Inheritance diagram for GeneProductRef:

Detailed Description

fbc Reference to a gene product of a reaction

GeneProductRef encodes a references to a GeneProduct object declared in a ListOfGeneProducts attached to the enclosing Model object. GeneProductRef is derived from the FbcAssociation class.

GeneProductRef objects are used to construct the content of GeneProductAssociation objects. As described more fully in the documentation of the latter, a GeneProductAssociation is a container that may contain either (i) a single GeneProductRef or (ii) a logical expression built up with FbcAnd and FbcOr and ultimately containing two or more GeneProductRef objects.

Note: This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (“fbc”) specification. In Version 1 of “fbc”, the information encoded by this class can be stored instead using the Association and GeneAssociation annotation classes. Please see the Version 1 and Version 2 “fbc” specifications for more details.

Public Member Functions
int	addCVTerm (CVTerm *term, bool newBag=false)
	Adds a copy of the given CVTerm object to this SBML object. More...

virtual int	appendAnnotation (const XMLNode *annotation)
	Appends the given `annotation` to the "annotation" subelement of this object. More...

virtual int	appendAnnotation (const std::string &annotation)
	Appends the given `annotation` to the "annotation" subelement of this object. More...

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

int	appendNotes (const std::string &notes)
	Appends the given `notes` to the "notes" subelement of this object. More...

virtual GeneProductRef *	clone () const
	Creates and returns a deep copy of this GeneProductRef object. More...

void	deleteDisabledPlugins (bool recursive=true)
	Deletes all information stored in disabled plugins. More...

int	disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
	Disables the given SBML Level 3 package on this object. More...

int	enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
	Enables or disables the given SBML Level 3 package on this object. More...

	GeneProductRef (unsigned int level=FbcExtension::getDefaultLevel(), unsigned int version=FbcExtension::getDefaultVersion(), unsigned int pkgVersion=FbcExtension::getDefaultPackageVersion())
	Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version. More...

	GeneProductRef (FbcPkgNamespaces *fbcns)
	Creates a new GeneProductRef with the given FbcPkgNamespaces object. More...

	GeneProductRef (const GeneProductRef &orig)
	Copy constructor for GeneProductRef. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...

virtual List *	getAllElementsFromPlugins (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects contained in SBML package plug-ins. More...

SBase *	getAncestorOfType (int type, const std::string &pkgName="core")
	Returns the first ancestor object that has the given SBML type code from the given package. More...

const SBase *	getAncestorOfType (int type, const std::string pkgName="core") const
	Returns the first ancestor object that has the given SBML type code from the given package. More...

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

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

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

std::string	getAnnotationString () const
	Returns the content of the "annotation" subelement of this object as a character string. More...

unsigned int	getColumn () const
	Returns the column number where this object first appears in the XML representation of the SBML document. More...

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

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

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

SBasePlugin *	getDisabledPlugin (unsigned int n)
	Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...

const SBasePlugin *	getDisabledPlugin (unsigned int n) const
	Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...

virtual SBase *	getElementByMetaId (const std::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...

const SBase *	getElementByMetaId (const std::string &metaid) const
	Returns the first child element it can find with a specific "metaid" attribute value, or `NULL` if no such object is found. More...

virtual SBase *	getElementBySId (const std::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...

const SBase *	getElementBySId (const std::string &id) const
	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...

virtual const std::string &	getElementName () const
	Returns the XML element name of this object. More...

virtual const std::string &	getGeneProduct () const
	Returns the value of the "geneProduct" attribute of this GeneProductRef. More...

virtual const std::string &	getId () const
	Returns the value of the "id" attribute of this GeneProductRef. More...

const std::string &	getIdAttribute () const
	Returns the value of the "id" attribute of this SBML object. More...

unsigned int	getLevel () const
	Returns the SBML Level of the SBMLDocument object containing this object. More...

unsigned int	getLine () const
	Returns the line number where this object first appears in the XML representation of the SBML document. More...

const std::string &	getMetaId () const
	Returns the value of the "metaid" attribute of this SBML object. More...

std::string &	getMetaId ()
	Returns the value of the "metaid" attribute of this SBML object. More...

const Model *	getModel () const
	Returns the Model object for the SBML Document in which the current object is located. More...

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

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

virtual const std::string &	getName () const
	Returns the value of the "name" attribute of this GeneProductRef object. More...

virtual XMLNamespaces *	getNamespaces () const
	Returns a list of the XML Namespaces declared on the SBML document owning this object. More...

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

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

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

std::string	getNotesString () const
	Returns the content of the "notes" subelement of this object as a string. More...

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

unsigned int	getNumDisabledPlugins () const
	Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...

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

unsigned int	getPackageCoreVersion () const
	Returns the SBML Core Version within the SBML Level of the actual object. More...

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

unsigned int	getPackageVersion () const
	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...

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

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

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

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

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

std::string	getPrefix () const
	Returns the XML namespace prefix of this element. More...

BiolQualifierType_t	getResourceBiologicalQualifier (std::string resource)
	Returns the MIRIAM biological qualifier associated with the given resource. More...

ModelQualifierType_t	getResourceModelQualifier (std::string resource)
	Returns the MIRIAM model qualifier associated with the given resource. More...

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

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

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

std::string	getSBOTermAsURL () const
	Returns the URL representation of the "sboTerm" attribute of this object. More...

std::string	getSBOTermID () const
	Returns the string representation of the "sboTerm" attribute of this object. More...

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

std::string	getURI () const
	Gets the namespace URI to which this element belongs to. More...

void *	getUserData () const
	Returns the user data that has been previously set via setUserData(). More...

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

virtual bool	hasRequiredAttributes () const
	Predicate returning `true` if all the required attributes for this GeneProductRef object have been set. More...

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

virtual bool	isFbcAnd () const
	Returns `true`, if this abstract FbcAssociation is of type FbcAnd. More...

virtual bool	isFbcOr () const
	Returns `true`, if this abstract FbcAssociation is of type FbcOr. More...

virtual bool	isGeneProductRef () const
	Returns `true`, if this abstract FbcAssociation is of type GeneProductRef. More...

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

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

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

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

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

virtual bool	isSetGeneProduct () const
	Predicate returning `true` if this GeneProductRef's "geneProduct" attribute is set. More...

virtual bool	isSetId () const
	Predicate returning `true` if this GeneProductRef's "id" attribute is set. More...

bool	isSetIdAttribute () const
	Predicate returning `true` if this object's "id" attribute is set. More...

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

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

virtual bool	isSetName () const
	Predicate returning `true` if this GeneProductRef's "name" attribute is set. More...

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

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

bool	isSetUserData () const
	Predicate returning true or false depending on whether the user data of this element has been set. More...

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

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

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

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

GeneProductRef &	operator= (const GeneProductRef &rhs)
	Assignment operator for GeneProductRef. More...

void	read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED)
	Reads (initializes) this SBML object by reading from the given XMLNode. More...

virtual int	removeFromParentAndDelete ()
	Removes this object from its parent. More...

int	removeTopLevelAnnotationElement (const std::string &elementName, const std::string elementURI="", bool removeEmpty=true)
	Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

int	replaceTopLevelAnnotationElement (const 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 (const std::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	setAnnotation (const XMLNode *annotation)
	Sets the value of the "annotation" subelement of this SBML object. More...

virtual int	setAnnotation (const std::string &annotation)
	Sets the value of the "annotation" subelement of this SBML object. More...

virtual int	setGeneProduct (const std::string &geneProduct)
	Sets the value of the "geneProduct" attribute of this GeneProductRef. More...

virtual int	setId (const std::string &sid)
	Sets the value of the "id" attribute of this GeneProductRef. More...

virtual int	setIdAttribute (const std::string &sid)
	Sets the value of the "id" attribute of this SBML object. More...

int	setMetaId (const std::string &metaid)
	Sets the value of the meta-identifier attribute of this SBML object. More...

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

virtual int	setName (const std::string &name)
	Sets the value of the "name" attribute of this GeneProductRef. More...

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

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

int	setNotes (const std::string &notes, bool addXHTMLMarkup=false)
	Sets the value of the "notes" subelement of this SBML object to a copy of the string `notes`. More...

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

virtual int	setSBOTerm (const std::string &sboid)
	Sets the value of the "sboTerm" attribute by string. More...

int	setUserData (void *userData)
	Sets the user data of this element. More...

virtual std::string	toInfix (bool usingId=false) const
	Converts this FbcAssociation object into an infix string representation. More...

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

XMLNode *	toXMLNode ()
	Returns this element as an XMLNode. More...

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

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

virtual int	unsetGeneProduct ()
	Unsets the value of the "geneProduct" attribute of this GeneProductRef. More...

virtual int	unsetId ()
	Unsets the value of the "id" attribute of this GeneProductRef. More...

int	unsetIdAttribute ()
	Unsets the value of the "id" attribute of this SBML object. More...

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

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

virtual int	unsetName ()
	Unsets the value of the "name" attribute of this GeneProductRef. More...

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

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

int	unsetUserData ()
	Unsets the user data of this element. More...

virtual	~GeneProductRef ()
	Destructor for GeneProductRef. More...

Static Public Member Functions
static FbcAssociation *	parseFbcInfixAssociation (const std::string &association, FbcModelPlugin *plugin, bool usingId=false, bool addMissingGP=true)
	Parses a gene association in infix format and returns a corresponding Association object. More...

Protected Member Functions
virtual void	setElementName (const std::string &name)

virtual void	setElementText (const std::string &text)
	When overridden allows SBase elements to use the text included in between the elements tags. More...

Constructor & Destructor Documentation

GeneProductRef::GeneProductRef	(	unsigned int	level = `FbcExtension::getDefaultLevel()`,
		unsigned int	version = `FbcExtension::getDefaultVersion()`,
		unsigned int	pkgVersion = `FbcExtension::getDefaultPackageVersion()`
	)

Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version.

Parameters

level	an unsigned int, the SBML Level to assign to this GeneProductRef.
version	an unsigned int, the SBML Version to assign to this GeneProductRef.
pkgVersion	an unsigned int, the SBML Fbc Version to assign to this GeneProductRef.

Note: Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.

GeneProductRef::GeneProductRef ( FbcPkgNamespaces * fbcns )

Creates a new GeneProductRef with the given FbcPkgNamespaces object.

: The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.

Parameters

fbcns the FbcPkgNamespaces object.

Note: Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.

GeneProductRef::GeneProductRef ( const GeneProductRef & orig )

Copy constructor for GeneProductRef.

Parameters

orig	the GeneProductRef instance to copy.

GeneProductRef::~GeneProductRef ( )

virtual

Destructor for GeneProductRef.

Member Function Documentation

int SBase::addCVTerm	(	CVTerm *	term,
		bool	newBag = `false`
	)

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 value is drawn from the enumeration OperationReturnValues_t. 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.; This method should be used with some caution. 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. 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. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

Examples:: addCVTerms.cpp, addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

int SBase::appendAnnotation ( const XMLNode * annotation )

virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE (if the parent element does not have the 'metaid' attribute set)
LIBSBML_DUPLICATE_ANNOTATION_NS (if the parent was already annotated with the annotation in question)

See also: getAnnotationString(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

Examples:: addingEvidenceCodes_2.cpp, and appendAnnotation.cpp.

int SBase::appendAnnotation ( const std::string & annotation )

virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE (if the parent element does not have the 'metaid' attribute set)
LIBSBML_DUPLICATE_ANNOTATION_NS (if the parent was already annotated with the annotation in question)

See also: getAnnotationString(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendNotes ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getNotesString(); isSetNotes(); setNotes(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int SBase::appendNotes ( const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getNotesString(); isSetNotes(); setNotes(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

GeneProductRef * GeneProductRef::clone ( ) const

virtual

Creates and returns a deep copy of this GeneProductRef object.

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

Reimplemented from FbcAssociation.

void SBase::deleteDisabledPlugins ( bool recursive = true )

inherited

Deletes all information stored in disabled plugins.

If the plugin is re-enabled later, it will then not have any previously-stored information.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

: If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

recursive if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.

See also: getNumDisabledPlugins()

int SBase::disablePackage	(	const std::string &	pkgURI,
		const std::string &	pkgPrefix
	)

inherited

Disables the given SBML Level 3 package on this object.

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

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

// We read in an SBML L3V1 model that uses the 'comp'
// package namespace.
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model.
Species* s1 = doc->getModel()->getSpecies(0);
// We construct a new model.  This model does not use the
// 'comp' package.
Model * newModel = new Model(3,1);
// The following will fail with an error, because addSpecies()
// will first check that the parent of the given object has
// namespaces declared, and will discover that s1 does but
// newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then
// the call to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
                   "comp");
newModel->addSpecies(s1);

Parameters

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

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: enablePackage(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)

int SBase::enablePackage	(	const std::string &	pkgURI,
		const std::string &	pkgPrefix,
		bool	flag
	)

inherited

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: disablePackage(const std::string& pkgURI, const std::string& pkgPrefix)

Examples:: addLayout.cpp.

List * SBase::getAllElements ( ElementFilter * filter = NULL )

virtualinherited

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a pointer to a List of pointers to all objects that are children of this object.

Reimplemented in RenderInformationBase, RenderGroup, Group, GradientBase, Layout, RenderCurve, Style, LineEnding, MultiSpeciesType, GlobalRenderInformation, Transition, LocalRenderInformation, ListOfFunctionTerms, ListOfGlobalRenderInformation, ListOfLocalRenderInformation, Model, Polygon, SBMLDocument, SpeciesFeature, Objective, Event, SpeciesFeatureType, ReactionGlyph, UnitDefinition, ListOf, GeneProductAssociation, GeneralGlyph, FbcAnd, FbcOr, Reaction, KineticLaw, Curve, Submodel, BoundingBox, SBaseRef, SpeciesReferenceGlyph, GraphicalObject, CubicBezier, LineSegment, and ReferenceGlyph.

List * SBase::getAllElementsFromPlugins ( ElementFilter * filter = NULL )

virtualinherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a pointer to a List of pointers to all children objects from plug-ins.

SBase * SBase::getAncestorOfType	(	int	type,
		const std::string &	pkgName = `"core"`
	)

inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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 from the given pkgName.

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 SBMLTypeCode_t value, or NULL if no ancestor exists.

Warning: The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.

const SBase * SBase::getAncestorOfType	(	int	type,
		const std::string	pkgName = `"core"`
	)		const

inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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 from the given pkgName.

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 SBMLTypeCode_t value, or NULL if no ancestor exists.

Warning: The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.

XMLNode * 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(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

XMLNode * SBase::getAnnotation ( ) const

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(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

std::string 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. See the method getAnnotation() for a version that returns annotations in XML form.

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

See also: getAnnotation(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

Examples:: printAnnotation.cpp.

std::string SBase::getAnnotationString ( ) const

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. See the method getAnnotation() for a version that returns annotations in XML form.

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

See also: getAnnotation(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

unsigned int SBase::getColumn ( ) const

inherited

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

Returns: the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

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()

CVTerm * SBase::getCVTerm ( unsigned int n )

inherited

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

Parameters

n	unsigned int the index of the CVTerm to retrieve.

Returns: the nth CVTerm in the list of CVTerms for this SBML object. If the index n is invalid, NULL is returned.

List * 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.

List * SBase::getCVTerms ( ) const

inherited

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

Returns: the list of CVTerms for this SBML object.

SBasePlugin * SBase::getDisabledPlugin ( unsigned int n )

inherited

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

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

: If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

n	the index of the disabled plug-in to return.

Returns: the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.

See also: getNumDisabledPlugins(); getPlugin(const std::string& package)

const SBasePlugin * SBase::getDisabledPlugin ( unsigned int n ) const

inherited

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

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

: If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

n	the index of the disabled plug-in to return.

Returns: the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.

See also: getNumDisabledPlugins(); getPlugin(const std::string& package)

SBase * SBase::getElementByMetaId ( const std::string & metaid )

virtualinherited

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

: 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

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.

Reimplemented in RenderInformationBase, RenderGroup, Group, GradientBase, RenderCurve, Style, LineEnding, GlobalRenderInformation, LocalRenderInformation, ListOfGlobalRenderInformation, ListOfLocalRenderInformation, Model, Polygon, SBMLDocument, Event, UnitDefinition, ListOf, Reaction, KineticLaw, Submodel, SBaseRef, and Transition.

const SBase * SBase::getElementByMetaId ( const std::string & metaid ) const

inherited

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

: 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

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 * SBase::getElementBySId ( const std::string & id )

virtualinherited

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.

Reimplemented in RenderInformationBase, RenderGroup, ListOfUnitDefinitions, ListOfRules, ListOfEventAssignments, ListOfInitialAssignments, Group, GradientBase, RenderCurve, Style, LineEnding, ListOfLocalParameters, GlobalRenderInformation, LocalRenderInformation, ListOfGlobalRenderInformation, ListOfLocalRenderInformation, Model, Polygon, SBMLDocument, Event, UnitDefinition, ListOf, Reaction, KineticLaw, Submodel, ListOfPorts, SBaseRef, and Transition.

const SBase * SBase::getElementBySId ( const std::string & id ) const

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.

const std::string & GeneProductRef::getElementName ( ) const

virtual

Returns the XML element name of this object.

For GeneProductRef, the XML element name is always "geneProductRef".

Returns: the name of this element, i.e. "geneProductRef".

Reimplemented from FbcAssociation.

const std::string & GeneProductRef::getGeneProduct ( ) const

virtual

Returns the value of the "geneProduct" attribute of this GeneProductRef.

Returns: the value of the "geneProduct" attribute of this GeneProductRef as a string.

const std::string & GeneProductRef::getId ( ) const

virtual

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

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns: the id of this GeneProductRef.

See also: getIdAttribute(); setIdAttribute(const std::string& sid); isSetIdAttribute(); unsetIdAttribute()

Reimplemented from SBase.

const string & SBase::getIdAttribute ( ) const

inherited

Returns the value of the "id" attribute of this SBML object.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns: the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.

See also: setIdAttribute(const std::string& sid); isSetIdAttribute(); unsetIdAttribute()

unsigned int SBase::getLevel ( ) const

inherited

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

: 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.)

Returns: the SBML level of this SBML object.

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

Examples:: addLayout.cpp, convertSBML.cpp, and printSBML.cpp.

unsigned int SBase::getLine ( ) const

inherited

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

Returns: the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

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()

const string & SBase::getMetaId ( ) const

inherited

Returns 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

Returns: the meta-identifier of this SBML object.

See also: isSetMetaId(); setMetaId(const std::string& metaid)

Examples:: addingEvidenceCodes_2.cpp.

string & SBase::getMetaId ( )

inherited

Returns 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

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

See also: isSetMetaId(); setMetaId(const std::string& metaid)

const Model * SBase::getModel ( ) const

inherited

Returns the Model object for the SBML Document in which the current object is located.

Returns: the Model object for the SBML Document of this SBML object.

See also: getParentSBMLObject(); getSBMLDocument()

ModelHistory * SBase::getModelHistory ( ) const

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.

ModelHistory * 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.

const std::string & GeneProductRef::getName ( ) const

virtual

Returns the value of the "name" attribute of this GeneProductRef object.

: In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns: the name of this SBML object, or the empty string if not set or unsettable.

See also: getIdAttribute(); isSetName(); setName(const std::string& sid); unsetName()

Reimplemented from SBase.

XMLNamespaces * SBase::getNamespaces ( ) const

virtualinherited

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

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.

Returns: the XML Namespaces associated with this SBML object, or NULL in certain very usual circumstances where a namespace is not set.

See also: getLevel(); getVersion()

Reimplemented in SBMLDocument.

XMLNode * 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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

XMLNode * SBase::getNotes ( ) const

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

std::string 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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

Examples:: printNotes.cpp, and SBMLHttpResolverExample.cpp.

std::string SBase::getNotesString ( ) const

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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

unsigned int 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.

unsigned int SBase::getNumDisabledPlugins ( ) const

inherited

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

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

: If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

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

unsigned int SBase::getNumPlugins ( ) const

inherited

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

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

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

See also: getPlugin(unsigned int n)

unsigned int SBase::getPackageCoreVersion ( ) const

inherited

Returns the SBML Core Version within the SBML Level of the actual object.

: 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.)

Returns: the SBML core version of this SBML object.

const std::string & SBase::getPackageName ( ) const

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.

unsigned int SBase::getPackageVersion ( ) const

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()

SBase * 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()

const SBase * SBase::getParentSBMLObject ( ) const

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 * SBase::getPlugin ( const std::string & package )

inherited

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

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

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.

See also: getPlugin(unsigned int n)

Examples:: addLayout.cpp, convertLayout.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.

const SBasePlugin * SBase::getPlugin ( const std::string & package ) const

inherited

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

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

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.

See also: getPlugin(unsigned int n)

SBasePlugin * SBase::getPlugin ( unsigned int n )

inherited

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

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

Parameters

n	the index of the plug-in to return.

Returns: the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.

See also: getNumPlugins(); getPlugin(const std::string& package)

const SBasePlugin * SBase::getPlugin ( unsigned int n ) const

inherited

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

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

: SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

Parameters

n	the index of the plug-in to return.

Returns: the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.

See also: getNumPlugins(); getPlugin(const std::string& package)

std::string SBase::getPrefix ( ) const

inherited

Returns the XML namespace prefix of this element.

This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.

Returns: a text string representing the XML namespace prefix.

BiolQualifierType_t SBase::getResourceBiologicalQualifier ( std::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 values from the enumeration type BiolQualifierType_t.

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 value from the enumeration type BiolQualifierType_t.

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 in the enumeration BiolQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

ModelQualifierType_t SBase::getResourceModelQualifier ( std::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 values from the enumeration type ModelQualifierType_t.

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 value from the enumeration type ModelQualifierType_t.

Parameters

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

Returns: the ModelQualifierType_t value associated with the resource, or BQM_UNKNOWN if the resource does not exist.

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

const SBMLDocument * SBase::getSBMLDocument ( ) const

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()

SBMLDocument * 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()

int SBase::getSBOTerm ( ) const

inherited

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

: Beginning with SBML Level 2 Version 2, 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". More details can be found in SBML specifications for Level 2 Version 2 and above.

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

Examples:: printSBML.cpp.

std::string SBase::getSBOTermAsURL ( ) const

inherited

Returns the 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". More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns: the value of the "sboTerm" attribute as an identifiers.org URL, or an empty string if the value is not set.

std::string SBase::getSBOTermID ( ) const

inherited

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

: Beginning with SBML Level 2 Version 2, 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". More details can be found in SBML specifications for Level 2 Version 2 and above.

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.

int GeneProductRef::getTypeCode ( ) const

virtual

Returns the libSBML type code for this SBML object.

: LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.

The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.

Returns: the SBML type code for this object: SBML_FBC_GENEPRODUCTREF (default).

Warning: The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf::getItemTypeCode()).

See also: getElementName(); getPackageName()

Reimplemented from FbcAssociation.

std::string SBase::getURI ( ) const

inherited

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns: the URI of this element, as a text string.

See also: getSBMLDocument(); getPackageName()

void * SBase::getUserData ( ) const

inherited

Returns the user data that has been previously set via setUserData().

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns: the user data of this node, or NULL if no user data has been set.

See also: ASTNode::setUserData(void *userData)

unsigned int SBase::getVersion ( ) const

inherited

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

: 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.)

Returns: the SBML version of this SBML object.

See also: getLevel(); getNamespaces()

Examples:: addLayout.cpp, convertSBML.cpp, and printSBML.cpp.

bool GeneProductRef::hasRequiredAttributes ( ) const

virtual

Predicate returning true if all the required attributes for this GeneProductRef object have been set.

Note

The required attributes for a GeneProductRef object are:

"geneProduct"

Returns: a boolean value indicating whether all the required attributes for this object have been defined.

Reimplemented from FbcAssociation.

bool 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 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
Level 3 Version 2 Core: "http://www.sbml.org/sbml/level3/version2/core"

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

bool FbcAssociation::isFbcAnd ( ) const

virtualinherited

Returns true, if this abstract FbcAssociation is of type FbcAnd.

Returns: true, if this abstract FbcAssociation is of type FbcAnd.

bool FbcAssociation::isFbcOr ( ) const

virtualinherited

Returns true, if this abstract FbcAssociation is of type FbcOr.

Returns: true, if this abstract FbcAssociation is of type FbcOr.

bool FbcAssociation::isGeneProductRef ( ) const

virtualinherited

Returns true, if this abstract FbcAssociation is of type GeneProductRef.

Returns: true, if this abstract FbcAssociation is of type GeneProductRef.

bool SBase::isPackageEnabled ( const std::string & pkgName ) const

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 SBase::isPackageURIEnabled ( const std::string & pkgURI ) const

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 SBase::isPkgEnabled ( const std::string & pkgName ) const

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 SBase::isPkgURIEnabled ( const std::string & pkgURI ) const

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 SBase::isSetAnnotation ( ) const

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(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

Examples:: printAnnotation.cpp.

bool GeneProductRef::isSetGeneProduct ( ) const

virtual

Predicate returning true if this GeneProductRef's "geneProduct" attribute is set.

Returns: true if this GeneProductRef's "geneProduct" attribute has been set, otherwise false is returned.

bool GeneProductRef::isSetId ( ) const

virtual

Predicate returning true if this GeneProductRef's "id" attribute is set.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

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

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, it is recommended that callers use isSetIdAttribute() instead.

See also: getIdAttribute(); setIdAttribute(const std::string& sid); unsetIdAttribute(); isSetIdAttribute()

Reimplemented from SBase.

bool SBase::isSetIdAttribute ( ) const

inherited

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

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

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

See also: getIdAttribute(); setIdAttribute(const std::string& sid); unsetIdAttribute()

bool SBase::isSetMetaId ( ) const

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

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

See also: getMetaId(); setMetaId(const std::string& metaid)

Examples:: addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

bool 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 GeneProductRef::isSetName ( ) const

virtual

Predicate returning true if this GeneProductRef's "name" attribute is set.

: In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

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

See also: getName(); setName(const std::string& sid); unsetName()

Reimplemented from SBase.

bool SBase::isSetNotes ( ) const

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(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

Examples:: getAllElementsWithNotes.cpp, printNotes.cpp, and SBMLHttpResolverExample.cpp.

bool SBase::isSetSBOTerm ( ) const

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.

Examples:: printSBML.cpp.

bool SBase::isSetUserData ( ) const

inherited

Predicate returning true or false depending on whether the user data of this element has been set.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns: boolean, true if this object's user data has been set, false otherwise.

bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase * sb )

inherited

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

: 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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an object to compare with respect to namespaces.

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

bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase * sb ) const

inherited

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

: 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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an object to compare with respect to namespaces.

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

bool SBase::matchesSBMLNamespaces ( const SBase * sb )

inherited

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

: 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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an object to compare with respect to namespaces.

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

bool SBase::matchesSBMLNamespaces ( const SBase * sb ) const

inherited

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

: 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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an object to compare with respect to namespaces.

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

GeneProductRef & GeneProductRef::operator= ( const GeneProductRef & rhs )

Assignment operator for GeneProductRef.

Parameters

rhs	the object whose values are used as the basis of the assignment.

FbcAssociation * FbcAssociation::parseFbcInfixAssociation	(	const std::string &	association,
		FbcModelPlugin *	plugin,
		bool	usingId = `false`,
		bool	addMissingGP = `true`
	)

staticinherited

Parses a gene association in infix format and returns a corresponding Association object.

This parses a string that has a list of gene names and conjunctions or disjunctions. For example:

  (b2422) and (b2425) and (b2423) and (b2424) or (b2422) and (b2423) and (b2424) and (b2413) and (b3917)

The 'and' operator takes precedence over the 'or' operator, meaning that the above input string would turn into two groups of gene names: either "b2422, b2425, b2423, and b2424" or "b2422, b2423, b2424, b2413, and b3917". Parentheses may be added to make things more clear, and to encode alternative schemes.

This method also creates missing GeneProduct objects, in case the unique reference does not yet exist.

Parameters

association	the string to parse.
plugin	the FbcModelPlugin on which to add the geneProduct elements.
usingId	boolean indicating whether the infix assumes identifiers (`true`) or labels (`false` default).
addMissingGP	boolean indicating whether to add missing geneProducts (`true` default) or not (`false`).

Returns: the parsed association, or NULL in case of an error.

void SBase::read	(	XMLNode &	node,
		XMLErrorSeverityOverride_t	flag = `LIBSBML_OVERRIDE_DISABLED`
	)

inherited

Reads (initializes) this SBML object by reading from the given XMLNode.

Parameters

node	the XMLNode to read from.
flag	an optional flag that determines how how errors are logged during the reading process.

Warning: This method is computationally expensive, because the given node has to be serialized to a string first. Attempting to serialize a large tree structure (e.g., a large Model) may consume significant computer memory and time.

int SBase::removeFromParentAndDelete ( )

virtualinherited

Removes this object from its parent.

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Trigger, Delay, ListOf, Priority, ModelDefinition, and ReplacedBy.

int SBase::removeTopLevelAnnotationElement	(	const std::string &	elementName,
		const std::string	elementURI = `""`,
		bool	removeEmpty = `true`
	)

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.
removeEmpty	if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: replaceTopLevelAnnotationElement(const XMLNode *); replaceTopLevelAnnotationElement(const std::string&)

void SBase::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier 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.

Reimplemented in Port, and GraphicalObject.

void GeneProductRef::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtual

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented from SBase.

void SBase::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented in Model, Species, Compartment, KineticLaw, Rule, Parameter, EventAssignment, InitialAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.

int SBase::replaceTopLevelAnnotationElement ( const 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) followed by calling 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI, bool removeEmpty); replaceTopLevelAnnotationElement(const std::string&)

int SBase::replaceTopLevelAnnotationElement ( const std::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) followed by calling 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI); replaceTopLevelAnnotationElement(const XMLNode*)

int SBase::setAnnotation ( const XMLNode * annotation )

virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getAnnotationString(); isSetAnnotation(); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::setAnnotation ( const std::string & annotation )

virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getAnnotationString(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation); unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

virtual void FbcAssociation::setElementName ( const std::string & name )

protectedvirtualinherited

void SBase::setElementText ( const std::string & text )

protectedvirtualinherited

When overridden allows SBase elements to use the text included in between the elements tags.

The default implementation does nothing.

Parameters

text	the text string found between the element tags.

int GeneProductRef::setGeneProduct ( const std::string & geneProduct )

virtual

Sets the value of the "geneProduct" attribute of this GeneProductRef.

Parameters

geneProduct the value of the "geneProduct" attribute to be set.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int GeneProductRef::setId ( const std::string & sid )

virtual

Sets the value of the "id" attribute of this GeneProductRef.

: The string sid is copied.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters

sid	the string to use as the identifier of this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getIdAttribute(); setIdAttribute(const std::string& sid); isSetIdAttribute(); unsetIdAttribute()

Reimplemented from SBase.

int SBase::setIdAttribute ( const std::string & sid )

virtualinherited

Sets the value of the "id" attribute of this SBML object.

: The string sid is copied.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters

sid	the string to use as the identifier of this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getIdAttribute(); setIdAttribute(const std::string& sid); isSetIdAttribute(); unsetIdAttribute()

int SBase::setMetaId ( const std::string & metaid )

inherited

Sets the value of the meta-identifier 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters

metaid the identifier string to use as the value of the "metaid" attribute.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getMetaId(); isSetMetaId()

Examples:: addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.

int 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 value is drawn from the enumeration OperationReturnValues_t. 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.

Examples:: addModelHistory.cpp.

int GeneProductRef::setName ( const std::string & name )

virtual

Sets the value of the "name" attribute of this GeneProductRef.

The string in name is copied.

Parameters

name	the new name for the SBML object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBase.

int 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int SBase::setNotes ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getNotesString(); isSetNotes(); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

Examples:: createExampleSBML.cpp.

int SBase::setNotes	(	const std::string &	notes,
		bool	addXHTMLMarkup = `false`
	)

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'><p>here is my note</p></body>");

Parameters

notes	an XML string that is to be used as the content of the "notes" subelement of this object.
addXHTMLMarkup	a boolean 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getNotesString(); isSetNotes(); setNotes(const XMLNode* notes); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int SBase::setSBOTerm ( int value )

virtualinherited

Sets the value of the "sboTerm" attribute.

: Beginning with SBML Level 2 Version 2, 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". More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

value the NNNNNNN integer portion of the SBO identifier.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: setSBOTerm(const std::string &sboid)

Examples:: groups_example1.cpp, and qual_example1.cpp.

int SBase::setSBOTerm ( const std::string & sboid )

virtualinherited

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

: Beginning with SBML Level 2 Version 2, 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". More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

sboid the SBO identifier string of the form "SBO:NNNNNNN".

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: setSBOTerm(int value)

int SBase::setUserData ( void * userData )

inherited

Sets the user data of this element.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Parameters

userData specifies the new user data.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

std::string GeneProductRef::toInfix ( bool usingId = false ) const

virtual

Converts this FbcAssociation object into an infix string representation.

Returns: the association as infix string.

Reimplemented from FbcAssociation.

char * 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.

XMLNode* SBase::toXMLNode ( )

inherited

Returns this element as an XMLNode.

Returns: this element as an XMLNode.

Warning: This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.

int 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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getAnnotation(); getAnnotationString(); isSetAnnotation(); setAnnotation(const XMLNode* annotation); setAnnotation(const std::string& annotation); appendAnnotation(const XMLNode* annotation); appendAnnotation(const std::string& annotation)

Examples:: unsetAnnotation.cpp.

int SBase::unsetCVTerms ( )

inherited

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

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int GeneProductRef::unsetGeneProduct ( )

virtual

Unsets the value of the "geneProduct" attribute of this GeneProductRef.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int GeneProductRef::unsetId ( )

virtual

Unsets the value of the "id" attribute of this GeneProductRef.

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

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

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getIdAttribute(); setIdAttribute(const std::string& sid); isSetIdAttribute(); unsetIdAttribute()

Reimplemented from SBase.

int SBase::unsetIdAttribute ( )

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.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getIdAttribute(); setIdAttribute(const std::string& sid); isSetIdAttribute()

int 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int SBase::unsetModelHistory ( )

inherited

Unsets the ModelHistory object attached to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. 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 GeneProductRef::unsetName ( )

virtual

Unsets the value of the "name" attribute of this GeneProductRef.

: In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: getName(); setName(const std::string& sid); isSetName()

Reimplemented from SBase.

int 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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getNotesString(); isSetNotes(); setNotes(const XMLNode* notes); setNotes(const std::string& notes, bool addXHTMLMarkup); appendNotes(const XMLNode* notes); appendNotes(const std::string& notes); SyntaxChecker::hasExpectedXHTMLSyntax()

Examples:: unsetNotes.cpp.

int SBase::unsetSBOTerm ( )

inherited

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

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int SBase::unsetUserData ( )

inherited

Unsets the user data of this element.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.

: The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

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