Inheritance diagram for libsbmlcs.Reaction:

Detailed Description

An SBML reaction between species in an SBML model.

A reaction represents any transformation, transport or binding process, typically a chemical reaction, that can change the quantity of one or more species. In SBML, a reaction is defined primarily in terms of the participating reactants and products (and their corresponding stoichiometries), along with optional modifier species, an optional rate at which the reaction takes place, and optional parameters.

As with other major objects in SBML, Reaction has a mandatory attribute, 'id', used to give the reaction an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. In SBML Level 2 and Level 3, the reaction 'id' identifier can be used in mathematical formulas elsewhere in an SBML model to represent the rate of that reaction; this usage is explained below. Reaction also has an optional 'name' attribute, of type string. The 'id' and 'name' must be used according to the guidelines described in the SBML specification.

The species participating as reactants, products, and/or modifiers in a reaction are declared using lists of SpeciesReference and/or ModifierSpeciesReference instances stored in subelements 'listOfReactants', 'listOfProducts' and 'listOfModifiers'. Certain restrictions are placed on the appearance of species in reaction definitions:

The ability of a species to appear as a reactant or product of any reaction in a model is governed by certain flags in that species' definition; see the definition of Species for more information.
Any species appearing in the mathematical formula of the subelement 'kineticLaw' (described below) of a Reaction must be declared in at least one of that Reaction's lists of reactants, products, and/or modifiers. Put another way, it is an error for a reaction's kinetic law formula to refer to species that have not been declared for that reaction.
For SBML Levels 1, 2, and SBML Level 3 Version 1, a reaction definition can contain an empty list of reactants or an empty list of products, but it must have at least one reactant or product; in other words, a reaction without any reactant or product species is not permitted. (This restriction does not apply to modifier species, which remain optional in all cases.) In SBML Level 3 Version 2, this requirement was dropped, allowing the creation of reactions with neither reactants nor products.

A reaction can contain up to one KineticLaw object in a subelement named 'kineticLaw'. It defines the speed at which the process defined by the reaction takes place. The description of KineticLaw provides more details about its use. Note that although the inclusion of a KineticLaw object in an instance of a Reaction component is optional, there is no useful default that can be substituted in place of a missing rate expression in a reaction. Moreover, a reaction's rate cannot be defined in any other way in SBML—InitialAssignment, AssignmentRule, RateRule, AlgebraicRule, Event, and other constructs in SBML cannot be used to set the reaction rate separately. Nevertheless, for some modeling applications, reactions without any defined rate can be perfectly acceptable.

Reaction also has a boolean attribute named 'reversible' for indicating whether the reaction is reversible. This attribute is optional in SBML Level 2, with a default of true; it is mandatory in SBML Level 3 (with no default value). To say that a reaction is reversible is to say it can proceed in either the forward or the reverse direction. Although the reversibility of a reaction can sometimes be deduced by inspecting its rate expression, this is not always the case, especially for complicated expressions. Moreover, the need in SBML to allow rate expressions (i.e., KineticLaw) to be optional leads to the need for a separate flag indicating reversibility. Note that labeling a reaction as irreversible is an assertion that the reaction always proceeds in the given forward direction. (Why else would it be flagged as irreversible?) This implies the rate expression in the KineticLaw always has a non-negative value during simulations. Software tools could provide a means of optionally testing that this condition holds. The presence of reversibility information in two places (i.e., the rate expression and the 'reversible' attribute on Reaction) leaves open the possibility that a model could contain contradictory information, but the creation of such a model would be an error on the part of the software generating it.

The Reaction object class has another boolean attribute called 'fast'. This attribute is optional in SBML Level 2, with a default of false; it is mandatory in SBML Level 3 (with no default value). In SBML Level 3 Version 2, a value of true for the 'fast' attribute is deprecated in favor of all reactions having a 'fast' value of false. It is used to indicate that a reaction occurs on a vastly faster time scale than others in a system. Readers are directed to the SBML Level 2 Version 4 specification, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. SBML Level 1 and Level 2 Version 1 incorrectly claimed that software tools could ignore this attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. SBML Level 2 Versions 2–4 therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Analysis software cannot ignore the value of the 'fast' attribute because doing so may lead to different results as compared to a software system that does make use of 'fast'.

In SBML Level 3 Version 2, the 'fast' attribute was removed. All reactions are assumed to be equivalent to reactions in previous levels/versions that have a 'fast' attribute value of false. Users should be aware that even for previous levels/versions of the specification, 'fast' attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.

In SBML Level 3, the Reaction object has an additional optional attribute named 'compartment', whose value must be the identifier of a compartment defined in the enclosing Model object. The 'compartment' attribute can be used to indicate the compartment in which the reaction is assumed to take place. If the attribute is present, its value must be the identifier of a Compartment object defined in the enclosing Model object. Similar to the 'reversible' attribute, the value of the 'compartment' attribute has no direct impact on the construction of mathematical equations for the SBML model. When a kinetic law is given for a reaction, the compartment location may already be implicit in the kinetic law (although this cannot always be guaranteed). Nevertheless, software tools may find the 'compartment' attribute value useful for such purposes as analyzing the structure of the model, guiding the modeler in constructing correct rate formulas, and visualization purposes.

Readers are urged to read the SBML specification for more details about the proper use of Reaction.

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

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

int	addModifier (ModifierSpeciesReference msr)
	Adds a given ModifierSpeciesReference object as a product in this Reaction. More...

int	addModifier (Species species, string id)
	Adds the given species as a modifier to this reaction. More...

int	addModifier (Species species)
	Adds the given species as a modifier to this reaction. More...

int	addProduct (SpeciesReference sr)
	Adds a given SpeciesReference object as a product in this Reaction. More...

int	addProduct (Species species, double stoichiometry, string id, bool constant)
	Adds the given species as a product with the given stoichiometry. More...

int	addProduct (Species species, double stoichiometry, string id)
	Adds the given species as a product with the given stoichiometry. More...

int	addProduct (Species species, double stoichiometry)
	Adds the given species as a product with the given stoichiometry. More...

int	addProduct (Species species)
	Adds the given species as a product with the given stoichiometry. More...

int	addReactant (SpeciesReference sr)
	Adds a given SpeciesReference object as a reactant in this Reaction. More...

int	addReactant (Species species, double stoichiometry, string id, bool constant)
	Adds the given species as a reactant with the given stoichiometry. More...

int	addReactant (Species species, double stoichiometry, string id)
	Adds the given species as a reactant with the given stoichiometry. More...

int	addReactant (Species species, double stoichiometry)
	Adds the given species as a reactant with the given stoichiometry. More...

int	addReactant (Species species)
	Adds the given species as a reactant with the given stoichiometry. More...

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

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

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

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

int	checkCompatibility (SBase arg0)

string	checkMathMLNamespace (XMLToken elem)

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

override void	connectToChild ()

KineticLaw	createKineticLaw ()
	Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it. More...

ModifierSpeciesReference	createModifier ()
	Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it. More...

SpeciesReference	createProduct ()
	Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it. More...

SpeciesReference	createReactant ()
	Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it. More...

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

void	deleteDisabledPlugins ()
	Deletes all information stored in disabled plugins. More...

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

override void	Dispose ()

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

override bool	Equals (Object sb)

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

SBase	getAncestorOfType (int type)
	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...

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

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

string	getCompartment ()
	(SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction. More...

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

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

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

new SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`, or `null` if no such object is found. More...

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

new string	getElementName ()
	Returns the XML element name of this object, which for Reaction, is always `'reaction'`. More...

bool	getFast ()
	Returns the value of the 'fast' attribute of this Reaction. More...

override int	GetHashCode ()

new string	getId ()
	Returns the value of the 'id' attribute of this Reaction. More...

string	getIdAttribute ()
	Returns the value of the 'id' attribute of this SBML object. More...

KineticLaw	getKineticLaw ()
	Returns the KineticLaw object contained in this Reaction. More...

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

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

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

SBaseList	getListOfAllElementsFromPlugins (ElementFilter filter)

SBaseList	getListOfAllElementsFromPlugins ()

ListOfSpeciesReferences	getListOfModifiers ()
	Returns the list of modifiers in this Reaction object. More...

ListOfSpeciesReferences	getListOfProducts ()
	Returns the list of products in this Reaction object. More...

ListOfSpeciesReferences	getListOfReactants ()
	Returns the list of reactants in this Reaction object. More...

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

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

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

ModifierSpeciesReference	getModifier (long n)
	Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction. More...

ModifierSpeciesReference	getModifier (string species)
	Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction. More...

new string	getName ()
	Returns the value of the 'name' attribute of this Reaction object. More...

new XMLNamespaces	getNamespaces ()
	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...

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

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

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

long	getNumModifiers ()
	Returns the number of modifier species in this Reaction. More...

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

long	getNumProducts ()
	Returns the number of product species in this Reaction. More...

long	getNumReactants ()
	Returns the number of reactant species in this Reaction. More...

long	getPackageCoreVersion ()
	Returns the SBML Core Version within the SBML Level of the actual object. More...

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

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

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

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

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

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

SpeciesReference	getProduct (long n)
	Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction. More...

SpeciesReference	getProduct (string species)
	Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction. More...

SpeciesReference	getReactant (long n)
	Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction. More...

SpeciesReference	getReactant (string species)
	Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction. More...

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

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

bool	getReversible ()
	Returns the value of the 'reversible' attribute on the Reaction as a boolean value. More...

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

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

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

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

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

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

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

new bool	hasRequiredAttributes ()
	Predicate returning `true` if all the required attributes for this Reaction 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...

void	initDefaults ()
	Initializes the fields of this Reaction object to 'typical' default values. More...

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

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

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

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

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

bool	isSetCompartment ()
	Predicate returning `true` if this Reaction's 'compartment' attribute is set. More...

bool	isSetFast ()
	Predicate returning `true` if the value of the 'fast' attribute on this Reaction is set. More...

new bool	isSetId ()
	Predicate returning `true` if this Reaction's 'id' attribute is set. More...

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

bool	isSetKineticLaw ()
	Predicate returning `true` if this Reaction contains a kinetic law object. More...

bool	isSetMetaId ()
	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...

new bool	isSetName ()
	Predicate returning `true` if this Reaction's 'name' attribute is set. More...

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

bool	isSetReversible ()
	Predicate returning `true` if this Reaction's 'reversible' attribute is set. More...

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

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

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

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

	Reaction (long level, long version)
	Creates a new Reaction using the given SBML `level` and `version` values. More...

	Reaction (SBMLNamespaces sbmlns)
	Creates a new Reaction using the given SBMLNamespaces object `sbmlns`. More...

	Reaction (Reaction orig)
	Copy constructor; creates a copy of this Reaction. More...

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

ModifierSpeciesReference	removeModifier (long n)
	Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it. More...

ModifierSpeciesReference	removeModifier (string species)
	Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it. More...

SpeciesReference	removeProduct (long n)
	Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it. More...

SpeciesReference	removeProduct (string species)
	Removes the product species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it. More...

SpeciesReference	removeReactant (long n)
	Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it. More...

SpeciesReference	removeReactant (string species)
	Removes the reactant species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it. More...

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

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

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

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

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

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

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

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

int	setCompartment (string sid)
	Sets the value of the 'compartment' attribute of this Reaction. More...

int	setFast (bool value)
	Sets the value of the 'fast' attribute of this Reaction. More...

new int	setId (string sid)
	Sets the value of the 'id' attribute of this Reaction. More...

new int	setIdAttribute (string sid)
	Sets the value of the 'id' attribute of this SBML object. More...

int	setKineticLaw (KineticLaw kl)
	Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object. More...

int	setMetaId (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...

new int	setName (string name)
	Sets the value of the 'name' attribute of this Reaction. More...

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

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

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

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

int	setReversible (bool value)
	Sets the value of the 'reversible' attribute of this Reaction. More...

void	setSBMLNamespacesAndOwn (SBMLNamespaces disownedNs)

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

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

string	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	unsetCompartment ()
	Unsets the value of the 'compartment' attribute of this Reaction. More...

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

int	unsetFast ()
	Unsets the value of the 'fast' attribute of this Reaction. More...

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

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

int	unsetKineticLaw ()
	Unsets the 'kineticLaw' subelement of this Reaction. 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...

new int	unsetName ()
	Unsets the value of the 'name' attribute of this Reaction. More...

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

int	unsetReversible ()
	Unsets the value of the 'reversible' attribute of this Reaction. 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...

Static Public Member Functions
static bool	operator!= (SBase lhs, SBase rhs)

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

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

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

Creates a new Reaction using the given SBML level and version values.

Parameters

level	a long integer, the SBML Level to assign to this Reaction.
version	a long integer, the SBML Version to assign to this Reaction.

Exceptions

SBMLConstructorException Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.

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.

libsbmlcs.Reaction.Reaction ( SBMLNamespaces sbmlns )

Creates a new Reaction using the given SBMLNamespaces object sbmlns.

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

sbmlns an SBMLNamespaces object.

Exceptions

SBMLConstructorException Thrown if the given sbmlns is inconsistent or incompatible with this 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.

libsbmlcs.Reaction.Reaction ( Reaction orig )

Copy constructor; creates a copy of this Reaction.

Parameters

orig	the object to copy.

Member Function Documentation

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

inherited

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

Parameters

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

Returns

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

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

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

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

int libsbmlcs.SBase.addCVTerm ( CVTerm term )

inherited

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

Parameters

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

Returns

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

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

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

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

int libsbmlcs.Reaction.addModifier ( ModifierSpeciesReference msr )

Adds a given ModifierSpeciesReference object as a product in this Reaction.

The ModifierSpeciesReference instance in msr is copied.

Parameters

msr	a ModifierSpeciesReference object referring to a Species in the enclosing Model.

Returns

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

Note: 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.

See also: createModifier()

int libsbmlcs.Reaction.addModifier	(	Species	species,
		string	id
	)

Adds the given species as a modifier to this reaction.

Parameters

species	the species to be added as modifier.
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createModifier()

int libsbmlcs.Reaction.addModifier ( Species species )

Adds the given species as a modifier to this reaction.

Parameters

species	the species to be added as modifier.
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createModifier()

int libsbmlcs.Reaction.addProduct ( SpeciesReference sr )

Adds a given SpeciesReference object as a product in this Reaction.

The SpeciesReference instance in sr is copied.

Parameters

sr	a SpeciesReference object referring to a Species in the enclosing Model.

Returns

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

Note: 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.

See also: createProduct()

int libsbmlcs.Reaction.addProduct	(	Species	species,
		double	stoichiometry,
		string	id,
		bool	constant
	)

Adds the given species as a product with the given stoichiometry.

Parameters

species	the species to be added as product.
stoichiometry	an optional parameter specifying the stoichiometry of the added product (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addProduct	(	Species	species,
		double	stoichiometry,
		string	id
	)

Adds the given species as a product with the given stoichiometry.

Parameters

species	the species to be added as product.
stoichiometry	an optional parameter specifying the stoichiometry of the added product (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addProduct	(	Species	species,
		double	stoichiometry
	)

Adds the given species as a product with the given stoichiometry.

Parameters

species	the species to be added as product.
stoichiometry	an optional parameter specifying the stoichiometry of the added product (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addProduct ( Species species )

Adds the given species as a product with the given stoichiometry.

Parameters

species	the species to be added as product.
stoichiometry	an optional parameter specifying the stoichiometry of the added product (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addReactant ( SpeciesReference sr )

Adds a given SpeciesReference object as a reactant in this Reaction.

The SpeciesReference instance in sr is copied.

Parameters

sr	a SpeciesReference object referring to a Species in the enclosing Model.

Returns

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

Note: 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.

See also: createReactant()

int libsbmlcs.Reaction.addReactant	(	Species	species,
		double	stoichiometry,
		string	id,
		bool	constant
	)

Adds the given species as a reactant with the given stoichiometry.

Parameters

species	the species to be added as reactant.
stoichiometry	an optional parameter specifying the stoichiometry of the added reactant (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addReactant	(	Species	species,
		double	stoichiometry,
		string	id
	)

Adds the given species as a reactant with the given stoichiometry.

Parameters

species	the species to be added as reactant.
stoichiometry	an optional parameter specifying the stoichiometry of the added reactant (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addReactant	(	Species	species,
		double	stoichiometry
	)

Adds the given species as a reactant with the given stoichiometry.

Parameters

species	the species to be added as reactant.
stoichiometry	an optional parameter specifying the stoichiometry of the added reactant (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

int libsbmlcs.Reaction.addReactant ( Species species )

Adds the given species as a reactant with the given stoichiometry.

Parameters

species	the species to be added as reactant.
stoichiometry	an optional parameter specifying the stoichiometry of the added reactant (defaulting to 1).
id	an optional id to be given to the species reference that will be created. (defaulting to empty string, i.e. not set).
constant	an attribute specifying whether the species reference is constant or not (defaulting to true).

Returns

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

Note: 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.; the Species object itself is NOT added to the model

See also: createProduct()

new int libsbmlcs.SBase.appendAnnotation ( XMLNode annotation )

inherited

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

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

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

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

Parameters

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

Returns

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

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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(string annotation); unsetAnnotation()

new int libsbmlcs.SBase.appendAnnotation ( string annotation )

inherited

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

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

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

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

Parameters

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

Returns

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

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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); unsetAnnotation()

int libsbmlcs.SBase.appendNotes ( XMLNode notes )

inherited

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

The content of notes is copied.

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

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

Parameters

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

Returns

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

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

int libsbmlcs.SBase.appendNotes ( string notes )

inherited

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

The content of the parameter notes is copied.

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

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

Parameters

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

Returns

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

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

int libsbmlcs.SBase.checkCompatibility ( SBase arg0 )

inherited

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken elem )

inherited

new Reaction libsbmlcs.Reaction.clone ( )

Creates and returns a deep copy of this Reaction object.

Returns: the (deep) copy of this Reaction object.

override void libsbmlcs.Reaction.connectToChild ( )

virtual

Reimplemented from libsbmlcs.SBase.

KineticLaw libsbmlcs.Reaction.createKineticLaw ( )

Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it.

If this Reaction had a previous KineticLaw, it will be destroyed.

Returns: the new KineticLaw object.

ModifierSpeciesReference libsbmlcs.Reaction.createModifier ( )

Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.

Returns: a new ModifierSpeciesReference object.

SpeciesReference libsbmlcs.Reaction.createProduct ( )

Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.

Returns: a new SpeciesReference object.

SpeciesReference libsbmlcs.Reaction.createReactant ( )

Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.

Returns: a new SpeciesReference object.

void libsbmlcs.SBase.deleteDisabledPlugins ( bool recursive )

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()

void libsbmlcs.SBase.deleteDisabledPlugins ( )

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 libsbmlcs.SBase.disablePackage	(	string	pkgURI,
		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:

Parameters

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

Returns

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

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

override void libsbmlcs.Reaction.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBase.

int libsbmlcs.SBase.enablePackage	(	string	pkgURI,
		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(string pkgURI, 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 possible values returned by this function are:

See also: disablePackage(string pkgURI, string pkgPrefix)

override bool libsbmlcs.SBase.Equals ( Object sb )

inherited

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

inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_. This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code 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 SBML object type code, 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.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

SBase libsbmlcs.SBase.getAncestorOfType ( int type )

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. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_. This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code 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 SBML object type code, 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.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

XMLNode libsbmlcs.SBase.getAnnotation ( )

inherited

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

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

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

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

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

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

string libsbmlcs.SBase.getAnnotationString ( )

inherited

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

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

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

The annotations returned by this method will be in string form. 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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

long libsbmlcs.SBase.getColumn ( )

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()

string libsbmlcs.Reaction.getCompartment ( )

(SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction.

Returns: the compartment of this Reaction.

Note: The 'compartment' attribute is available in SBML Level 3, but is not present on Reaction in lower Levels of SBML.

CVTerm libsbmlcs.SBase.getCVTerm ( long 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.

CVTermList libsbmlcs.SBase.getCVTerms ( )

inherited

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

Returns: the list of CVTerms for this SBML object.

SBasePlugin libsbmlcs.SBase.getDisabledPlugin ( long 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(string package)

new SBase libsbmlcs.Reaction.getElementByMetaId ( string metaid )

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters

metaid string representing the metaid of the object to find.

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

new SBase libsbmlcs.Reaction.getElementBySId ( string id )

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

Parameters

id	string representing the id of the object to find.

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

new string libsbmlcs.Reaction.getElementName ( )

Returns the XML element name of this object, which for Reaction, is always 'reaction'.

Returns: the name of this element, i.e., 'reaction'.

bool libsbmlcs.Reaction.getFast ( )

Returns the value of the 'fast' attribute of this Reaction.

In SBML Level 3 Version 2, the 'fast' attribute was removed. All reactions are assumed to be equivalent to reactions in previous levels/versions that have a 'fast' attribute value of false. Users should be aware that even for previous levels/versions of the specification, 'fast' attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.

Returns: the 'fast' status of this Reaction.

Warning: SBML definitions before SBML Level 2 Version 2 incorrectly indicated that software tools could ignore the 'fast' attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.

override int libsbmlcs.SBase.GetHashCode ( )

inherited

new string libsbmlcs.Reaction.getId ( )

Returns the value of the 'id' attribute of this Reaction.

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 Reaction.

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

string libsbmlcs.SBase.getIdAttribute ( )

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(string sid); isSetIdAttribute(); unsetIdAttribute()

KineticLaw libsbmlcs.Reaction.getKineticLaw ( )

Returns the KineticLaw object contained in this Reaction.

Returns: the KineticLaw instance.

long libsbmlcs.SBase.getLevel ( )

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()

long libsbmlcs.SBase.getLine ( )

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()

SBaseList libsbmlcs.SBase.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElements ( )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )

inherited

ListOfSpeciesReferences libsbmlcs.Reaction.getListOfModifiers ( )

Returns the list of modifiers in this Reaction object.

Returns: the ListOfSpeciesReferences containing the references to the species acting as modifiers in this reaction.

ListOfSpeciesReferences libsbmlcs.Reaction.getListOfProducts ( )

Returns the list of products in this Reaction object.

Returns: the ListOfSpeciesReferences containing the references to the species acting as products in this reaction.

ListOfSpeciesReferences libsbmlcs.Reaction.getListOfReactants ( )

Returns the list of reactants in this Reaction object.

Returns: the ListOfSpeciesReferences containing the references to the species acting as reactants in this reaction.

string libsbmlcs.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.

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

Model libsbmlcs.SBase.getModel ( )

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 libsbmlcs.SBase.getModelHistory ( )

inherited

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

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

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

ModifierSpeciesReference libsbmlcs.Reaction.getModifier ( long n )

Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.

Callers should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.

Parameters

n	the index of the modifier species sought.

Returns: the nth modifier (as a ModifierSpeciesReference object) of this Reaction. If the index n is invalid, null is returned.

ModifierSpeciesReference libsbmlcs.Reaction.getModifier ( string species )

Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.

Parameters

species the identifier of the modifier Species ('species' attribute of the ModifierSpeciesReference object).

Returns: a ModifierSpeciesReference object, or null if no species with the given identifier species appears as a modifier in this Reaction.

new string libsbmlcs.Reaction.getName ( )

Returns the value of the 'name' attribute of this Reaction 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(string sid); unsetName()

new XMLNamespaces libsbmlcs.SBase.getNamespaces ( )

inherited

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()

XMLNode libsbmlcs.SBase.getNotes ( )

inherited

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

The optional SBML element named 'notes', present on every major SBML component type (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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

string libsbmlcs.SBase.getNotesString ( )

inherited

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

The optional SBML element named 'notes', present on every major SBML component type (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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

long libsbmlcs.SBase.getNumCVTerms ( )

inherited

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

Returns: the number of CVTerms for this SBML object.

long libsbmlcs.SBase.getNumDisabledPlugins ( )

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.

long libsbmlcs.Reaction.getNumModifiers ( )

Returns the number of modifier species in this Reaction.

Returns: the number of modifiers in this Reaction.

long libsbmlcs.SBase.getNumPlugins ( )

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)

long libsbmlcs.Reaction.getNumProducts ( )

Returns the number of product species in this Reaction.

Returns: the number of products in this Reaction.

long libsbmlcs.Reaction.getNumReactants ( )

Returns the number of reactant species in this Reaction.

Returns: the number of reactants in this Reaction.

long libsbmlcs.SBase.getPackageCoreVersion ( )

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.

string libsbmlcs.SBase.getPackageName ( )

inherited

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

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

long libsbmlcs.SBase.getPackageVersion ( )

inherited

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

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

See also: getLevel(); getVersion()

SBase libsbmlcs.SBase.getParentSBMLObject ( )

inherited

Returns the parent SBML object containing this object.

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

Returns: the parent SBML object of this SBML object.

See also: getSBMLDocument(); getModel()

SBasePlugin libsbmlcs.SBase.getPlugin ( string package )

inherited

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

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 libsbmlcs.SBase.getPlugin ( long 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(string package)

string libsbmlcs.SBase.getPrefix ( )

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.

SpeciesReference libsbmlcs.Reaction.getProduct ( long n )

Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.

Callers should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.

Parameters

n	the index of the product sought.

Returns: the nth product (as a SpeciesReference object) of this Reaction. If the index n is invalid, null is returned.

SpeciesReference libsbmlcs.Reaction.getProduct ( string species )

Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.

Parameters

species the identifier of the product Species ('species' attribute of the product SpeciesReference object).

Returns: a SpeciesReference object, or null if no species with the given identifier species appears as a product in this Reaction.

SpeciesReference libsbmlcs.Reaction.getReactant ( long n )

Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.

Callers should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.

Parameters

n	the index of the reactant sought.

Returns: the nth reactant (as a SpeciesReference object) of this Reaction. If the index n is invalid, null is returned.

SpeciesReference libsbmlcs.Reaction.getReactant ( string species )

Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.

Parameters

species the identifier of the reactant Species ('species' attribute of the reactant SpeciesReference object).

Returns: a SpeciesReference object, or null if no species with the given identifier species appears as a reactant in this Reaction.

int libsbmlcs.SBase.getResourceBiologicalQualifier ( string resource )

inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml. This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

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

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

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

int libsbmlcs.SBase.getResourceModelQualifier ( string resource )

inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml. This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

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

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

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

bool libsbmlcs.Reaction.getReversible ( )

Returns the value of the 'reversible' attribute on the Reaction as a boolean value.

Returns: the reversibility status of this Reaction.

SBMLDocument libsbmlcs.SBase.getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

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

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

Returns: the parent SBMLDocument object of this SBML object.

See also: getParentSBMLObject(); getModel()

int libsbmlcs.SBase.getSBOTerm ( )

inherited

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

Beginning with SBML Level 2 Version 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.

string libsbmlcs.SBase.getSBOTermAsURL ( )

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.

string libsbmlcs.SBase.getSBOTermID ( )

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.

new int libsbmlcs.Reaction.getTypeCode ( )

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_. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml.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_REACTION (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()

string libsbmlcs.SBase.getURI ( )

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()

long libsbmlcs.SBase.getVersion ( )

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()

new bool libsbmlcs.Reaction.hasRequiredAttributes ( )

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

The required attributes for a Reaction object are:

'id' (or 'name' in SBML Level 1)
'fast' (in Level 3 Version 1 only, where it is defined as a required attribute)
'reversible' (in Level 3 only, where it is defined as a required attribute)

Returns: true if the required attributes have been set, false otherwise.

bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )

inherited

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

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

Level 1 Version 2: "http://www.sbml.org/sbml/level1"
Level 2 Version 1: "http://www.sbml.org/sbml/level2"
Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
Level 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.

void libsbmlcs.Reaction.initDefaults ( )

Initializes the fields of this Reaction object to 'typical' default values.

The SBML Reaction component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:

Sets the 'reversible' attribute to true
Sets the 'fast' attribute to false
Marks the 'fast' attribute as not having been set for SBML Level 2, but as having been set for SBML Level 1 and SBML Level 3.

Warning: SBML definitions before SBML Level 2 Version 2 incorrectly indicated that software tools could ignore the 'fast' attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.

bool libsbmlcs.SBase.isPackageEnabled ( string pkgName )

inherited

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

The search ignores the package version.

Parameters

pkgName the name of the package.

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

See also: isPackageURIEnabled()

bool libsbmlcs.SBase.isPackageURIEnabled ( string pkgURI )

inherited

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

Parameters

pkgURI the URI of the package.

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

See also: isPackageEnabled()

bool libsbmlcs.SBase.isPkgEnabled ( string pkgName )

inherited

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

The search ignores the package version.

Parameters

pkgName the name of the package.

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

See also: isPkgURIEnabled()

bool libsbmlcs.SBase.isPkgURIEnabled ( string pkgURI )

inherited

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

Parameters

pkgURI the URI of the package.

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

See also: isPkgEnabled()

bool libsbmlcs.SBase.isSetAnnotation ( )

inherited

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

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

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

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

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

bool libsbmlcs.Reaction.isSetCompartment ( )

Predicate returning true if this Reaction's 'compartment' attribute is set.

Returns: true if the 'compartment' attribute of this Reaction is set, false otherwise.

Note: The 'compartment' attribute is available in SBML Level 3, but is not present on Reaction in lower Levels of SBML.

bool libsbmlcs.Reaction.isSetFast ( )

Predicate returning true if the value of the 'fast' attribute on this Reaction is set.

In SBML Level 3 Version 2, the 'fast' attribute was removed. All reactions are assumed to be equivalent to reactions in previous levels/versions that have a 'fast' attribute value of false. Users should be aware that even for previous levels/versions of the specification, 'fast' attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.

Returns: true if the 'fast' attribute is set, false otherwise.

Warning: SBML definitions before SBML Level 2 Version 2 incorrectly indicated that software tools could ignore the 'fast' attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.

new bool libsbmlcs.Reaction.isSetId ( )

Predicate returning true if this Reaction'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(string sid); unsetIdAttribute(); isSetIdAttribute()

bool libsbmlcs.SBase.isSetIdAttribute ( )

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(string sid); unsetIdAttribute()

bool libsbmlcs.Reaction.isSetKineticLaw ( )

Predicate returning true if this Reaction contains a kinetic law object.

Returns: true if a KineticLaw is present in this Reaction,, false otherwise.

bool libsbmlcs.SBase.isSetMetaId ( )

inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. 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(string metaid)

bool libsbmlcs.SBase.isSetModelHistory ( )

inherited

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

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

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

new bool libsbmlcs.Reaction.isSetName ( )

Predicate returning true if this Reaction'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(string sid); unsetName()

bool libsbmlcs.SBase.isSetNotes ( )

inherited

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

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

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

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

See also: getNotes(); getNotesString(); setNotes(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

bool libsbmlcs.Reaction.isSetReversible ( )

Predicate returning true if this Reaction's 'reversible' attribute is set.

Returns: true if the 'reversible' attribute of this Reaction is set, false otherwise.

bool libsbmlcs.SBase.isSetSBOTerm ( )

inherited

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

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

bool libsbmlcs.SBase.isSetUserData ( )

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 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 libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase sb )

inherited

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

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 libsbmlcs.SBase.matchesSBMLNamespaces ( SBase sb )

inherited

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

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.

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

staticinherited

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

staticinherited

new int libsbmlcs.SBase.removeFromParentAndDelete ( )

inherited

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 possible values returned by this function are:

ModifierSpeciesReference libsbmlcs.Reaction.removeModifier ( long n )

Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. The caller should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.

Parameters

n	the index of the ModifierSpeciesReference object to remove.

Returns: the removed ModifierSpeciesReference object, or null if the given index is out of range.

ModifierSpeciesReference libsbmlcs.Reaction.removeModifier ( string species )

Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.

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

Parameters

species the 'species' attribute of the ModifierSpeciesReference object.

Returns: the removed ModifierSpeciesReference object, or null if no ModifierSpeciesReference object with the given 'species' attribute species exists in this Reaction.

SpeciesReference libsbmlcs.Reaction.removeProduct ( long n )

Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. The caller should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.

Parameters

n	the index of the product SpeciesReference object to remove.

Returns: the removed product SpeciesReference object, or null if the given index is out of range.

SpeciesReference libsbmlcs.Reaction.removeProduct ( string species )

Removes the product species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.

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

Parameters

species the 'species' attribute of the product SpeciesReference object.

Returns: the removed product SpeciesReference object, or null if no product SpeciesReference object with the given 'species' attribute species exists in this Reaction.

SpeciesReference libsbmlcs.Reaction.removeReactant ( long n )

Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. The caller should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.

Parameters

n	the index of the reactant SpeciesReference object to remove.

Returns: the removed reactant SpeciesReference object, or null if the given index is out of range.

SpeciesReference libsbmlcs.Reaction.removeReactant ( string species )

Removes the reactant species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.

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

Parameters

species the 'species' attribute of the reactant SpeciesReference object.

Returns: the removed reactant SpeciesReference object, or null if no reactant SpeciesReference object with the given 'species' attribute species exists in this Reaction.

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

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 possible values returned by this function are:

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

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

inherited

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

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

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

Parameters

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
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 possible values returned by this function are:

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

int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string elementName )

inherited

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

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

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

Parameters

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
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 possible values returned by this function are:

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

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

inherited

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.

new void libsbmlcs.Reaction.renameSIdRefs	(	string	oldid,
		string	newid
	)

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.

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

inherited

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.

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode annotation )

inherited

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

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

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) 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 possible values returned by this function are:

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

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string annotation )

inherited

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

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

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) 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 possible values returned by this function are:

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

new int libsbmlcs.SBase.setAnnotation ( XMLNode annotation )

inherited

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

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

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

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

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

Parameters

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

Returns

integer value indicating success/failure of the function. 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(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

new int libsbmlcs.SBase.setAnnotation ( string annotation )

inherited

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

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

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

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

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

Parameters

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

Returns

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

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

int libsbmlcs.Reaction.setCompartment ( string sid )

Sets the value of the 'compartment' attribute of this Reaction.

The string sid is copied.

Parameters

sid	the string to use as the compartment of this Reaction.

Returns

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

Note: The 'compartment' attribute is available in SBML Level 3, but is not present on Reaction in lower Levels of SBML.

int libsbmlcs.Reaction.setFast ( bool value )

Sets the value of the 'fast' attribute of this Reaction.

In SBML Level 3 Version 2, the 'fast' attribute was removed. All reactions are assumed to be equivalent to reactions in previous levels/versions that have a 'fast' attribute value of false. Users should be aware that even for previous levels/versions of the specification, 'fast' attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.

Calling this function with an argument of true for an SBML Level 3 Version 2 Reaction will not set the value, as the attribute does not exist for that level/version.

LIBSBML_UNEXPECTED_ATTRIBUTE

Parameters

value the value of the 'fast' attribute.

Returns

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

Warning: SBML definitions before SBML Level 2 Version 2 incorrectly indicated that software tools could ignore the 'fast' attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.

new int libsbmlcs.Reaction.setId ( string sid )

Sets the value of the 'id' attribute of this Reaction.

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 possible values returned by this function are:

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

new int libsbmlcs.SBase.setIdAttribute ( string sid )

inherited

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 possible values returned by this function are:

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

int libsbmlcs.Reaction.setKineticLaw ( KineticLaw kl )

Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object.

Parameters

kl	the KineticLaw object to use.

Returns

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

int libsbmlcs.SBase.setMetaId ( 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 possible values returned by this function are:

See also: getMetaId(); isSetMetaId()

int libsbmlcs.SBase.setModelHistory ( ModelHistory history )

inherited

Sets the ModelHistory of this object.

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

Parameters

history ModelHistory of this object.

Returns

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

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

new int libsbmlcs.Reaction.setName ( string name )

Sets the value of the 'name' attribute of this Reaction.

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 possible values returned by this function are:

int libsbmlcs.SBase.setNamespaces ( XMLNamespaces xmlns )

inherited

Sets the namespaces relevant of this SBML object.

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

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

Parameters

xmlns the namespaces to set.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.SBase.setNotes ( XMLNode notes )

inherited

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

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

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

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

Parameters

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

Returns

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

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

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

inherited

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

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

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

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

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

SBMLDocument s = new SBMLDocument(3, 1);

s.setNotes('<body xmlns='http://www.w3.org/1999/xhtml'><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 possible values returned by this function are:

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

int libsbmlcs.SBase.setNotes ( string notes )

inherited

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

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

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

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

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

SBMLDocument s = new SBMLDocument(3, 1);

s.setNotes('<body xmlns='http://www.w3.org/1999/xhtml'><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 possible values returned by this function are:

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

int libsbmlcs.Reaction.setReversible ( bool value )

Sets the value of the 'reversible' attribute of this Reaction.

Parameters

value the value of the 'reversible' attribute.

Returns

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

LIBSBML_OPERATION_SUCCESS

void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces disownedNs )

inherited

new int libsbmlcs.SBase.setSBOTerm ( int value )

inherited

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 possible values returned by this function are:

See also: setSBOTerm(string &sboid)

new int libsbmlcs.SBase.setSBOTerm ( string sboid )

inherited

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 possible values returned by this function are:

See also: setSBOTerm(int value)

string libsbmlcs.SBase.toSBML ( )

inherited

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

Returns: the partial SBML that describes this SBML object.

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

XMLNode libsbmlcs.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 libsbmlcs.SBase.unsetAnnotation ( )

inherited

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

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

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

Returns

integer value indicating success/failure of the function. 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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation)

int libsbmlcs.Reaction.unsetCompartment ( )

Unsets the value of the 'compartment' attribute of this Reaction.

Returns

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

Note: The 'compartment' attribute is available in SBML Level 3, but is not present on Reaction in lower Levels of SBML.

int libsbmlcs.SBase.unsetCVTerms ( )

inherited

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

Returns

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

int libsbmlcs.Reaction.unsetFast ( )

Unsets the value of the 'fast' attribute of this Reaction.

In SBML Level 3 Version 2, the 'fast' attribute was removed. All reactions are assumed to be equivalent to reactions in previous levels/versions that have a 'fast' attribute value of false. Users should be aware that even for previous levels/versions of the specification, 'fast' attribute values of true never achieved widespread support, and many software packages may ignore it. To achieve the same or similar effects as setting the fast attribute to true for a given reaction, the KineticLaw attribute should be constructed to produce a value in the desired time scale, or else the reaction could be replaced with an AssignmentRule or AlgebraicRule.

Returns

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

Warning: SBML definitions before SBML Level 2 Version 2 incorrectly indicated that software tools could ignore the 'fast' attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to true. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to true, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.

new int libsbmlcs.SBase.unsetId ( )

inherited

Unsets 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

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

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

int libsbmlcs.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 possible values returned by this function are:

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute()

int libsbmlcs.Reaction.unsetKineticLaw ( )

Unsets the 'kineticLaw' subelement of this Reaction.

Returns

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

int libsbmlcs.SBase.unsetMetaId ( )

inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. 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 possible values returned by this function are:

int libsbmlcs.SBase.unsetModelHistory ( )

inherited

Unsets the ModelHistory object attached to this object.

Returns

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

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

new int libsbmlcs.Reaction.unsetName ( )

Unsets the value of the 'name' attribute of this Reaction.

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 possible values returned by this function are:

See also: getName(); setName(string sid); isSetName()

int libsbmlcs.SBase.unsetNotes ( )

inherited

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

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

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

Returns

integer value indicating success/failure of the function. 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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.Reaction.unsetReversible ( )

Unsets the value of the 'reversible' attribute of this Reaction.

Returns

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

int libsbmlcs.SBase.unsetSBOTerm ( )

inherited

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

Returns

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

int libsbmlcs.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 data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns

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

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation