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libSBML C# API
5.18.0
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libSBML C# API
5.18.0
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The rule type AlgebraicRule is derived from the parent class Rule. It is used to express equations that are neither assignments of model variables nor rates of change. AlgebraicRule does not add any attributes to the basic Rule; its role is simply to distinguish this case from the other cases.
In the context of a simulation, algebraic rules are in effect at all times, t >= 0. For purposes of evaluating expressions that involve the delay 'csymbol' (see the SBML specification), algebraic rules are considered to apply also at t <= 0. Please consult the relevant SBML specification for additional information about the semantics of assignments, rules, and entity values for simulation time t <= 0.
An SBML model must not be overdetermined. The ability to define arbitrary algebraic expressions in an SBML model introduces the possibility that a model is mathematically overdetermined by the overall system of equations constructed from its rules, reactions and events. Therefore, if an algebraic rule is introduced in a model, for at least one of the entities referenced in the rule's 'math' element the value of that entity must not be completely determined by other constructs in the model. This means that at least this entity must not have the attribute 'constant'=true and there must also not be a rate rule or assignment rule for it. Furthermore, if the entity is a Species object, its value must not be determined by reactions, which means that it must either have the attribute 'boundaryCondition'=true or else not be involved in any reaction at all. These restrictions are explained in more detail in the SBML specification documents.
In SBML Levels 2 and 3, Reaction object identifiers can be referenced in the 'math' expression of an algebraic rule, but reaction rates can never be determined by algebraic rules. This is true even when a reaction does not contain a KineticLaw object. (In such cases of missing kinetic law definitions, the model is valid but incomplete; the rates of reactions lacking kinetic laws are simply undefined, and not determined by the algebraic rule.)
In SBML Level 2 and Level 3 Version 1, the 'math' subelement of the AlgebraicRule is required. In SBML Level 3 Version 2, this rule is relaxed, and the subelement is optional. If an AlgebraicRule with no 'math' child is present in the model, no additional mathematical constraints on the model are added by the rule. This may represent a situation where the model itself is unfinished, or the missing information may be provided by an SBML Level 3 package.
Finally, any symbol that appears as the target of a rateOf csymbol (AST_FUNCTION_RATE_OF, introduced in SBML Level 3 Version 2) may not be determined by an AlgebraicRule. This is because the rateOf csymbol is defined as applying only to symbols whose rates of change are easily determinable.
Users should note that these rules about what symbols may not be determined by an AlgebraicRule may be used to discover what symbol is being determined by an AlgebraicRule. If three symbols appear in the math element of an AlgebraicRule, the first of which is flagged constant=true, and the second of which appears as the target of a rateOf csymbol, one may conclude that the AlgebraicRule must be used to determine the value of the third symbol. This is, in fact, a principle use (outside of validation) of the constant attribute: its use in allowing software to properly identify the dependent variable in an AlgebraicRule.
In SBML Level 3 as well as Level 2, rules are separated into three subclasses for the benefit of model analysis software. The three subclasses are based on the following three different possible functional forms (where x is a variable, f is some arbitrary function returning a numerical result, V is a vector of variables that does not include x, and W is a vector of variables that may include x):
| Algebraic: | left-hand side is zero | 0 = f(W) |
| Assignment: | left-hand side is a scalar: | x = f(V) |
| Rate: | left-hand side is a rate-of-change: | dx/dt = f(W) |
In their general form given above, there is little to distinguish between assignment and algebraic rules. They are treated as separate cases for the following reasons:
The approach taken to covering these cases in SBML is to define an abstract Rule structure containing a subelement, 'math', to hold the right-hand side expression, then to derive subtypes of Rule that add attributes to distinguish the cases of algebraic, assignment and rate rules. The 'math' subelement must contain a MathML expression defining the mathematical formula of the rule. This MathML formula must return a numerical value. The formula can be an arbitrary expression referencing the variables and other entities in an SBML model.
Each of the three subclasses of Rule (AssignmentRule, AlgebraicRule, RateRule) inherit the the 'math' subelement and other fields from SBase. The AssignmentRule and RateRule classes add an additional attribute, 'variable'. See the definitions of AssignmentRule, AlgebraicRule and RateRule for details about the structure and interpretation of each one.
An important design goal of SBML rule semantics is to ensure that a model's simulation and analysis results will not be dependent on when or how often rules are evaluated. To achieve this, SBML needs to place two restrictions on rule use. The first concerns algebraic loops in the system of assignments in a model, and the second concerns overdetermined systems.
The combined set of InitialAssignment, AssignmentRule and KineticLaw objects in a model constitute a set of assignment statements that should be considered as a whole. (A KineticLaw object is counted as an assignment because it assigns a value to the symbol contained in the 'id' attribute of the Reaction object in which it is defined.) This combined set of assignment statements must not contain algebraic loops—dependency chains between these statements must terminate. To put this more formally, consider a directed graph in which nodes are assignment statements and directed arcs exist for each occurrence of an SBML species, compartment or parameter symbol in an assignment statement's 'math' subelement. Let the directed arcs point from the statement assigning the symbol to the statements that contain the symbol in their 'math' subelement expressions. This graph must be acyclic.
Similarly, the combined set of RateRule and Reaction objects constitute a set of definitions for the rates of change of various model entities (namely, the objects identified by the values of the 'variable' attributes of the RateRule objects, and the 'species' attributes of the SpeciesReference objects in each Reaction). In SBML Level 3 Version 2, these rates of change may be referenced directly using the rateOf csymbol, but may not thereby contain algebraic loops—dependency chains between these statements must terminate. More formally, consider a directed graph in which the nodes are the definitions of different variables' rates of change, and directed arcs exist for each occurrence of a variable referenced by a rateOf csymbol from any RateRule or KineticLaw object in the model. Let the directed arcs point from the variable referenced by the rateOf csymbol (call it x) to the variable(s) determined by the 'math' expression in which x appears. This graph must be acyclic.
SBML does not specify when or how often rules should be evaluated. Eliminating algebraic loops ensures that assignment statements can be evaluated any number of times without the result of those evaluations changing. As an example, consider the set of equations x = x + 1, y = z + 200 and z = y + 100. If this set of equations were interpreted as a set of assignment statements, it would be invalid because the rule for x refers to x (exhibiting one type of loop), and the rule for y refers to z while the rule for z refers back to y (exhibiting another type of loop). Conversely, the following set of equations would constitute a valid set of assignment statements: x = 10, y = z + 200, and z = x + 100.
An SBML model must not be overdetermined; that is, a model must not define more equations than there are unknowns in a model. A valid SBML model that does not contain AlgebraicRule structures cannot be overdetermined.
LibSBML implements the static analysis procedure described in Appendix B of the SBML Level 3 specification for assessing whether a model is overdetermined.
(In summary, assessing whether a given continuous, deterministic, mathematical model is overdetermined does not require dynamic analysis; it can be done by analyzing the system of equations created from the model. One approach is to construct a bipartite graph in which one set of vertices represents the variables and the other the set of vertices represents the equations. Place edges between vertices such that variables in the system are linked to the equations that determine them. For algebraic equations, there will be edges between the equation and each variable occurring in the equation. For ordinary differential equations (such as those defined by rate rules or implied by the reaction rate definitions), there will be a single edge between the equation and the variable determined by that differential equation. A mathematical model is overdetermined if the maximal matchings of the bipartite graph contain disconnected vertexes representing equations. If one maximal matching has this property, then all the maximal matchings will have this property; i.e., it is only necessary to find one maximal matching.)
SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for distinguishing rules; specifically, it uses an attribute whose value is drawn from an enumeration of 3 values. LibSBML supports this using methods that work with the enumeration values listed below.
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... | |
| AlgebraicRule (long level, long version) | |
Creates a new AlgebraicRule object using the given SBML level and version values. More... | |
| AlgebraicRule (SBMLNamespaces sbmlns) | |
Creates a new AlgebraicRule object using the given SBMLNamespaces object sbmlns. 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 AlgebraicRule | clone () |
| Creates and returns a deep copy of this AlgebraicRule object. More... | |
| virtual void | connectToChild () |
| bool | containsUndeclaredUnits () |
Predicate returning true if the math expression of this Rule contains parameters/numbers with undeclared units. More... | |
| void | deleteDisabledPlugins (bool recursive) |
| Deletes all information stored in disabled plugins. More... | |
| void | deleteDisabledPlugins () |
| Deletes all information stored in disabled plugins. More... | |
| int | disablePackage (string pkgURI, string pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| override void | Dispose () |
| int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| override bool | Equals (Object sb) |
| SBase | getAncestorOfType (int type, string pkgName) |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| SBase | getAncestorOfType (int type) |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| XMLNode | getAnnotation () |
| Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
| string | getAnnotationString () |
| Returns the content of the 'annotation' subelement of this object as a character string. More... | |
| long | getColumn () |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| 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 () |
| Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule. 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. More... | |
| string | getFormula () |
| Returns the mathematical expression of this Rule in text-string form. More... | |
| override int | GetHashCode () |
| new string | getId () |
| Returns the value of the 'variable' attribute of this Rule (NOT the 'id'). More... | |
| string | getIdAttribute () |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| int | getL1TypeCode () |
| Returns the SBML Level 1 type code for this Rule object. 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 () |
| new ASTNode | getMath () |
| Get the mathematical formula of this Rule as an ASTNode tree. More... | |
| string | getMetaId () |
| Returns the value of the 'metaid' attribute of this SBML object. More... | |
| Model | getModel () |
| Returns the Model object for the SBML Document in which the current object is located. More... | |
| ModelHistory | getModelHistory () |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| new string | getName () |
| Returns the value of the 'name' attribute of this SBML 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... | |
| int | getType () |
| Returns a code representing the type of rule this is. More... | |
| new int | getTypeCode () |
| Returns the libSBML type code for this SBML object. More... | |
| string | getUnits () |
| Returns the units for the mathematical formula of this Rule. More... | |
| string | getURI () |
| Gets the namespace URI to which this element belongs to. More... | |
| string | getVariable () |
| Get the value of the 'variable' attribute of this Rule object. 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 AlgebraicRule object have been set. More... | |
| new bool | hasRequiredElements () |
Predicate returning true if all the required elements for this Rule 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... | |
| bool | isAlgebraic () |
Predicate returning true if this Rule is an AlgebraicRule. More... | |
| bool | isAssignment () |
Predicate returning true if this Rule is an AssignmentRule. More... | |
| bool | isCompartmentVolume () |
Predicate returning true if this Rule is an CompartmentVolumeRule or equivalent. 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 | isParameter () |
Predicate returning true if this Rule is an ParameterRule or equivalent. 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 | isRate () |
Predicate returning true if this Rule is a RateRule (SBML Levels 2–3) or has a 'type' attribute value of 'rate' (SBML Level 1). More... | |
| bool | isScalar () |
Predicate returning true if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of 'scalar' (SBML Level 1). More... | |
| bool | isSetAnnotation () |
Predicate returning true if this object's 'annotation' subelement exists and has content. More... | |
| bool | isSetFormula () |
Predicate returning true if this Rule's mathematical expression is set. More... | |
| new bool | isSetId () |
Predicate returning true if a call to getId() returns a non-empty string. More... | |
| bool | isSetIdAttribute () |
Predicate returning true if this object's 'id' attribute is set. More... | |
| bool | isSetMath () |
Predicate returning true if this Rule's mathematical expression 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 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 | isSetUnits () |
Predicate returning true if this Rule'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 | isSetVariable () |
Predicate returning true if this Rule's 'variable' attribute is set. More... | |
| bool | isSpeciesConcentration () |
Predicate returning true if this Rule is a SpeciesConcentrationRule or equivalent. 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 | setFormula (string formula) |
| Sets the 'math' subelement of this Rule to an expression in text-string form. More... | |
| new int | setId (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| new int | setIdAttribute (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| int | setL1TypeCode (int type) |
| Sets the SBML Level 1 type code for this Rule. More... | |
| new int | setMath (ASTNode math) |
| Sets the 'math' subelement of this Rule to a copy of the given ASTNode. 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 SBML object. 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 | setUnits (string sname) |
| Sets the units for this Rule. More... | |
| int | setVariable (string sid) |
| Sets the 'variable' attribute value of this Rule 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 | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML 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 | 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 SBML 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 | unsetUnits () |
| Unsets the 'units' for this Rule. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| int | unsetVariable () |
| Unsets the value of the 'variable' attribute of this Rule object. More... | |
Static Public Member Functions | |
| static bool | operator!= (SBase lhs, SBase rhs) |
| static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
| bool | swigCMemOwn |
| libsbmlcs.AlgebraicRule.AlgebraicRule | ( | long | level, |
| long | version | ||
| ) |
Creates a new AlgebraicRule object using the given SBML level and version values.
| level | the SBML Level to assign to this AlgebraicRule object. |
| version | the SBML Version to assign to this AlgebraicRule object. |
| SBMLConstructorException | Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version. |
| libsbmlcs.AlgebraicRule.AlgebraicRule | ( | SBMLNamespaces | sbmlns | ) |
Creates a new AlgebraicRule object 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.
| sbmlns | an SBMLNamespaces object. |
| SBMLConstructorException | Thrown if the given sbmlns is inconsistent or incompatible with this object. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| 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. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| 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. |
create) for alternatives that do not lead to these issues.
|
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.
| annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
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.
| annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
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.
| notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object. |
|
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.
| notes | an XML string that is to appended to the content of the 'notes' subelement of this object. |
|
inherited |
|
inherited |
| new AlgebraicRule libsbmlcs.AlgebraicRule.clone | ( | ) |
Creates and returns a deep copy of this AlgebraicRule object.
|
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.
|
inherited |
Predicate returning true if the math expression of this Rule contains parameters/numbers with undeclared units.
true if the math expression of this Rule includes parameters/numbers with undeclared units, false otherwise.true indicates that the UnitDefinition returned by getDerivedUnitDefinition() may not accurately represent the units of the expression.
|
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.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
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.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
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:
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
|
virtual |
Reimplemented from libsbmlcs.SBase.
|
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).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
inherited |
|
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.
| 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. |
null if no ancestor exists.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.
|
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.
| 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. |
null if no ancestor exists.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.
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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.
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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.
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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule.
The units are calculated based on the mathematical expression in the Rule and the model quantities referenced by <ci> elements used within that expression. The method Rule::getDerivedUnitDefinition() returns the calculated units, to the extent that libSBML can compute them.
null.null if one cannot be constructed.
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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.
| n | the index of the disabled plug-in to return. |
n is invalid, null is returned.
|
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.
| metaid | string representing the 'metaid' attribute value of the object to find. |
|
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.
| id | string representing the 'id' attribute value of the object to find. |
|
inherited |
Returns the XML element name of this object.
The returned value can be any of a number of different strings, depending on the SBML Level in use and the kind of Rule object this is. The rules as of libSBML version 5.18.0 are the following:
'rateRule' 'assignmentRule' 'algebraicRule' 'specieConcentrationRule' 'speciesConcentrationRule' 'compartmentVolumeRule' 'parameterRule' 'unknownRule' Beware that the last ('unknownRule') is not a valid SBML element name.
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inherited |
Returns the mathematical expression of this Rule in text-string form.
The text string is produced by libsbml.formulaToString(); please consult the documentation for that function to find out more about the format of the text-string formula.
|
inherited |
|
inherited |
Returns the value of the 'variable' attribute of this Rule (NOT the 'id').
The 'variable' attribute of a Rule indicates the element which the results of the 'math' are to be applied. An AlgebraicRule has no 'variable', and will always return an empty string.
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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.
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inherited |
Returns the SBML Level 1 type code for this Rule object.
This method only applies to SBML Level 1 model objects. If this is not an SBML Level 1 rule object, this method will return SBML_UNKNOWN.
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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.)
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get the mathematical formula of this Rule as an ASTNode tree.
|
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.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null if none exist.
|
inherited |
Returns the value of the 'name' attribute of this SBML 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.
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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.
null in certain very usual circumstances where a namespace is not set.
|
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().
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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.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
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.
|
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.
|
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.)
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inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"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.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0 will be returned if this element belongs to the SBML Level 3 Core package.
|
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.
|
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.
| package | the name or URI of the package. |
|
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.
| n | the index of the plug-in to return. |
n is invalid, null is returned.
|
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.
|
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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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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.
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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.
-1 if the value is not set.
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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.
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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.
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Returns a code representing the type of rule this is.
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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.
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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.
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Get the value of the 'variable' attribute of this Rule object.
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.
The 'variable' attribute of a Rule indicates the element which the results of the 'math' are to be applied. An AlgebraicRule has no 'variable', and will always return an empty string.
null if this object is an AlgebraicRule object, or if the attribute is unset.
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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.)
| new bool libsbmlcs.AlgebraicRule.hasRequiredAttributes | ( | ) |
Predicate returning true if all the required attributes for this AlgebraicRule object have been set.
In SBML Levels 2–3, there is no required attribute for an AlgebraicRule object. For Level 1, the only required attribute is 'formula'.
true if the required attributes have been set, false otherwise.
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Predicate returning true if all the required elements for this Rule object have been set.
The only required element for a Rule object is the 'math' subelement in SBML Level 2 and Level 3 Version 1. In SBML Level 3 Version 2+, it is no longer required.
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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:
http://www.sbml.org/sbml/level1" http://www.sbml.org/sbml/level2" http://www.sbml.org/sbml/level2/version2" http://www.sbml.org/sbml/level2/version3" http://www.sbml.org/sbml/level2/version4" http://www.sbml.org/sbml/level2/version5" http://www.sbml.org/sbml/level3/version1/core" http://www.sbml.org/sbml/level3/version2/core" true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
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Predicate returning true if this Rule is an AlgebraicRule.
true if this Rule is an AlgebraicRule, false otherwise.
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Predicate returning true if this Rule is an AssignmentRule.
true if this Rule is an AssignmentRule, false otherwise.
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Predicate returning true if this Rule is an CompartmentVolumeRule or equivalent.
This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit CompartmentVolumeRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns true if the symbol is the identifier of a Compartment object defined in the model.
true if this Rule is a CompartmentVolumeRule, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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Predicate returning true if this Rule is an ParameterRule or equivalent.
This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit ParameterRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns true if the symbol is the identifier of a Parameter object defined in the model.
true if this Rule is a ParameterRule, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
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inherited |
Predicate returning true if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of 'scalar' (SBML Level 1).
true if this Rule is an AssignmentRule (Level 2) or has type 'scalar' (Level 1), false otherwise.
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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.
true if a 'annotation' subelement exists, false otherwise.
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inherited |
Predicate returning true if this Rule's mathematical expression is set.
This method is equivalent to isSetMath(). This version is present for easier compatibility with SBML Level 1, in which mathematical formulas were written in text-string form.
true if the mathematical formula for this Rule is set, false otherwise.
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inherited |
Predicate returning true if a call to getId() returns a non-empty string.
For most objects, this function will return true if its 'id' attribute is set, and false if it is not, or if the object has no 'id' attribute at all. However, for an EventAssignment or a Rule, isSetId() checks whether the 'variable' attribute is set, and for an InitialAssignment, it checks whether the 'symbol' attribute is set. Because those elements will also have an 'id' attribute in SBML Level 3 Version 2 which isSetId() will not check, the function itself is deprecated, and it is recommended to use isSetIdAttribute() in all cases where one needs to know whether the 'id' attribute is set, and to use EventAssignment::isSetVariable(), Rule::isSetVariable() and InitialAssignment::isSetSymbol() when the status of the 'variable' or 'symbol' attributes need to be checked.
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.
true if the 'id' attribute of this SBML object is set, false otherwise.
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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.
true if the 'id' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this Rule's mathematical expression is set.
This method is equivalent to isSetFormula().
true if the formula (or equivalently the math) for this Rule is set, false otherwise.
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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.
true if the 'metaid' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object has a ModelHistory object attached to it.
true if the ModelHistory of this object is set, false otherwise.
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inherited |
Predicate returning true if this 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.
true if the 'name' attribute of this SBML object is set, false otherwise.
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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.
true if a 'notes' subelement exists, false otherwise.
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inherited |
Predicate returning true if this object's 'sboTerm' attribute is set.
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
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inherited |
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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.
true if this object's user data has been set, false otherwise.
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inherited |
Predicate returning true if this Rule's 'variable' attribute is set.
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.
true if the 'variable' attribute value of this Rule is set, false otherwise.
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inherited |
Predicate returning true if this Rule is a SpeciesConcentrationRule or equivalent.
This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit SpeciesConcentrationRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns true if the symbol is the identifier of a Species object defined in the model.
true if this Rule is a SpeciesConcentrationRule, false otherwise.
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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.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is a subset of sb's, false otherwise.
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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.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is the same as sb's, false otherwise.
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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.
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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.
| 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). |
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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.
| 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). |
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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.
| 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). |
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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.
| oldid | the old identifier. |
| newid | the new identifier. |
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inherited |
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.
| oldid | the old identifier. |
| newid | the new identifier. |
|
inherited |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
|
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.
| annotation | XMLNode representing the replacement top level 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.
| annotation | string representing the replacement top level 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).
| annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object. |
|
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).
| annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object. |
|
inherited |
Sets the 'math' subelement of this Rule to an expression in text-string form.
This is equivalent to setMath(ASTNode math). The provision of using text-string formulas is retained for easier SBML Level 1 compatibility. The formula is converted to an ASTNode internally.
| formula | a mathematical formula in text-string form. |
|
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.
| sid | the string to use as the identifier of this object. |
|
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.
| sid | the string to use as the identifier of this object. |
|
inherited |
Sets the SBML Level 1 type code for this Rule.
| type | the SBML Level 1 type code for this Rule. The allowable values are SBML_COMPARTMENT_VOLUME_RULE, SBML_PARAMETER_RULE, and SBML_SPECIES_CONCENTRATION_RULE. |
type value is not one of the above.
|
inherited |
Sets the 'math' subelement of this Rule to a copy of the given ASTNode.
| math | the AST structure of the mathematical formula. |
|
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.
| metaid | the identifier string to use as the value of the 'metaid' attribute. |
|
inherited |
Sets the ModelHistory of this object.
The content of history is copied, and this object's existing model history content is deleted.
| history | ModelHistory of this object. |
|
inherited |
Sets the value of the 'name' attribute of this SBML object.
The string in name is copied.
| name | the new name for the SBML object. |
|
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.
| xmlns | the namespaces to set. |
|
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.
| notes | an XML structure that is to be used as the content of the 'notes' subelement of this object. |
|
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.
| 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. |
|
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.
| 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. |
|
inherited |
|
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.
| value | the NNNNNNN integer portion of the SBO identifier. |
|
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.
|
inherited |
Sets the units for this Rule.
| sname | the identifier of the units. |
|
inherited |
Sets the 'variable' attribute value of this Rule object.
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.
| sid | the identifier of a Compartment, Species or Parameter elsewhere in the enclosing Model object. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
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.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
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.
|
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.
|
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.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
inherited |
Unsets the value of the 'name' attribute of this SBML 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.
|
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.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
|
inherited |
Unsets the 'units' for this Rule.
|
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.
|
inherited |
Unsets the value of the 'variable' attribute of this Rule object.
|
protectedinherited |