Inheritance diagram for libsbmlcs.ReplacedElement:

[legend]

Public Member Functions
virtual bool	acceptComp (SWIGTYPE_p_CompVisitor v)

int	addCVTerm (CVTerm term, bool newBag)
	Adds a copy of the given CVTerm object to this SBML object. More...

int	addCVTerm (CVTerm term)
	Adds a copy of the given CVTerm object to this SBML object. More...

int	appendAnnotation (XMLNode annotation)
	Appends the given `annotation` to the 'annotation' subelement of this object. More...

int	appendAnnotation (string annotation)
	Appends the given `annotation` to the 'annotation' subelement of this object. More...

int	appendNotes (XMLNode notes)
	Appends the given `notes` to the 'notes' subelement of this object. More...

int	appendNotes (string notes)
	Appends the given `notes` to the 'notes' subelement of this object. More...

int	checkCompatibility (SBase arg0)
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

string	checkMathMLNamespace (XMLToken elem)
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

virtual void	clearReferencedElement ()

SBase	clone ()
	Creates and returns a deep copy of this SBase object. More...

void	connectToChild ()
	Sets this SBML object to child SBML objects (if any). More...

void	connectToParent (SBase parent)
	Sets the parent SBML object of this SBML object. More...

SBaseRef	createSBaseRef ()

int	disablePackage (string pkgURI, string pkgPrefix)
	Disables the given SBML Level 3 package. More...

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

int	enablePackage (string pkgURI, string pkgPrefix, bool flag)
	Enables or disables the given SBML Level 3 package. More...

void	enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
	Enables/Disables the given package with this element and child elements (if any). More...

override bool	Equals (Object sb)

SBase	getAncestorOfType (int type, string pkgName)
	Returns the first ancestor object that has the given SBML type code. More...

SBase	getAncestorOfType (int type)
	Returns the first ancestor object that has the given SBML type code. More...

XMLNode	getAnnotation ()
	Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...

string	getAnnotationString ()
	Returns the content of the 'annotation' subelement of this object as a character string. More...

long	getColumn ()
	Returns the column number on which this object first appears in the XML representation of the SBML document. More...

virtual string	getConversionFactor ()

CVTerm	getCVTerm (long n)
	Returns the nth CVTerm in the list of CVTerms of this SBML object. More...

CVTermList	getCVTerms ()
	Returns a list of CVTerm objects in the annotations of this SBML object. More...

virtual string	getDeletion ()

SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with a specific 'metaid' attribute value, or `null` if no such object is found. More...

SBase	getElementBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide `SId` namespace, or `null` if no such object is found. More...

SBase	getElementFromPluginsByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid` from all plug-ins associated with this element, or `null` if no such object is found. More...

SBase	getElementFromPluginsBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace from all plug-ins associated with this element, or `null` if no such object is found. More...

string	getElementName ()
	Returns the XML element name of this object. More...

override int	GetHashCode ()

string	getId ()
	Returns the value of the 'metaid' attribute of this object. More...

virtual string	getIdRef ()

long	getLevel ()
	Returns the SBML Level of the SBMLDocument object containing this object. More...

long	getLine ()
	Returns the line number on which this object first appears in the XML representation of the SBML document. More...

SBaseList	getListOfAllElements ()

SBaseList	getListOfAllElementsFromPlugins ()

string	getMetaId ()
	Returns the value of the 'metaid' attribute of this object. More...

virtual string	getMetaIdRef ()

Model	getModel ()
	Returns the Model object in which the current object is located. More...

ModelHistory	getModelHistory ()
	Returns the ModelHistory object, if any, attached to this object. More...

string	getName ()
	Returns the value of the 'metaid' attribute of this object. More...

XMLNamespaces	getNamespaces ()
	Returns a list of the XML Namespaces declared on this SBML document. More...

XMLNode	getNotes ()
	Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...

string	getNotesString ()
	Returns the content of the 'notes' subelement of this object as a string. More...

long	getNumCVTerms ()
	Returns the number of CVTerm objects in the annotations of this SBML object. More...

long	getNumPlugins ()
	Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...

override int	getNumReferents ()

string	getPackageName ()
	Returns the name of the SBML Level 3 package in which this element is defined. More...

string	getPackageURI ()

long	getPackageVersion ()
	Returns the Version of the SBML Level 3 package to which this element belongs to. More...

SBase	getParentSBMLObject ()
	Returns the parent SBML object containing this object. More...

SBasePlugin	getPlugin (string package)
	Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...

SBasePlugin	getPlugin (long n)
	Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...

virtual string	getPortRef ()

string	getPrefix ()
	Return the prefix of this element. More...

virtual SBase	getReferencedElement ()

override SBase	getReferencedElementFrom (Model model)

int	getResourceBiologicalQualifier (string resource)
	Returns the MIRIAM biological qualifier associated with the given resource. More...

int	getResourceModelQualifier (string resource)
	Returns the MIRIAM model qualifier associated with the given resource. More...

SBaseRef	getSBaseRef ()

SBMLDocument	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

SBMLNamespaces	getSBMLNamespaces ()
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

int	getSBOTerm ()
	Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...

string	getSBOTermAsURL ()
	Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More...

string	getSBOTermID ()
	Returns the string representation of the 'sboTerm' attribute of this object. More...

virtual string	getSubmodelRef ()

int	getTypeCode ()
	Returns the libSBML type code for this object. More...

virtual string	getUnitRef ()

long	getVersion ()
	Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...

bool	hasNonstandardIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements excluding 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...

bool	hasRequiredAttributes ()
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

bool	hasRequiredElements ()
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

bool	hasValidLevelVersionNamespaceCombination ()
	Predicate returning `true` if this object's level/version and namespace values correspond to a valid SBML specification. More...

bool	isPackageEnabled (string pkgName)
	Predicate returning `true` if the given SBML Level 3 package is enabled with this object. More...

bool	isPackageURIEnabled (string pkgURI)
	Predicate returning `true` if an SBML Level 3 package with the given URI is enabled with this object. More...

bool	isPkgEnabled (string pkgName)
	Predicate returning `true` if the given SBML Level 3 package is enabled with this object. More...

bool	isPkgURIEnabled (string pkgURI)
	Predicate returning `true` if an SBML Level 3 package with the given URI is enabled with this object. More...

bool	isSetAnnotation ()
	Predicate returning `true` if this object's 'annotation' subelement exists and has content. More...

virtual bool	isSetConversionFactor ()

virtual bool	isSetDeletion ()

bool	isSetId ()
	Predicate returning `true` if this object's 'metaid' attribute is set. More...

virtual bool	isSetIdRef ()

bool	isSetMetaId ()
	Predicate returning `true` if this object's 'metaid' attribute is set. More...

virtual bool	isSetMetaIdRef ()

bool	isSetModelHistory ()
	Predicate returning `true` if this object has a ModelHistory object attached to it. More...

bool	isSetName ()
	Predicate returning `true` if this object's 'metaid' attribute is set. More...

bool	isSetNotes ()
	Predicate returning `true` if this object's 'notes' subelement exists and has content. More...

virtual bool	isSetPortRef ()

bool	isSetSBaseRef ()

bool	isSetSBOTerm ()
	Predicate returning `true` if this object's 'sboTerm' attribute is set. More...

virtual bool	isSetSubmodelRef ()

virtual bool	isSetUnitRef ()

bool	matchesRequiredSBMLNamespacesForAddition (SBase sb)
	Returns `true` if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...

bool	matchesSBMLNamespaces (SBase sb)
	Returns `true` if this object's set of XML namespaces are the same as the given object's XML namespaces. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

virtual int	performDeletion ()

override int	performReplacement ()

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the object. More...

int	removeFromParentAndDelete ()
	Removes itself from its parent. More...

int	removeTopLevelAnnotationElement (string elementName, string elementURI)
	Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

int	removeTopLevelAnnotationElement (string elementName)
	Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

void	renameMetaIdRefs (string oldid, string newid)
	Renames all the `MetaIdRef` attributes on this element. More...

void	renameSIdRefs (string oldid, string newid)
	Renames all the `SIdRef` attributes on this element, including any found in MathML content (if such exists). More...

void	renameUnitSIdRefs (string oldid, string newid)
	Renames all the `UnitSIdRef` attributes on this element. More...

	ReplacedElement (long level, long version, long pkgVersion)

	ReplacedElement (long level, long version)

	ReplacedElement (long level)

	ReplacedElement ()

	ReplacedElement (CompPkgNamespaces compns)

	ReplacedElement (ReplacedElement source)

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...

int	replaceTopLevelAnnotationElement (XMLNode annotation)
	Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...

int	replaceTopLevelAnnotationElement (string annotation)
	Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...

virtual int	replaceWithAndMaybeDelete (SBase replacement, bool deleteme, ASTNode conversionFactor)

override int	saveReferencedElement ()

int	setAnnotation (XMLNode annotation)
	Sets the value of the 'annotation' subelement of this SBML object. More...

int	setAnnotation (string annotation)
	Sets the value of the 'annotation' subelement of this SBML object. More...

virtual int	setConversionFactor (string id)

virtual int	setDeletion (string id)

int	setId (string sid)
	Predicate returning `true` if this object has a ModelHistory object attached to it. More...

virtual int	setIdRef (string id)

int	setMetaId (string metaid)
	Sets the value of the 'metaid' attribute of this object. More...

virtual int	setMetaIdRef (string id)

int	setModelHistory (ModelHistory history)
	Sets the ModelHistory of this object. More...

int	setName (string name)
	Predicate returning `true` if this object has a ModelHistory object attached to it. More...

int	setNamespaces (XMLNamespaces xmlns)
	Sets the namespaces relevant of this SBML object. More...

int	setNotes (XMLNode notes)
	Sets the value of the 'notes' subelement of this SBML object. More...

int	setNotes (string notes, bool addXHTMLMarkup)
	Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`. More...

int	setNotes (string notes)
	Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`. More...

virtual int	setPortRef (string id)

int	setSBaseRef (SBaseRef sBaseRef)

void	setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns)
	Subclasses should override this method to write out their contained SBML objects as XML elements. More...

int	setSBOTerm (int value)
	Sets the value of the 'sboTerm' attribute. More...

int	setSBOTerm (string sboid)
	Sets the value of the 'sboTerm' attribute by string. More...

virtual int	setSubmodelRef (string id)

virtual int	setUnitRef (string id)

string	toSBML ()
	Returns a string consisting of a partial SBML corresponding to just this object. More...

int	unsetAnnotation ()
	Unsets the value of the 'annotation' subelement of this SBML object. More...

virtual int	unsetConversionFactor ()

int	unsetCVTerms ()
	Clears the list of CVTerm objects attached to this SBML object. More...

virtual int	unsetDeletion ()

int	unsetId ()
	Unsets the value of the 'id' attribute of this SBML object. More...

virtual int	unsetIdRef ()

int	unsetMetaId ()
	Unsets the value of the 'metaid' attribute of this SBML object. More...

virtual int	unsetMetaIdRef ()

int	unsetModelHistory ()
	Unsets the ModelHistory object attached to this object. More...

int	unsetName ()
	Unsets the value of the 'name' attribute of this SBML object. More...

int	unsetNotes ()
	Unsets the value of the 'notes' subelement of this SBML object. More...

virtual int	unsetPortRef ()

virtual int	unsetSBaseRef ()

int	unsetSBOTerm ()
	Unsets the value of the 'sboTerm' attribute of this SBML object. More...

virtual int	unsetSubmodelRef ()

virtual int	unsetUnitRef ()

void	writeExtensionElements (XMLOutputStream stream)
	Writes out contained SBML objects of package extensions (if any) as XML elements. More...

Static Public Member Functions
static Model	getParentModel (SBase child)

static bool	operator!= (SBase lhs, SBase rhs)

static bool	operator== (SBase lhs, SBase rhs)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.ReplacedElement.ReplacedElement	(	long	level,
		long	version,
		long	pkgVersion
	)

libsbmlcs.ReplacedElement.ReplacedElement	(	long	level,
		long	version
	)

libsbmlcs.ReplacedElement.ReplacedElement ( long level )

libsbmlcs.ReplacedElement.ReplacedElement ( )

libsbmlcs.ReplacedElement.ReplacedElement ( CompPkgNamespaces compns )

libsbmlcs.ReplacedElement.ReplacedElement ( ReplacedElement source )

Member Function Documentation

virtual bool libsbmlcs.ReplacedElement.acceptComp ( SWIGTYPE_p_CompVisitor v )

virtual

int libsbmlcs.SBase.addCVTerm	(	CVTerm	term,
		bool	newBag
	)

inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters

term	the CVTerm to assign.
newBag	if `true`, creates a new RDF bag with the same identifier as a previous bag, and if `false`, adds the term to an existing RDF bag with the same type of qualifier as the term being added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning: The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

int libsbmlcs.SBase.addCVTerm ( CVTerm term )

inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters

term	the CVTerm to assign.
newBag	if `true`, creates a new RDF bag with the same identifier as a previous bag, and if `false`, adds the term to an existing RDF bag with the same type of qualifier as the term being added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning: The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

int libsbmlcs.SBase.appendAnnotation ( XMLNode annotation )

inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters

annotation an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(string annotation); unsetAnnotation()

int libsbmlcs.SBase.appendAnnotation ( string annotation )

inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters

annotation an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); unsetAnnotation()

int libsbmlcs.SBase.appendNotes ( XMLNode notes )

inherited

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters

notes an XML node structure that is to appended to the content of the 'notes' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.appendNotes ( string notes )

inherited

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters

notes an XML string that is to appended to the content of the 'notes' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(XMLNode notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.checkCompatibility ( SBase arg0 )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken elem )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

virtual void libsbmlcs.SBaseRef.clearReferencedElement ( )

virtualinherited

SBase libsbmlcs.ReplacedElement.clone ( )

Creates and returns a deep copy of this SBase object.

Returns: a (deep) copy of this SBase object.

void libsbmlcs.Replacing.connectToChild ( )

inherited

Sets this SBML object to child SBML objects (if any).

(Creates a child-parent relationship by the parent)

Subclasses must override this function if they define one ore more child elements. Basically, this function needs to be called in constructor, copy constructor, assignment operator.

void libsbmlcs.SBase.connectToParent ( SBase parent )

inherited

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters

parent the SBML object to use

SBaseRef libsbmlcs.SBaseRef.createSBaseRef ( )

inherited

int libsbmlcs.SBase.disablePackage	(	string	pkgURI,
		string	pkgPrefix
	)

inherited

Disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters

pkgURI	the URI of the package
pkgPrefix	the XML prefix of the package

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

override void libsbmlcs.ReplacedElement.Dispose ( )

virtual

Reimplemented from libsbmlcs.CompBase.

void libsbmlcs.SBase.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself—subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBase.enablePackage	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

inherited

Enables or disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters

pkgURI	the URI of the package
pkgPrefix	the XML prefix of the package
flag	whether to enable (`true`) or disable (`false`) the package

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

void libsbmlcs.SBase.enablePackageInternal	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

inherited

Enables/Disables the given package with this element and child elements (if any).

(This is an internal implementation for enablePackage function)

Note: Subclasses in which one or more child elements are defined must override this function.

See Also: connectToChild()

override bool libsbmlcs.SBase.Equals ( Object sb )

inherited

SBase libsbmlcs.SBase.getAncestorOfType	(	int	type,
		string	pkgName
	)

inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters

type	the SBML type code of the object sought
pkgName	(optional) the short name of an SBML Level 3 package to which the sought-after object must belong

Returns: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.

SBase libsbmlcs.SBase.getAncestorOfType ( int type )

inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters

type	the SBML type code of the object sought
pkgName	(optional) the short name of an SBML Level 3 package to which the sought-after object must belong

Returns: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.

XMLNode libsbmlcs.SBase.getAnnotation ( )

inherited

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns: the annotation of this SBML object as a tree of XMLNode objects.

See Also: getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

string libsbmlcs.SBase.getAnnotationString ( )

inherited

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns: the annotation of this SBML object as a character string.

See Also: getAnnotation(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

long libsbmlcs.SBase.getColumn ( )

inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns: the column number of this SBML object.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See Also: getLine()

virtual string libsbmlcs.ReplacedElement.getConversionFactor ( )

virtual

CVTerm libsbmlcs.SBase.getCVTerm ( long n )

inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters

n	long the index of the CVTerm to retrieve

Returns: the nth CVTerm in the list of CVTerms for this SBML object.

CVTermList libsbmlcs.SBase.getCVTerms ( )

inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns: the list of CVTerms for this SBML object.

virtual string libsbmlcs.ReplacedElement.getDeletion ( )

virtual

SBase libsbmlcs.SBaseRef.getElementByMetaId ( string metaid )

inherited

Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.

Parameters

metaid string representing the 'metaid' attribute value of the object to find.

Returns: pointer to the first element found with the given meta-identifier.

SBase libsbmlcs.SBaseRef.getElementBySId ( string id )

inherited

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Parameters

id	string representing the 'id' attribute value of the object to find.

Returns: pointer to the first element found with the given identifier.

SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string metaid )

inherited

Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found.

Parameters

metaid string representing the metaid of objects to find

Returns: pointer to the first element found with the given metaid.

SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string id )

inherited

Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found.

Parameters

id	string representing the id of objects to find

Returns: pointer to the first element found with the given id.

string libsbmlcs.ReplacedElement.getElementName ( )

Returns the XML element name of this object.

This is overridden by subclasses to return a string appropriate to the SBML component. For example, Model defines it as returning 'model', CompartmentType defines it as returning 'compartmentType', and so on.

override int libsbmlcs.SBase.GetHashCode ( )

inherited

string libsbmlcs.SBase.getId ( )

inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: the meta-identifier of this SBML object, as a string.

See Also: isSetMetaId(); setMetaId(string metaid)

virtual string libsbmlcs.SBaseRef.getIdRef ( )

virtualinherited

long libsbmlcs.SBase.getLevel ( )

inherited

Returns the SBML Level of the SBMLDocument object containing this object.

Returns: the SBML level of this SBML object.

See Also: getVersion(); getNamespaces(); getPackageVersion()

long libsbmlcs.SBase.getLine ( )

inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns: the line number of this SBML object.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See Also: getColumn()

SBaseList libsbmlcs.SBase.getListOfAllElements ( )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )

inherited

string libsbmlcs.SBase.getMetaId ( )

inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: the meta-identifier of this SBML object.

See Also: isSetMetaId(); setMetaId(string metaid)

virtual string libsbmlcs.SBaseRef.getMetaIdRef ( )

virtualinherited

Model libsbmlcs.SBase.getModel ( )

inherited

Returns the Model object in which the current object is located.

Returns: the parent Model of this SBML object.

See Also: getParentSBMLObject(); getSBMLDocument()

ModelHistory libsbmlcs.SBase.getModelHistory ( )

inherited

Returns the ModelHistory object, if any, attached to this object.

Returns: the ModelHistory object attached to this object, or null if none exist.

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

string libsbmlcs.SBase.getName ( )

inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: the meta-identifier of this SBML object, as a string.

See Also: isSetMetaId(); setMetaId(string metaid)

XMLNamespaces libsbmlcs.SBase.getNamespaces ( )

inherited

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns: the XML Namespaces associated with this SBML object

See Also: getLevel(); getVersion()

XMLNode libsbmlcs.SBase.getNotes ( )

inherited

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns: the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

string libsbmlcs.SBase.getNotesString ( )

inherited

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns: the content of the 'notes' subelement of this SBML object as a string.

See Also: getNotes(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

long libsbmlcs.SBase.getNumCVTerms ( )

inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns: the number of CVTerms for this SBML object.

long libsbmlcs.SBase.getNumPlugins ( )

inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns: the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

override int libsbmlcs.ReplacedElement.getNumReferents ( )

virtual

Reimplemented from libsbmlcs.SBaseRef.

string libsbmlcs.CompBase.getPackageName ( )

inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns: the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.

string libsbmlcs.CompBase.getPackageURI ( )

inherited

long libsbmlcs.CompBase.getPackageVersion ( )

inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns: the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.

See Also: getLevel(); getVersion()

static Model libsbmlcs.CompBase.getParentModel ( SBase child )

staticinherited

SBase libsbmlcs.SBase.getParentSBMLObject ( )

inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns: the parent SBML object of this SBML object.

See Also: getSBMLDocument(); getModel()

SBasePlugin libsbmlcs.SBase.getPlugin ( string package )

inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters

package the name or URI of the package

Returns: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

SBasePlugin libsbmlcs.SBase.getPlugin ( long n )

inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters

n	the index of the plug-in to return

Returns: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

virtual string libsbmlcs.SBaseRef.getPortRef ( )

virtualinherited

string libsbmlcs.CompBase.getPrefix ( )

inherited

Return the prefix of this element.

virtual SBase libsbmlcs.SBaseRef.getReferencedElement ( )

virtualinherited

override SBase libsbmlcs.ReplacedElement.getReferencedElementFrom ( Model model )

virtual

Reimplemented from libsbmlcs.SBaseRef.

int libsbmlcs.SBase.getResourceBiologicalQualifier ( string resource )

inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

resource string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.

Returns: the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.

Note: The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

int libsbmlcs.SBase.getResourceModelQualifier ( string resource )

inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

resource string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.

Returns: the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.

Note: The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

SBaseRef libsbmlcs.SBaseRef.getSBaseRef ( )

inherited

SBMLDocument libsbmlcs.SBase.getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this SBML object.

See Also: getParentSBMLObject(); getModel()

SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.getSBOTerm ( )

inherited

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns: the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.

string libsbmlcs.SBase.getSBOTermAsURL ( )

inherited

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns: the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.

string libsbmlcs.SBase.getSBOTermID ( )

inherited

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns: the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.

virtual string libsbmlcs.Replacing.getSubmodelRef ( )

virtualinherited

int libsbmlcs.ReplacedElement.getTypeCode ( )

Returns the libSBML type code for this object.

This method may return the type code of this SBML object, or it may return SBML_UNKNOWN. This is because subclasses of SBase are not required to implement this method to return a type code. This method is meant primarily for the LibSBML C interface, in which class and subclass information is not readily available.

Returns: the SBML object type code of this SBML object or SBML_UNKNOWN (the default).

See Also: getElementName(); getPackageName()

virtual string libsbmlcs.SBaseRef.getUnitRef ( )

virtualinherited

long libsbmlcs.SBase.getVersion ( )

inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns: the SBML version of this SBML object.

See Also: getLevel(); getNamespaces()

bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').

bool libsbmlcs.Replacing.hasRequiredAttributes ( )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.SBase.hasRequiredElements ( )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )

inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

Level 1 Version 2: 'http://www.sbml.org/sbml/level1'
Level 2 Version 1: 'http://www.sbml.org/sbml/level2'
Level 2 Version 2: 'http://www.sbml.org/sbml/level2/version2'
Level 2 Version 3: 'http://www.sbml.org/sbml/level2/version3'
Level 2 Version 4: 'http://www.sbml.org/sbml/level2/version4'
Level 3 Version 1 Core: 'http://www.sbml.org/sbml/level3/version1/core'

Returns: true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.

bool libsbmlcs.SBase.isPackageEnabled ( string pkgName )

inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters

pkgName the name of the package

Returns: true if the given package is enabled within this object, false otherwise.

See Also: isPackageURIEnabled()

bool libsbmlcs.SBase.isPackageURIEnabled ( string pkgURI )

inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters

pkgURI the URI of the package

Returns: true if the given package is enabled within this object, false otherwise.

See Also: isPackageEnabled()

bool libsbmlcs.SBase.isPkgEnabled ( string pkgName )

inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters

pkgName the name of the package

Returns: true if the given package is enabled within this object, false otherwise.

See Also: isPkgURIEnabled()

bool libsbmlcs.SBase.isPkgURIEnabled ( string pkgURI )

inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters

pkgURI the URI of the package

Returns: true if the given package is enabled within this object, false otherwise.

See Also: isPkgEnabled()

bool libsbmlcs.SBase.isSetAnnotation ( )

inherited

Predicate returning true if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns: true if a 'annotation' subelement exists, false otherwise.

See Also: getAnnotation(); getAnnotationString(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

virtual bool libsbmlcs.ReplacedElement.isSetConversionFactor ( )

virtual

virtual bool libsbmlcs.ReplacedElement.isSetDeletion ( )

virtual

bool libsbmlcs.SBase.isSetId ( )

inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See Also: getMetaId(); setMetaId(string metaid)

virtual bool libsbmlcs.SBaseRef.isSetIdRef ( )

virtualinherited

bool libsbmlcs.SBase.isSetMetaId ( )

inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See Also: getMetaId(); setMetaId(string metaid)

virtual bool libsbmlcs.SBaseRef.isSetMetaIdRef ( )

virtualinherited

bool libsbmlcs.SBase.isSetModelHistory ( )

inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns: true if the ModelHistory of this object is set, false otherwise.

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

bool libsbmlcs.SBase.isSetName ( )

inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See Also: getMetaId(); setMetaId(string metaid)

bool libsbmlcs.SBase.isSetNotes ( )

inherited

Predicate returning true if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns: true if a 'notes' subelement exists, false otherwise.

See Also: getNotes(); getNotesString(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

virtual bool libsbmlcs.SBaseRef.isSetPortRef ( )

virtualinherited

bool libsbmlcs.SBaseRef.isSetSBaseRef ( )

inherited

bool libsbmlcs.SBase.isSetSBOTerm ( )

inherited

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns: true if the 'sboTerm' attribute of this SBML object is set, false otherwise.

virtual bool libsbmlcs.Replacing.isSetSubmodelRef ( )

virtualinherited

virtual bool libsbmlcs.SBaseRef.isSetUnitRef ( )

virtualinherited

bool libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase sb )

inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters

sb	an object to compare with respect to namespaces

Returns: bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.

bool libsbmlcs.SBase.matchesSBMLNamespaces ( SBase sb )

inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters

sb	an object to compare with respect to namespaces

Returns: bool, true if this object's collection of namespaces is the same as sb's, false otherwise.

void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

static bool libsbmlcs.SBase.operator!=	(	SBase	lhs,
		SBase	rhs
	)

staticinherited

static bool libsbmlcs.SBase.operator==	(	SBase	lhs,
		SBase	rhs
	)

staticinherited

virtual int libsbmlcs.SBaseRef.performDeletion ( )

virtualinherited

override int libsbmlcs.ReplacedElement.performReplacement ( )

virtual

Reimplemented from libsbmlcs.Replacing.

int libsbmlcs.SBase.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

int libsbmlcs.SBaseRef.removeFromParentAndDelete ( )

inherited

Removes itself from its parent.

If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.SBase.removeTopLevelAnnotationElement	(	string	elementName,
		string	elementURI
	)

inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters

elementName	a string representing the name of the top level annotation element that is to be removed
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: replaceTopLevelAnnotationElement(XMLNode ); replaceTopLevelAnnotationElement(string)

int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string elementName )

inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters

elementName	a string representing the name of the top level annotation element that is to be removed
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: replaceTopLevelAnnotationElement(XMLNode ); replaceTopLevelAnnotationElement(string)

void libsbmlcs.SBase.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier
newid	the new identifier

void libsbmlcs.ReplacedElement.renameSIdRefs	(	string	oldid,
		string	newid
	)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier
newid	the new identifier

void libsbmlcs.SBase.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

inherited

Renames all the UnitSIdRef attributes on this element.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier
newid	the new identifier

void libsbmlcs.SBase.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself—subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode annotation )

inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters

annotation XMLNode representing the replacement top level annotation

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: removeTopLevelAnnotationElement(string elementName, string elementURI); replaceTopLevelAnnotationElement(string)

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string annotation )

inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters

annotation string representing the replacement top level annotation

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: removeTopLevelAnnotationElement(string elementName, string elementURI); replaceTopLevelAnnotationElement(XMLNode)

virtual int libsbmlcs.Replacing.replaceWithAndMaybeDelete	(	SBase	replacement,
		bool	deleteme,
		ASTNode	conversionFactor
	)

virtualinherited

override int libsbmlcs.Replacing.saveReferencedElement ( )

virtualinherited

Reimplemented from libsbmlcs.SBaseRef.

int libsbmlcs.SBase.setAnnotation ( XMLNode annotation )

inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters

annotation an XML structure that is to be used as the new content of the 'annotation' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See Also: getAnnotationString(); isSetAnnotation(); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

int libsbmlcs.SBase.setAnnotation ( string annotation )

inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters

annotation an XML string that is to be used as the content of the 'annotation' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

virtual int libsbmlcs.ReplacedElement.setConversionFactor ( string id )

virtual

virtual int libsbmlcs.ReplacedElement.setDeletion ( string id )

virtual

int libsbmlcs.SBase.setId ( string sid )

inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns: true if the ModelHistory of this object is set, false otherwise.

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

virtual int libsbmlcs.SBaseRef.setIdRef ( string id )

virtualinherited

int libsbmlcs.SBase.setMetaId ( string metaid )

inherited

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters

metaid the identifier string to use as the value of the 'metaid' attribute

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getMetaId(); isSetMetaId()

virtual int libsbmlcs.SBaseRef.setMetaIdRef ( string id )

virtualinherited

int libsbmlcs.SBase.setModelHistory ( ModelHistory history )

inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters

history ModelHistory of this object.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

int libsbmlcs.SBase.setName ( string name )

inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns: true if the ModelHistory of this object is set, false otherwise.

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

int libsbmlcs.SBase.setNamespaces ( XMLNamespaces xmlns )

inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters

xmlns the namespaces to set

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.SBase.setNotes ( XMLNode notes )

inherited

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters

notes an XML structure that is to be used as the content of the 'notes' subelement of this object

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getNotesString(); isSetNotes(); setNotes(string notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.setNotes	(	string	notes,
		bool	addXHTMLMarkup
	)

inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters

notes	an XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkup	a bool indicating whether to wrap the contents of the `notes` argument with XHTML paragraph (`<p>`) tags. This is appropriate when the string in `notes` does not already containg the appropriate XHTML markup.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.setNotes ( string notes )

inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters

notes	an XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkup	a bool indicating whether to wrap the contents of the `notes` argument with XHTML paragraph (`<p>`) tags. This is appropriate when the string in `notes` does not already containg the appropriate XHTML markup.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

virtual int libsbmlcs.SBaseRef.setPortRef ( string id )

virtualinherited

Reimplemented in libsbmlcs.Port.

int libsbmlcs.SBaseRef.setSBaseRef ( SBaseRef sBaseRef )

inherited

void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces sbmlns )

inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.setSBOTerm ( int value )

inherited

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters

value the NNNNNNN integer portion of the SBO identifier

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: setSBOTerm(string sboid)

int libsbmlcs.SBase.setSBOTerm ( string sboid )

inherited

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters

sboid the SBO identifier string of the form 'SBO:NNNNNNN'

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also: setSBOTerm(int value)

virtual int libsbmlcs.Replacing.setSubmodelRef ( string id )

virtualinherited

virtual int libsbmlcs.SBaseRef.setUnitRef ( string id )

virtualinherited

string libsbmlcs.SBase.toSBML ( )

inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns: the partial SBML that describes this SBML object.

Warning: This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

int libsbmlcs.SBase.unsetAnnotation ( )

inherited

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See Also: getAnnotation(); getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation)

virtual int libsbmlcs.ReplacedElement.unsetConversionFactor ( )

virtual

int libsbmlcs.SBase.unsetCVTerms ( )

inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

virtual int libsbmlcs.ReplacedElement.unsetDeletion ( )

virtual

int libsbmlcs.SBase.unsetId ( )

inherited

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

virtual int libsbmlcs.SBaseRef.unsetIdRef ( )

virtualinherited

int libsbmlcs.SBase.unsetMetaId ( )

inherited

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

virtual int libsbmlcs.SBaseRef.unsetMetaIdRef ( )

virtualinherited

int libsbmlcs.SBase.unsetModelHistory ( )

inherited

Unsets the ModelHistory object attached to this object.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

int libsbmlcs.SBase.unsetName ( )

inherited

Unsets the value of the 'name' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.SBase.unsetNotes ( )

inherited

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See Also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes); appendNotes(XMLNode notes); appendNotes(string notes); SyntaxChecker::hasExpectedXHTMLSyntax()

virtual int libsbmlcs.SBaseRef.unsetPortRef ( )

virtualinherited

virtual int libsbmlcs.SBaseRef.unsetSBaseRef ( )

virtualinherited

int libsbmlcs.SBase.unsetSBOTerm ( )

inherited

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

virtual int libsbmlcs.Replacing.unsetSubmodelRef ( )

virtualinherited

virtual int libsbmlcs.SBaseRef.unsetUnitRef ( )

virtualinherited

void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream stream )

inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn

protectedinherited

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation