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

#include <OntologyTerm.h>

Inheritance diagram for OntologyTerms:
NUMLList NMBase

Public Member Functions

virtual OntologyTermsclone () const
 Creates and returns a deep copy of this OntologyTerms instance. More...
 
virtual NUMLTypeCode_t getTypeCode () const
 Returns the libNUML type code for this NUML object. More...
 
virtual NUMLTypeCode_t getItemTypeCode () const
 Returns the libNUML type code for the objects contained in this NUMLList (i.e., OntologyTerm objects, if the list is non-empty). More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object. More...
 
virtual OntologyTermget (unsigned int n)
 Get a OntologyTerm from the OntologyTerms. More...
 
virtual const OntologyTermget (unsigned int n) const
 Get a OntologyTerm from the OntologyTerms. More...
 
virtual OntologyTermget (const std::string &sid)
 Get a OntologyTerm from the OntologyTerms based on its identifier. More...
 
virtual const OntologyTermget (const std::string &sid) const
 Get a OntologyTerm from the OntologyTerms based on its identifier. More...
 
virtual OntologyTermremove (unsigned int n)
 Removes the nth item from this OntologyTerms items and returns a pointer to it. More...
 
virtual OntologyTermremove (const std::string &sid)
 Removes item in this OntologyTerms items with the given identifier. More...
 
virtual int getElementPosition () const
 Get the ordinal position of this element in the containing object (which in this case is the Model object). More...
 
- Public Member Functions inherited from NUMLList
 NUMLList (unsigned int level, unsigned int version)
 Creates a new NUMLList using the given NUML level and version values. More...
 
 NUMLList (NUMLNamespaces *numlns)
 Creates a new DimensionDescription using the given NUMLNamespaces object numlns. More...
 
 NUMLList ()
 
virtual ~NUMLList ()
 
 NUMLList (const NUMLList &orig)
 Copy constructor. More...
 
NUMLListoperator= (const NUMLList &rhs)
 Assignment operator for NUMLList. More...
 
virtual bool accept (NUMLVisitor &v) const
 Accepts the given NUMLVisitor. More...
 
virtual NMBaseclone () const
 Creates and returns a deep copy of this NUMLList. More...
 
void append (const NMBase *item)
 Adds item to the end of this NUMLList. More...
 
void appendAndOwn (NMBase *item)
 Adds item to the end of this NUMLList. More...
 
virtual const NMBaseget (unsigned int n) const
 Get an item from the list. More...
 
virtual NMBaseget (unsigned int n)
 Get an item from the list. More...
 
void clear (bool doDelete=true)
 Removes all items in this NUMLList object. More...
 
virtual NMBaseremove (unsigned int n)
 Removes the nth item from this NUMLList items and returns a pointer to it. More...
 
unsigned int size () const
 Get the size of this NUMLList. More...
 
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...
 
virtual NUMLTypeCode_t getTypeCode () const
 Get the type code of the objects contained in this SedListOf. More...
 
virtual NUMLTypeCode_t getItemTypeCode () const
 Get the type code of the objects contained in this NUMLList. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for NUMLList, is always "listOf". 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...
 
- 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

virtual NMBasecreateObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream)
 
- Protected Member Functions inherited from NUMLList
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...
 
- 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...
 

Additional Inherited Members

- Protected Attributes inherited from NUMLList
std::vector< NMBase * > mItems
 
- 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
 

Member Function Documentation

◆ clone()

OntologyTerms * OntologyTerms::clone ( ) const
virtual

Creates and returns a deep copy of this OntologyTerms instance.

Returns
a (deep) copy of this OntologyTerms.

Reimplemented from NUMLList.

◆ createObject()

NMBase * OntologyTerms::createObject ( LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &  stream)
protectedvirtual
Returns
the NUML object corresponding to next XMLToken in the XMLInputStream or NULL if the token was not recognized.

Reimplemented from NMBase.

◆ get() [1/4]

OntologyTerm * OntologyTerms::get ( const std::string &  sid)
virtual

Get a OntologyTerm from the OntologyTerms based on its identifier.

Parameters
sida string representing the identifier of the OntologyTerm to get.
Returns
OntologyTerm in this OntologyTerms with the given id or NULL if no such OntologyTerm exists.
See also
get(unsigned int n)
size()

◆ get() [2/4]

const OntologyTerm * OntologyTerms::get ( const std::string &  sid) const
virtual

Get a OntologyTerm from the OntologyTerms based on its identifier.

Parameters
sida string representing the identifier of the OntologyTerm to get.
Returns
OntologyTerm in this OntologyTerms with the given id or NULL if no such OntologyTerm exists.
See also
get(unsigned int n)
size()

◆ get() [3/4]

OntologyTerm * OntologyTerms::get ( unsigned int  n)
virtual

Get a OntologyTerm from the OntologyTerms.

Parameters
nthe index number of the OntologyTerm to get.
Returns
the nth OntologyTerm in this OntologyTerms.
See also
size()

Reimplemented from NUMLList.

◆ get() [4/4]

const OntologyTerm * OntologyTerms::get ( unsigned int  n) const
virtual

Get a OntologyTerm from the OntologyTerms.

Parameters
nthe index number of the OntologyTerm to get.
Returns
the nth OntologyTerm in this OntologyTerms.
See also
size()

Reimplemented from NUMLList.

◆ getElementName()

const string & OntologyTerms::getElementName ( ) const
virtual

Returns the XML element name of this object.

For OntologyTerms, the XML element name is "OntologyTerms".

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

Reimplemented from NUMLList.

◆ getElementPosition()

int OntologyTerms::getElementPosition ( ) const
virtual

Get the ordinal position of this element in the containing object (which in this case is the Model object).

The ordering of elements in the XML form of NUML is generally fixed for most components in NUML. So, for example, the OntologyTerms in a model is (in NUML Level 2 Version 4) the sixth NUMLList. (However, it differs for different Levels and Versions of NUML.)

Returns
the ordinal position of the element with respect to its siblings, or -1 (default) to indicate the position is not significant.

Reimplemented from NMBase.

◆ getItemTypeCode()

NUMLTypeCode_t OntologyTerms::getItemTypeCode ( ) const
virtual

Returns the libNUML type code for the objects contained in this NUMLList (i.e., OntologyTerm objects, if the list is non-empty).

Returns
the NUML type code for the objects contained in this NUMLList instance, or NUML_UNKNOWN (default).
See also
getElementName()

Reimplemented from NUMLList.

◆ getTypeCode()

virtual NUMLTypeCode_t OntologyTerms::getTypeCode ( ) const
inlinevirtual

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 NUMLList.

◆ remove() [1/2]

OntologyTerm * OntologyTerms::remove ( const std::string &  sid)
virtual

Removes item in this OntologyTerms items with the given identifier.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the item to remove
Returns
the item removed. As mentioned above, the caller owns the returned item.

◆ remove() [2/2]

OntologyTerm * OntologyTerms::remove ( unsigned int  n)
virtual

Removes the nth item from this OntologyTerms items and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters
nthe index of the item to remove
See also
size()

Reimplemented from NUMLList.


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