Inheritance diagram for libsbmlcs.Species:

Detailed Description

An SBML species – a pool of entities.

A species in SBML refers to a pool of entities that (a) are considered indistinguishable from each other for the purposes of the model, (b) participate in reactions, and (c) are located in a specific compartment. The SBML Species object class is intended to represent these pools.

As with other major constructs in SBML, Species has a mandatory attribute, 'id', used to give the species type an identifier in the model. The identifier must be a text string conforming to the identifer syntax permitted in SBML. Species also has an optional 'name' attribute, of type string. The 'id' and 'name' must be used according to the guidelines described in the SBML specifications.

The required attribute 'compartment' is used to identify the compartment in which the species is located. The attribute's value must be the identifier of an existing Compartment object. It is important to note that there is no default value for the 'compartment' attribute on Species; every species in an SBML model must be assigned a compartment explicitly. (This also implies that every model with one or more Species objects must define at least one Compartment object.)

The initial amount and concentration of a species

The optional attributes 'initialAmount' and 'initialConcentration', both having a data type of double, can be used to set the initial quantity of the species in the compartment where the species is located. These attributes are mutually exclusive; i.e., only one can have a value on any given instance of a Species object. Missing 'initialAmount' and 'initialConcentration' values implies that their values either are unknown, or to be obtained from an external source, or determined by an InitialAssignment or other SBML construct elsewhere in the model.

A species' initial quantity in SBML is set by the 'initialAmount' or 'initialConcentration' attribute exactly once. If the 'constant' attribute is true, then the value of the species' quantity is fixed and cannot be changed except by an InitialAssignment. These methods differ in that the 'initialAmount' and 'initialConcentration' attributes can only be used to set the species quantity to a literal floating-point number, whereas the use of an InitialAssignment object allows the value to be set using an arbitrary mathematical expression (which, thanks to MathML's expressiveness, may evaluate to a rational number). If the species' 'constant' attribute is false, the species' quantity value may be overridden by an InitialAssignment or changed by AssignmentRule or AlgebraicRule, and in addition, for t > 0, it may also be changed by a RateRule, Event objects, and as a result of being a reactant or product in one or more Reaction objects. (However, some constructs are mutually exclusive; see the SBML specifications for the precise details.) It is not an error to define 'initialAmount' or 'initialConcentration' on a species and also redefine the value using an InitialAssignment, but the 'initialAmount' or 'initialConcentration' setting in that case is ignored. The SBML specifications provide additional information about the semantics of assignments, rules and values for simulation time t <= 0.

SBML Level 2 additionally stipulates that in cases where a species' compartment has a 'spatialDimensions' value of 0 (zero), the species cannot have a value for 'initialConcentration' because the concepts of concentration and density break down when a container has zero dimensions.

The units of a species' amount or concentration

When the attribute 'initialAmount' is set, the unit of measurement associated with the value of 'initialAmount' is specified by the Species attribute 'substanceUnits'. When the 'initialConcentration' attribute is set, the unit of measurement associated with this concentration value is {unit of amount} divided by {unit of size}, where the {unit of amount} is specified by the Species 'substanceUnits' attribute, and the {unit of size} is specified by the 'units' attribute of the Compartment object in which the species is located. Note that in either case, a unit of amount is involved and determined by the 'substanceUnits' attribute. Note these two attributes alone do not determine the units of the species when the species identifier appears in a mathematical expression; that aspect is determined by the attribute 'hasOnlySubstanceUnits' discussed below.

In SBML Level 3, if the 'substanceUnits' attribute is not set on a given Species object instance, then the unit of amount for that species is inherited from the 'substanceUnits' attribute on the enclosing Model object instance. If that attribute on Model is not set either, then the unit associated with the species' quantity is undefined.

In SBML Level 2, if the 'substanceUnits' attribute is not set on a given Species object instance, then the unit of amount for that species is taken from the predefined SBML unit identifier 'substance'. The value assigned to 'substanceUnits' must be chosen from one of the following possibilities: one of the base unit identifiers defined in SBML, the built-in unit identifier 'substance', or the identifier of a new unit defined in the list of unit definitions in the enclosing Model object. The chosen units for 'substanceUnits' must be be 'dimensionless', 'mole', 'item', 'kilogram', 'gram', or units derived from these.

As noted at the beginning of this section, simply setting 'initialAmount' or 'initialConcentration' alone does not determine whether a species identifier represents an amount or a concentration when it appears elsewhere in an SBML model. The role of the attribute 'hasOnlySubstanceUnits' is to indicate whether the units of the species, when the species identifier appears in mathematical formulas, are intended to be concentration or amount. The attribute takes on a boolean value. In SBML Level 3, the attribute has no default value and must always be set in a model; in SBML Level 2, it has a default value of false.

The units of the species are used in the following ways:

When the species' identifier appears in a MathML formula, it represents the species' quantity, and the unit of measurement associated with the quantity is as described above.
The 'math' elements of AssignmentRule, InitialAssignment and EventAssignment objects referring to this species should all have the same units as the unit of measurement associated with the species quantity.
In a RateRule object that defines the rate of change of the species' quantity, the unit associated with the rule's 'math' element should be equal to the unit of the species' quantity divided by the model-wide unit of time; in other words, {unit of species quantity}/{unit of time}.

The 'constant' and 'boundaryCondition' attributes

The Species object class has two boolean attributes named 'constant' and 'boundaryCondition', used to indicate whether and how the quantity of that species can vary during a simulation. In SBML Level 2 they are optional; in SBML Level 3 they are mandatory. The following table shows how to interpret the combined values of these attributes.

Interpretation of species' `constant` and `boundaryCondition` attributes.
`constant` value	`boundaryCondition` value	Can have assignment or rate rule?	Can be reactant or product?	Species' quantity can be changed by
`true`	`true`	no	yes	(never changes)
`false`	`true`	yes	yes	rules and events
`true`	`false`	no	no	(never changes)
`false`	`false`	yes	yes	reactions or rules (but not both at the same time), and events

By default, when a species is a product or reactant of one or more reactions, its quantity is determined by those reactions. In SBML, it is possible to indicate that a given species' quantity is not determined by the set of reactions even when that species occurs as a product or reactant; i.e., the species is on the boundary of the reaction system, and its quantity is not determined by the reactions. The boolean attribute 'boundaryCondition' can be used to indicate this. A value of false indicates that the species is part of the reaction system. In SBML Level 2, the attribute has a default value of false, while in SBML Level 3, it has no default.

The 'constant' attribute indicates whether the species' quantity can be changed at all, regardless of whether by reactions, rules, or constructs other than InitialAssignment. A value of false indicates that the species' quantity can be changed. (This is also a common value because the purpose of most simulations is precisely to calculate changes in species quantities.) In SBML Level 2, the attribute has a default value of false, while in SBML Level 3, it has no default. Note that the initial quantity of a species can be set by an InitialAssignment irrespective of the value of the 'constant' attribute.

In practice, a 'boundaryCondition' value of true means a differential equation derived from the reaction definitions should not be generated for the species. However, the species' quantity may still be changed by AssignmentRule, RateRule, AlgebraicRule, Event, and InitialAssignment constructs if its 'constant' attribute is false. Conversely, if the species' 'constant' attribute is true, then its value cannot be changed by anything except InitialAssignment.

A species having 'boundaryCondition'=false and 'constant'=false can appear as a product and/or reactant of one or more reactions in the model. If the species is a reactant or product of a reaction, it must not also appear as the target of any AssignmentRule or RateRule object in the model. If instead the species has 'boundaryCondition'= false and 'constant'=true, then it cannot appear as a reactant or product, or as the target of any AssignmentRule, RateRule or EventAssignment object in the model.

Finally, it is worth clarifying that while the constant and boundaryCondition attributes restrict whether and how the species amount changes, the same is not true of a species' concentration. In SBML, the concentration of a species is a quantity that depends on the size of the compartment in which it is located. A compartment's size may change, and therefore, so can the concentration of a species even if the amount of the species remains unchanged. A species' concentration may therefore vary even if the Species object's constant attribute is set to true in a model.

The conversionFactor attribute in SBML Level 3

In SBML Level 3, Species has an additional optional attribute, 'conversionFactor', that defines a conversion factor that applies to a particular species. The value must be the identifier of a Parameter object instance defined in the model. That Parameter object must be a constant, meaning its 'constant' attribute must be set to true. If a given Species object definition defines a value for its 'conversionFactor' attribute, it takes precedence over any factor defined by the Model object's 'conversionFactor' attribute.

The unit of measurement associated with a species' quantity can be different from the unit of extent of reactions in the model. SBML Level 3 avoids implicit unit conversions by providing an explicit way to indicate any unit conversion that might be required. The use of a conversion factor in computing the effects of reactions on a species' quantity is explained in detail in the SBML Level 3 specification document. Because the value of the 'conversionFactor' attribute is the identifier of a Parameter object, and because parameters can have units attached to them, the transformation from reaction extent units to species units can be completely specified using this approach.

Note that the unit conversion factor is only applied when calculating the effect of a reaction on a species. It is not used in any rules or other SBML constructs that affect the species, and it is also not used when the value of the species is referenced in a mathematical expression.

The speciesType attribute in SBML Level 2 Versions 2–4

In SBML Level 2 Versions 2–4, each species in a model may optionally be designated as belonging to a particular species type. The optional attribute 'speciesType' is used to identify the species type of the chemical entities that make up the pool represented by the Species objects. The attribute's value must be the identifier of an existing SpeciesType object in the model. If the 'speciesType' attribute is not present on a particular species definition, it means the pool contains chemical entities of a type unique to that pool; in effect, a virtual species type is assumed for that species, and no other species can belong to that species type. The value of 'speciesType' attributes on species have no effect on the numerical interpretation of a model; simulators and other numerical analysis software may ignore 'speciesType' attributes.

There can be only one species of a given species type in any given compartment of a model. More specifically, for all Species objects having a value for the 'speciesType' attribute, the pair

('speciesType' attribute value, 'compartment' attribute value)

must be unique across the set of all Species object in a model.

The spatialSizeUnits attribute in SBML Level 2 Versions 1–2

In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because many software tools do no properly interpret this unit declaration and it is incompatible with all SBML specifications after Level 2 Version 3.

Additional considerations for interpreting the numerical value of a species

Species are unique in SBML in that they have a kind of duality: a species identifier may stand for either substance amount (meaning, a count of the number of individual entities) or a concentration or density (meaning, amount divided by a compartment size). The previous sections explain the meaning of a species identifier when it is referenced in a mathematical formula or in rules or other SBML constructs; however, it remains to specify what happens to a species when the compartment in which it is located changes in size.

When a species definition has a 'hasOnlySubstanceUnits' attribute value of false and the size of the compartment in which the species is located changes, the default in SBML is to assume that it is the concentration that must be updated to account for the size change. This follows from the principle that, all other things held constant, if a compartment simply changes in size, the size change does not in itself cause an increase or decrease in the number of entities of any species in that compartment. In a sense, the default is that the amount of a species is preserved across compartment size changes. Upon such size changes, the value of the concentration or density must be recalculated from the simple relationship concentration = amount / size if the value of the concentration is needed (for example, if the species identifier appears in a mathematical formula or is otherwise referenced in an SBML construct). There is one exception: if the species' quantity is determined by an AssignmentRule, RateRule, AlgebraicRule, or an EventAssignment and the species has a 'hasOnlySubstanceUnits' attribute value of false, it means that the concentration is assigned by the rule or event; in that case, the amount must be calculated when the compartment size changes. (Events also require additional care in this situation, because an event with multiple assignments could conceivably reassign both a species quantity and a compartment size simultaneously. Please refer to the SBML specifications for the details.)

Note that the above only matters if a species has a 'hasOnlySubstanceUnits' attribute value of false, meaning that the species identifier refers to a concentration wherever the identifier appears in a mathematical formula. If instead the attribute's value is true, then the identifier of the species always stands for an amount wherever it appears in a mathematical formula or is referenced by an SBML construct. In that case, there is never a question about whether an assignment or event is meant to affect the amount or concentration: it is always the amount.

A particularly confusing situation can occur when the species has 'constant' attribute value of true in combination with a 'hasOnlySubstanceUnits' attribute value of false. Suppose this species is given a value for 'initialConcentration'. Does a 'constant' value of true mean that the concentration is held constant if the compartment size changes? No; it is still the amount that is kept constant across a compartment size change. The fact that the species was initialized using a concentration value is irrelevant.

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...

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

virtual void	connectToChild ()

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...

bool	getBoundaryCondition ()
	Get the value of the 'boundaryCondition' attribute. More...

int	getCharge ()
	Get the value of the 'charge' attribute. More...

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

string	getCompartment ()
	Get the compartment in which this species is located. More...

bool	getConstant ()
	Get the value of the 'constant' attribute. More...

string	getConversionFactor ()
	Get the value of the 'conversionFactor' attribute. 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...

UnitDefinition	getDerivedUnitDefinition ()
	Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration. 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 a specific 'metaid' attribute value, 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 Species, is always `'species'`. More...

override int	GetHashCode ()

bool	getHasOnlySubstanceUnits ()
	Get the value of the 'hasOnlySubstanceUnits' attribute. More...

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

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

double	getInitialAmount ()
	Get the value of the 'initialAmount' attribute. More...

double	getInitialConcentration ()
	Get the value of the 'initialConcentration' attribute. 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 ()

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...

new string	getName ()
	Returns the value of the 'name' attribute of this Species 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	getNumPlugins ()
	Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. 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...

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...

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...

string	getSpatialSizeUnits ()
	Get the value of the 'spatialSizeUnits' attribute. More...

string	getSpeciesType ()
	Get the type of this Species object object. More...

string	getSubstanceUnits ()
	Get the value of the 'substanceUnits' attribute. More...

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

string	getUnits ()
	Get the value of the 'units' attribute. 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 Species 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 Species object to 'typical' defaults 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	isSetBoundaryCondition ()
	Predicate returning `true` if this Species object's 'boundaryCondition' attribute is set. More...

bool	isSetCharge ()
	Predicate returning `true` if this Species object's 'charge' attribute is set. More...

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

bool	isSetConstant ()
	Predicate returning `true` if this Species object's 'constant' attribute is set. More...

bool	isSetConversionFactor ()
	Predicate returning `true` if this Species object's 'conversionFactor' attribute is set. More...

bool	isSetHasOnlySubstanceUnits ()
	Predicate returning `true` if this Species object's 'hasOnlySubstanceUnits' attribute is set. More...

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

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

bool	isSetInitialAmount ()
	Predicate returning `true` if this Species object's 'initialAmount' attribute is set. More...

bool	isSetInitialConcentration ()
	Predicate returning `true` if this Species object's 'initialConcentration' attribute is set. 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 Species object's 'name' attribute is set. More...

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

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

bool	isSetSpatialSizeUnits ()
	Predicate returning `true` if this Species object's 'spatialSizeUnits' attribute is set. More...

bool	isSetSpeciesType ()
	Predicate returning `true` if this Species object's 'speciesType' attribute is set. More...

bool	isSetSubstanceUnits ()
	Predicate returning `true` if this Species object's 'substanceUnits' attribute is set. More...

bool	isSetUnits ()
	Predicate returning `true` if this Species object's 'units' 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...

new int	removeFromParentAndDelete ()
	Removes this object from its parent. 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	setBoundaryCondition (bool value)
	Sets the 'boundaryCondition' attribute of this Species object. More...

int	setCharge (int value)
	Sets the 'charge' attribute of this Species object. More...

int	setCompartment (string sid)
	Sets the 'compartment' attribute of this Species object. More...

int	setConstant (bool value)
	Sets the 'constant' attribute of this Species object. More...

int	setConversionFactor (string sid)
	Sets the value of the 'conversionFactor' attribute of this Species object. More...

int	setHasOnlySubstanceUnits (bool value)
	Sets the 'hasOnlySubstanceUnits' attribute of this Species object. More...

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

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

int	setInitialAmount (double value)
	Sets the 'initialAmount' attribute of this Species and marks the field as set. More...

int	setInitialConcentration (double value)
	Sets the 'initialConcentration' attribute of this Species and marks the field as set. 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 Species. 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...

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...

int	setSpatialSizeUnits (string sid)
	(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object. More...

int	setSpeciesType (string sid)
	Sets the 'speciesType' attribute of this Species object. More...

int	setSubstanceUnits (string sid)
	Sets the 'substanceUnits' attribute of this Species object. More...

int	setUnits (string sname)
	(SBML Level 1 only) Sets the units of this Species object. More...

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

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

	Species (Species orig)
	Copy constructor; creates a copy of this Species object. 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	unsetBoundaryCondition ()
	Unsets the 'boundaryCondition' attribute value of this Species object. More...

int	unsetCharge ()
	Unsets the 'charge' attribute value of this Species object. More...

int	unsetCompartment ()
	Unsets the 'compartment' attribute value of this Species object. More...

int	unsetConstant ()
	Unsets the value of the 'constant' attribute of this Species object. More...

int	unsetConversionFactor ()
	Unsets the 'conversionFactor' attribute value of this Species object. More...

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

int	unsetHasOnlySubstanceUnits ()
	Unsets the 'hasOnlySubstanceUnits' attribute value of this Species object. 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	unsetInitialAmount ()
	Unsets the 'initialAmount' attribute value of this Species object. More...

int	unsetInitialConcentration ()
	Unsets the 'initialConcentration' attribute value of this Species object. More...

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

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

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

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

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

int	unsetSpatialSizeUnits ()
	Unsets the 'spatialSizeUnits' attribute value of this Species object. More...

int	unsetSpeciesType ()
	Unsets the 'speciesType' attribute value of this Species object. More...

int	unsetSubstanceUnits ()
	Unsets the 'substanceUnits' attribute value of this Species object. More...

int	unsetUnits ()
	Unsets the 'units' attribute value of this Species 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.Species.Species	(	long	level,
		long	version
	)

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

Parameters

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

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.Species.Species ( SBMLNamespaces sbmlns )

Creates a new Species 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.

It is worth emphasizing that although this constructor does not take an identifier argument, in SBML Level 2 and beyond, the 'id' (identifier) attribute of a Species is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method Species::setId().

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.Species.Species ( Species orig )

Copy constructor; creates a copy of this Species object.

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.

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 Species libsbmlcs.Species.clone ( )

Creates and returns a deep copy of this Species object.

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

virtual void libsbmlcs.SBase.connectToChild ( )

virtualinherited

Reimplemented in libsbmlcs.Model, libsbmlcs.Reaction, libsbmlcs.Event, libsbmlcs.Layout, libsbmlcs.Submodel, libsbmlcs.UnitDefinition, libsbmlcs.KineticLaw, libsbmlcs.BoundingBox, libsbmlcs.SBaseRef, libsbmlcs.GraphicalObject, libsbmlcs.GeneralGlyph, libsbmlcs.ReactionGlyph, libsbmlcs.ListOf, libsbmlcs.SpeciesReferenceGlyph, libsbmlcs.ReferenceGlyph, libsbmlcs.CubicBezier, libsbmlcs.LineSegment, and libsbmlcs.Curve.

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.Species.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()

bool libsbmlcs.Species.getBoundaryCondition ( )

Get the value of the 'boundaryCondition' attribute.

Returns: true if this Species' 'boundaryCondition' attribute value is true, false otherwise.

int libsbmlcs.Species.getCharge ( )

Get the value of the 'charge' attribute.

Returns: the charge of this Species object.

Note: Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species is deprecated and in SBML Level 3 it does not exist at all. Its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

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.Species.getCompartment ( )

Get the compartment in which this species is located.

The compartment is designated by its identifier.

Returns: the value of the 'compartment' attribute of this Species object, as a string.

bool libsbmlcs.Species.getConstant ( )

Get the value of the 'constant' attribute.

Returns: true if this Species's 'constant' attribute value is true, false otherwise.

Note: The attribute 'constant' is only available in SBML Levels 2 and 3. It does not exist on Species in Level 1.

string libsbmlcs.Species.getConversionFactor ( )

Get the value of the 'conversionFactor' attribute.

Returns: the conversionFactor of this Species, as a string.

Note: The 'conversionFactor' attribute was introduced in SBML Level 3. It does not exist on Species in SBML Levels 1 and 2.

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.

UnitDefinition libsbmlcs.Species.getDerivedUnitDefinition ( )

Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration.

Species in SBML have an attribute ('substanceUnits') for declaring the units of measurement intended for the species' amount or concentration (depending on which one applies). In the absence of a value given for 'substanceUnits', the units are taken from the enclosing Model's definition of 'substance' or 'substance'/(size of the compartment) in which the species is located, or finally, if these are not redefined by the Model, the relevant SBML default units for those quantities. Following that procedure, the method getDerivedUnitDefinition()returns a UnitDefinition based on the interpreted units of this species's amount or concentration.

Note that the functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return null.

Note also that unit declarations for Species are in terms of the identifier of a unit, but this method returns a UnitDefinition object, not a unit identifier. It does this by constructing an appropriate UnitDefinition. Callers may find this particularly useful when used in conjunction with the helper methods on UnitDefinition for comparing different UnitDefinition objects.

In SBML Level 2 specifications prior to Version 3, Species includes an additional attribute named 'spatialSizeUnits', which allows explicitly setting the units of size for initial concentration. The getDerivedUnitDefinition()takes this into account for models expressed in SBML Level 2 Versions 1 and 2.

Returns: a UnitDefinition that expresses the units of this Species, or null if one cannot be constructed.

See also: getSubstanceUnits()

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.SBase.getElementByMetaId ( string metaid )

inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

Parameters

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

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

new SBase libsbmlcs.SBase.getElementBySId ( string id )

inherited

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

Parameters

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

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

new string libsbmlcs.Species.getElementName ( )

Returns the XML element name of this object, which for Species, is always 'species'.

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

override int libsbmlcs.SBase.GetHashCode ( )

inherited

bool libsbmlcs.Species.getHasOnlySubstanceUnits ( )

Get the value of the 'hasOnlySubstanceUnits' attribute.

Returns: true if this Species' 'hasOnlySubstanceUnits' attribute value is true, false otherwise.

Note: The 'hasOnlySubstanceUnits' attribute does not exist in SBML Level 1.

new string libsbmlcs.Species.getId ( )

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

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 Species.

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()

double libsbmlcs.Species.getInitialAmount ( )

Get the value of the 'initialAmount' attribute.

Returns: the initialAmount of this Species, as a floating point number.

double libsbmlcs.Species.getInitialConcentration ( )

Get the value of the 'initialConcentration' attribute.

Returns: the initialConcentration of this Species,, as a floating point number.

Note: The attribute 'initialConcentration' is only available in SBML Level 2 and 3. It does not exist on Species in Level 1.

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

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.

new string libsbmlcs.Species.getName ( )

Returns the value of the 'name' attribute of this Species 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.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.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.

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.

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.

string libsbmlcs.Species.getSpatialSizeUnits ( )

Get the value of the 'spatialSizeUnits' attribute.

Returns: the value of the 'spatialSizeUnits' attribute of this Species object, as a string.

Warning: In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with levels and versions of SBML beyond Level 2 Version 2.

string libsbmlcs.Species.getSpeciesType ( )

Get the type of this Species object object.

Returns: the value of the 'speciesType' attribute of this Species as a string.

Note: The 'speciesType' attribute is only available in SBML Level 2 Versions 2–4.

string libsbmlcs.Species.getSubstanceUnits ( )

Get the value of the 'substanceUnits' attribute.

Returns: the value of the 'substanceUnits' attribute of this Species, as a string. An empty string indicates that no units have been assigned.

Note: There is an important distinction to be made between no units assigned, and assuming a value without units has any specific unit such as dimensionless. In SBML, default units are never attributed to numbers, and numbers without units are not automatically assumed to have the unit dimensionless. Please consult the relevant SBML specification document for a more in-depth explanation of this topic and the SBML unit system.

See also: isSetSubstanceUnits(); setSubstanceUnits(string sid)

new int libsbmlcs.Species.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_SPECIES (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.Species.getUnits ( )

Get the value of the 'units' attribute.

Returns: the units of this Species (L1 only).

Note: The 'units' attribute is defined only in SBML Level 1. In SBML Level 2 and Level 3, it has been replaced by a combination of 'substanceUnits' and the units of the Compartment object in which a species is located. In SBML Level 2 Versions 1–2, an additional attribute 'spatialSizeUnits' helps determine the units of the species quantity, but this attribute was removed in later versions of SBML Level 2.

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.Species.hasRequiredAttributes ( )

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

The required attributes for a Species object are:

'id' (or 'name' in SBML Level 1)
'compartment'
'initialAmount' (required in SBML Level 1 only; optional otherwise)
'hasOnlySubstanceUnits' (required in SBML Level 3; optional in SBML Level 2)
'boundaryCondition' (required in SBML Level 3; optional in Levels 1 and 2)
'constant' (required in SBML Level 3; optional in SBML Level 2)

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.Species.initDefaults ( )

Initializes the fields of this Species object to 'typical' defaults values.

The SBML Species 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 'boundaryCondition' to false
Sets 'constant' to false
sets 'hasOnlySubstanceUnits' to false
(Applies to Level 3 models only) Sets attribute 'substanceUnits' to mole

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.Species.isSetBoundaryCondition ( )

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

Returns: true if the 'boundaryCondition' attribute of this Species is set, false otherwise.

bool libsbmlcs.Species.isSetCharge ( )

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

Returns: true if the 'charge' attribute of this Species is set, false otherwise.

Note: Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species is deprecated and in SBML Level 3 it does not exist at all. Its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

bool libsbmlcs.Species.isSetCompartment ( )

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

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

bool libsbmlcs.Species.isSetConstant ( )

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

Returns: true if the 'constant' attribute of this Species is set, false otherwise.

Note: The attribute 'constant' is only available in SBML Levels 2 and 3. It does not exist on Species in Level 1.

bool libsbmlcs.Species.isSetConversionFactor ( )

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

Returns: true if the 'conversionFactor' attribute of this Species is set, false otherwise.

Note: The 'conversionFactor' attribute was introduced in SBML Level 3. It does not exist on Species in SBML Levels 1 and 2.

bool libsbmlcs.Species.isSetHasOnlySubstanceUnits ( )

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

Returns: true if the 'hasOnlySubstanceUnits' attribute of this Species is set, false otherwise.

Note: The 'hasOnlySubstanceUnits' attribute does not exist in SBML Level 1.

new bool libsbmlcs.Species.isSetId ( )

Predicate returning true if this Species 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.

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.Species.isSetInitialAmount ( )

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

Returns: true if the 'initialAmount' attribute of this Species is set, false otherwise.

Note: In SBML Level 1, Species' 'initialAmount' is required and therefore should always be set. (However, in Level 1, the attribute has no default value either, so this method will not return true until a value has been assigned.) In SBML Level 2, 'initialAmount' is optional and as such may or may not be set.

bool libsbmlcs.Species.isSetInitialConcentration ( )

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

Returns: true if the 'initialConcentration' attribute of this Species is set, false otherwise.

Note: The attribute 'initialConcentration' is only available in SBML Level 2 and 3. It does not exist on Species in Level 1.

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.Species.isSetName ( )

Predicate returning true if this Species object'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.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.Species.isSetSpatialSizeUnits ( )

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

Returns: true if the 'spatialSizeUnits' attribute of this Species is set, false otherwise.

Warning: In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with levels and versions of SBML beyond Level 2 Version 2.

bool libsbmlcs.Species.isSetSpeciesType ( )

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

Returns: true if the 'speciesType' attribute of this Species is set, false otherwise.

Note: The 'speciesType' attribute is only available in SBML Level 2 Versions 2–4.

bool libsbmlcs.Species.isSetSubstanceUnits ( )

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

Returns: true if the 'substanceUnits' attribute of this Species is set, false otherwise.

bool libsbmlcs.Species.isSetUnits ( )

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

Returns: true if the 'units' attribute of this Species 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:

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.Species.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.Species.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

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.Species.setBoundaryCondition ( bool value )

Sets the 'boundaryCondition' attribute of this Species object.

Parameters

value boolean value for the 'boundaryCondition' attribute.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.Species.setCharge ( int value )

Sets the 'charge' attribute of this Species object.

Parameters

value an integer to which to set the 'charge' to.

Note: Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species is deprecated and in SBML Level 3 it does not exist at all. Its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

Returns

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

int libsbmlcs.Species.setCompartment ( string sid )

Sets the 'compartment' attribute of this Species object.

Parameters

sid	the identifier of a Compartment object defined elsewhere in this Model.

Returns

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

int libsbmlcs.Species.setConstant ( bool value )

Sets the 'constant' attribute of this Species object.

Parameters

value a boolean value for the 'constant' attribute.

Returns

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

Note: The attribute 'constant' is only available in SBML Levels 2 and 3. It does not exist on Species in Level 1.

int libsbmlcs.Species.setConversionFactor ( string sid )

Sets the value of the 'conversionFactor' attribute of this Species object.

The string in sid is copied.

Parameters

sid	the new conversionFactor for the Species.

Returns

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

Note: The 'conversionFactor' attribute was introduced in SBML Level 3. It does not exist on Species in SBML Levels 1 and 2.

int libsbmlcs.Species.setHasOnlySubstanceUnits ( bool value )

Sets the 'hasOnlySubstanceUnits' attribute of this Species object.

Parameters

value boolean value for the 'hasOnlySubstanceUnits' attribute.

Returns

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

Note: The 'hasOnlySubstanceUnits' attribute does not exist in SBML Level 1.

new int libsbmlcs.Species.setId ( string sid )

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

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.Species.setInitialAmount ( double value )

Sets the 'initialAmount' attribute of this Species and marks the field as set.

This method also unsets the 'initialConcentration' attribute.

Parameters

value the value to which the 'initialAmount' attribute should be set.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.Species.setInitialConcentration ( double value )

Sets the 'initialConcentration' attribute of this Species and marks the field as set.

This method also unsets the 'initialAmount' attribute.

Parameters

value the value to which the 'initialConcentration' attribute should be set.

Returns

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

Note: The attribute 'initialConcentration' is only available in SBML Level 2 and 3. It does not exist on Species in Level 1.

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.Species.setName ( string name )

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

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()

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)

int libsbmlcs.Species.setSpatialSizeUnits ( string sid )

(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object.

Parameters

sid	the identifier of the unit to use.

Returns

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

Warning: In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with levels and versions of SBML beyond Level 2 Version 2.

int libsbmlcs.Species.setSpeciesType ( string sid )

Sets the 'speciesType' attribute of this Species object.

Parameters

sid	the identifier of a SpeciesType object defined elsewhere in this Model.

Returns

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

Note: The 'speciesType' attribute is only available in SBML Level 2 Versions 2–4.

int libsbmlcs.Species.setSubstanceUnits ( string sid )

Sets the 'substanceUnits' attribute of this Species object.

Parameters

sid	the identifier of the unit to use.

Returns

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

int libsbmlcs.Species.setUnits ( string sname )

(SBML Level 1 only) Sets the units of this Species object.

Parameters

sname the identifier of the unit to use.

Returns

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

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.Species.unsetBoundaryCondition ( )

Unsets the 'boundaryCondition' attribute value of this Species object.

Returns

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

int libsbmlcs.Species.unsetCharge ( )

Unsets the 'charge' attribute value of this Species object.

Returns

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

Note: Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species is deprecated and in SBML Level 3 it does not exist at all. Its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

int libsbmlcs.Species.unsetCompartment ( )

Unsets the 'compartment' attribute value of this Species object.

Returns

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

int libsbmlcs.Species.unsetConstant ( )

Unsets the value of the 'constant' attribute of this Species object.

Returns

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

See also: isSetConstant(); setConstant(); getConstant()

int libsbmlcs.Species.unsetConversionFactor ( )

Unsets the 'conversionFactor' attribute value of this Species object.

Returns

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

Note: The 'conversionFactor' attribute was introduced in SBML Level 3. It does not exist on Species in SBML Levels 1 and 2.

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.Species.unsetHasOnlySubstanceUnits ( )

Unsets the 'hasOnlySubstanceUnits' attribute value of this Species object.

Returns

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

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.Species.unsetInitialAmount ( )

Unsets the 'initialAmount' attribute value of this Species object.

Returns

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

int libsbmlcs.Species.unsetInitialConcentration ( )

Unsets the 'initialConcentration' attribute value of this Species object.

Returns

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

Note: The attribute 'initialConcentration' is only available in SBML Level 2 and 3. It does not exist on Species in Level 1.

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.Species.unsetName ( )

Unsets the value of the 'name' attribute of this Species 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

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.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.Species.unsetSpatialSizeUnits ( )

Unsets the 'spatialSizeUnits' attribute value of this Species object.

Returns

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

Warning: In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with levels and versions of SBML beyond Level 2 Version 2.

int libsbmlcs.Species.unsetSpeciesType ( )

Unsets the 'speciesType' attribute value of this Species object.

Returns

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

Note: The attribute 'speciesType' is only available in SBML Level 2 Versions 2–4.

int libsbmlcs.Species.unsetSubstanceUnits ( )

Unsets the 'substanceUnits' attribute value of this Species object.

Returns

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

int libsbmlcs.Species.unsetUnits ( )

Unsets the 'units' attribute value of this Species 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

The initial amount and concentration of a species

The units of a species' amount or concentration

The 'constant' and 'boundaryCondition' attributes

The conversionFactor attribute in SBML Level 3

The speciesType attribute in SBML Level 2 Versions 2–4

The spatialSizeUnits attribute in SBML Level 2 Versions 1–2

Additional considerations for interpreting the numerical value of a species

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation