclone () 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 NUMLDocumentgetNUMLDocument () const
 Returns the parent NUMLDocument object. More...
 
NUMLDocumentgetNUMLDocument ()
 Returns the parent NUMLDocument object. More...
 
NMBasegetParentNUMLObject ()
 Returns the parent NUML object. More...
 
NMBasegetAncestorOfType (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)
 
NUMLNamespacesgetNUMLNamespaces () 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 &notes, bool addXHTMLMarkup=false)
 
int appendNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes)
 
int appendNotes (const std::string &notes)
 
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 ()
 
- Protected Member Functions inherited from NMBase
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 NMBasecreateObject (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...
 
NUMLErrorLoggetErrorLog ()
 
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
 
- Protected Attributes inherited from NMBase
std::string mMetaId
 
std::string mId
 
std::string mName
 
NUMLDocumentmNUML
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * mNotes
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * mAnnotation
 
NUMLNamespacesmNUMLNamespaces
 
unsigned int mLine
 
unsigned int mColumn
 
int mDept
 
NMBasemParentNUMLObject
 
bool mHasBeenDeleted
 
std::string mEmptyString
 

Friends

class Validator
 
class ConsistencyValidator
 
class IdentifierConsistencyValidator
 
class InternalConsistencyValidator
 

Detailed Description

ontology terms store information about what individual elements represents

Constructor & Destructor Documentation

◆ OntologyTerm() [1/3]

LIBNUML_CPP_NAMESPACE_BEGIN OntologyTerm::OntologyTerm ( unsigned int  level,
unsigned int  version 
)

Creates an new OntologyTerm using the given NUML level and version values.

Parameters
levelan unsigned int, the NUML Level to assign to thisOntologyTerm
versionan unsigned int, the NUML Version to assign to this OntologyTerm
Note
Once an OntologyTerm has been added to an NUMLDocument, the 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() [2/3]

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

Parameters
numlnsan NUMLNamespaces object.
Note
Once an OntologyTerm has been added to an NUMLDocument, the 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.

◆ ~OntologyTerm()

OntologyTerm::~OntologyTerm ( )
virtual

◆ OntologyTerm() [3/3]

OntologyTerm::OntologyTerm ( )
protected

Member Function Documentation

◆ accept()

bool OntologyTerm::accept ( NUMLVisitor v) const
virtual

Accepts the given NUMLVisitor for this instance of OntologyTerm.

Parameters
vthe NUMLVisitor instance to be used.
Returns
the result of calling v.visit().

Implements NMBase.

◆ clone()

OntologyTerm * OntologyTerm::clone ( ) const
virtual

Creates and returns a deep copy of this OntologyTerm.

Returns
a (deep) copy of this OntologyTerm.

Implements NMBase.

◆ getElementName()

const string & OntologyTerm::getElementName ( ) const
virtual

Returns the XML element name of this object, which for OntologyTerm, is always "ontologyTerm".

Returns
the name of this element, i.e., "ontologyTerm".

Implements NMBase.

◆ getId()

const string & OntologyTerm::getId ( ) const
virtual

Returns the value of the "id" attribute of this OntologyTerm.

Returns
the id of this OntologyTerm.

Reimplemented from NMBase.

◆ getOntologyURI()

const string & OntologyTerm::getOntologyURI ( ) const

Returns the value of the "ontologyURI" attribute of this OntologyTerm.

Returns
the ontologyURI of this OntologyTerm.

◆ getSourceTermId()

const string & OntologyTerm::getSourceTermId ( ) const

Returns the value of the "sourceTermId" attribute of this OntologyTerm.

Returns
the sourceTermId of this OntologyTerm.

◆ getTerm()

const string & OntologyTerm::getTerm ( ) const

Returns the value of the "term" attribute of this OntologyTerm.

Returns
the term of this OntologyTerm.

◆ getTypeCode()

NUMLTypeCode_t OntologyTerm::getTypeCode ( ) const
virtual

Returns the libNUML type code for this NUML object.

Returns
the NUML type code for this object, or NUML_UNKNOWN (default).
See also
getElementName()

Reimplemented from NMBase.

◆ readAttributes()

void OntologyTerm::readAttributes ( const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &  attributes)
virtual

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.

◆ setId()

int OntologyTerm::setId ( const std::string &  sid)
virtual

Reimplemented from NMBase.

◆ setOntologyURI()

int OntologyTerm::setOntologyURI ( const std::string &  ontologyURI)

Sets the value of the "ontologyURI" attribute of this NUML object.

The string in ontologyURI is copied.

Parameters
ontologyURIthe new ontologyURI for the object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBNUML_OPERATION_SUCCESS
  • LIBNUML_INVALID_ATTRIBUTE_VALUE

◆ setSourceTermId()

int OntologyTerm::setSourceTermId ( const std::string &  sourceTermId)

Sets the value of the "sourceTermId" attribute of this NUML object.

The string in sourceTermId is copied.

Parameters
sourceTermIdthe new sourceTermId for the object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBNUML_OPERATION_SUCCESS
  • LIBNUML_INVALID_ATTRIBUTE_VALUE

◆ setTerm()

int OntologyTerm::setTerm ( const std::string &  term)

Sets the value of the "term" attribute of this NUML object.

The string in term is copied.

Parameters
termthe new term for the object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBNUML_OPERATION_SUCCESS
  • LIBNUML_INVALID_ATTRIBUTE_VALUE

◆ writeAttributes()

void OntologyTerm::writeAttributes ( LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &  stream) const
virtual

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.

Friends And Related Function Documentation

◆ ConsistencyValidator

friend class ConsistencyValidator
friend

◆ IdentifierConsistencyValidator

friend class IdentifierConsistencyValidator
friend

◆ InternalConsistencyValidator

friend class InternalConsistencyValidator
friend

◆ Validator

friend class Validator
friend

Member Data Documentation

◆ mId

std::string OntologyTerm::mId
protected

◆ mOntologyURI

std::string OntologyTerm::mOntologyURI
protected

◆ mSourceTermId

std::string OntologyTerm::mSourceTermId
protected

◆ mTerm

std::string OntologyTerm::mTerm
protected

The documentation for this class was generated from the following files: