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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial values to entities in a model. The simplest and most basic is to set the values of the appropriate attributes in the relevant components; for example, the initial value of a model parameter (whether it is a constant or a variable) can be assigned by setting its 'value' attribute directly in the model definition. However, this approach is not suitable when the value must be calculated, because the initial value attributes on different components such as species, compartments, and parameters are single values and not mathematical expressions. In those situations, the InitialAssignment construct can be used; it permits the calculation of the value of a constant or the initial value of a variable from the values of other quantities in a model.
As explained below, the provision of InitialAssignment does not mean that models necessarily must use this construct when defining initial values of quantities in a model. If a value can be set directly using the relevant attribute of a component in a model, then that approach may be more efficient and more portable to other software tools. InitialAssignment should be used when the other mechanism is insufficient for the needs of a particular model.
The InitialAssignment construct has some similarities to AssignmentRule. The main differences are: (a) an InitialAssignment can set the value of a constant whereas an AssignmentRule cannot, and (b) unlike AssignmentRule, an InitialAssignment definition only applies up to and including the beginning of simulation time, i.e., t <= 0, while an AssignmentRule applies at all times.
InitialAssignment has a required attribute, 'symbol', whose value must follow the guidelines for identifiers described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification). The value of this attribute in an InitialAssignment object can be the identifier of a Compartment, Species, SpeciesReference (in SBML Level 3), global Parameter, or (as of SBML Level 3 Version 2) the identifier of a SBML Level 3 package element with mathematical meaning. The InitialAssignment defines the initial value of the constant or variable referred to by the 'symbol' attribute. (The attribute's name is 'symbol' rather than 'variable' because it may assign values to constants as well as variables in a model.) Note that an initial assignment cannot be made to reaction identifiers, that is, the 'symbol' attribute value of an InitialAssignment cannot be an identifier that is the 'id' attribute value of a Reaction object in the model. This is identical to a restriction placed on rules.
InitialAssignment also has a 'math' subelement that contains a MathML expression used to calculate the value of the constant or the initial value of the variable. This subelement is required in SBML Level 2 and SBML Level 3 Version 1, but the requirement was relaxed in SBML Level 3 Version 2, making it optional. The units of the value computed by the formula in the 'math' subelement should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the units associated with the identifier given in the 'symbol' attribute. (That is, the units are the units of the species, compartment, or parameter, as appropriate for the kind of object identified by the value of 'symbol'.)
InitialAssignment was introduced in SBML Level 2 Version 2. It is not available in SBML Level 2 Version 1 nor in any version of Level 1.
The value calculated by an InitialAssignment object overrides the value assigned to the given symbol by the object defining that symbol. For example, if a compartment's 'size' attribute is set in its definition, and the model also contains an InitialAssignment having that compartment's identifier as its 'symbol' attribute value, then the interpretation is that the 'size' assigned in the Compartment object should be ignored and the value assigned based on the computation defined in the InitialAssignment. Initial assignments can take place for Compartment, Species, global Parameter, SpeciesReference (in Level 3), and SBML Level 3 package elements (in Level 3 Version 2), regardless of the value of their 'constant' attribute.
The actions of all InitialAssignment objects are in general terms the same, but differ in the precise details depending on the type of variable being set:
In the case of a species, an InitialAssignment sets the referenced species' initial quantity (concentration or amount of substance) to the value determined by the formula in the 'math' subelement. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the species.
In the case of a compartment, an InitialAssignment sets the referenced compartment's initial size to the size determined by the formula in 'math'. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the size of the compartment.
In the case of a parameter, an InitialAssignment sets the referenced parameter's initial value to that determined by the formula in 'math'. The overall units of the formula should (in SBML Level 2 Version 4 and SBML Level 3) or must (in previous Versions) be the same as the units defined for the parameter.
(For SBML Level 3 only) In the case of a species reference, an initial assignment sets the initial value of the stoichiometry of the referenced reactant or product to the value determined by the formula in 'math'. The unit associated with the value produced by the 'math' formula should be consistent with the unit 'dimensionless', because reactant and product stoichiometries in reactions are dimensionless quantities.
(For SBML Level 3 Version 2 only) In the case of an object from an SBML Level 3 package, an InitialAssignment sets the referenced object's initial value (however such values are defined by the package) to the value of the formula in math. The unit of measurement associated with the value produced by the formula should be the same as that object's units attribute value (if it has such an attribute), or be equal to the units of model components of that type (if objects of that class are defined by the package as having the same units).
If the symbol attribute of an InitialAssignment object references an object in an SBML namespace that is not understood by the interpreter reading a given SBML document (that is, if the object is defined by an SBML Level 3 package that the software does not support), the assignment must be ignored–the object's initial value will not need to be set, as the interpreter could not understand that package. If an interpreter cannot establish whether a referenced object is missing from the model or instead is defined in an SBML namespace not understood by the interpreter, it may produce a warning to the user. (The latter situation may only arise if an SBML package is present in the SBML document with a package:required attribute of 'true'.)
In the context of a simulation, initial assignments establish values that are in effect prior to and including the start of simulation time, i.e., t <= 0. Section 3.4.8 in the SBML Level 2 Version 4 and SBML Level 3 specifications provides information about the interpretation of assignments, rules, and entity values for simulation time up to and including the start time t = 0; this is important for establishing the initial conditions of a simulation if the model involves expressions containing the delay 'csymbol'.
There cannot be two initial assignments for the same symbol in a model; that is, a model must not contain two or more InitialAssignment objects that both have the same identifier as their 'symbol' attribute value. A model must also not define initial assignments and assignment rules for the same entity. That is, there cannot be both an InitialAssignment and an AssignmentRule for the same symbol in a model, because both kinds of constructs apply prior to and at the start of simulated time—allowing both to exist for a given symbol would result in indeterminism).
The ordering of InitialAssignment objects is not significant. The combined set of InitialAssignment, AssignmentRule and KineticLaw objects form a set of assignment statements that must be considered as a whole. The combined set of assignment statements should not contain algebraic loops: a chain of dependency between these statements should terminate. (More formally, consider the directed graph of assignment statements where nodes are a model's assignment statements and directed arcs exist for each occurrence of a symbol in an assignment statement 'math' attribute. The directed arcs in this graph start from the statement assigning the symbol and end at the statement that contains the symbol in their math elements. Such a graph must be acyclic.)
Finally, it is worth being explicit about the expected behavior in the following situation. Suppose (1) a given symbol has a value x assigned to it in its definition, and (2) there is an initial assignment having the identifier as its 'symbol' value and reassigning the value to y, and (3) the identifier is also used in the mathematical formula of a second initial assignment. What value should the second initial assignment use? It is y, the value assigned to the symbol by the first initial assignment, not whatever value was given in the symbol's definition. This follows directly from the behavior described above: if an InitialAssignment object exists for a given symbol, then the symbol's value is overridden by that initial assignment.
Public Member Functions | |
| def | __init__ (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | addCVTerm (self, term, newBag=False) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| def | appendAnnotation (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | appendNotes (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | clone (self) |
| Creates and returns a deep copy of this InitialAssignment object. More... | |
| def | connectToChild (self) |
| def | containsUndeclaredUnits (self, args) |
Predicate returning True if the math expression of this InitialAssignment contains parameters/numbers with undeclared units. More... | |
| def | deleteDisabledPlugins (self, recursive=True) |
| Deletes all information stored in disabled plugins. More... | |
| def | disablePackage (self, pkgURI, pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| def | enablePackage (self, pkgURI, pkgPrefix, flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| def | getAncestorOfType (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getAnnotation (self, args) |
| Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
| def | getAnnotationString (self, args) |
| Returns the content of the 'annotation' subelement of this object as a character string. More... | |
| def | getColumn (self) |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| def | getCVTerm (self, n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| def | getCVTerms (self, args) |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| def | getDerivedUnitDefinition (self, args) |
| Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this InitialAssignment. More... | |
| def | getDisabledPlugin (self, args) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| def | getElementByMetaId (self, args) |
Returns the first child element it can find with a specific 'metaid' attribute value, or None if no such object is found. More... | |
| def | getElementBySId (self, args) |
Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found. More... | |
| def | getElementName (self) |
Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'. More... | |
| def | getId (self) |
| Returns the value of the 'symbol' attribute of this InitialAssignment (NOT the 'id'). More... | |
| def | getIdAttribute (self) |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| def | getLevel (self) |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| def | getLine (self) |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| def | getListOfAllElements (self, filter=None) |
| Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More... | |
| def | getListOfAllElementsFromPlugins (self, filter=None) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| def | getMath (self) |
| Get the mathematical formula of this InitialAssignment. More... | |
| def | getMetaId (self) |
| Returns the value of the 'metaid' attribute of this SBML object. More... | |
| def | getModel (self) |
| Returns the Model object for the SBML Document in which the current object is located. More... | |
| def | getModelHistory (self, args) |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| def | getName (self) |
| Returns the value of the 'name' attribute of this SBML object. More... | |
| def | getNamespaces (self) |
| Returns a list of the XML Namespaces declared on the SBML document owning this object. More... | |
| def | getNotes (self, args) |
| Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
| def | getNotesString (self, args) |
| Returns the content of the 'notes' subelement of this object as a string. More... | |
| def | getNumCVTerms (self) |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| def | getNumDisabledPlugins (self) |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| def | getNumPlugins (self) |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| def | getPackageCoreVersion (self) |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| def | getPackageName (self) |
| Returns the name of the SBML Level 3 package in which this element is defined. More... | |
| def | getPackageVersion (self) |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| def | getParentSBMLObject (self, args) |
| Returns the parent SBML object containing this object. More... | |
| def | getPlugin (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getPrefix (self) |
| Returns the XML namespace prefix of this element. More... | |
| def | getResourceBiologicalQualifier (self, resource) |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| def | getResourceModelQualifier (self, resource) |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| def | getSBMLDocument (self, args) |
| Returns the SBMLDocument object containing this object instance. More... | |
| def | getSBOTerm (self) |
| Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermAsURL (self) |
| Returns the URL representation of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermID (self) |
| Returns the string representation of the 'sboTerm' attribute of this object. More... | |
| def | getSymbol (self) |
| Get the value of the 'symbol' attribute of this InitialAssignment. More... | |
| def | getTypeCode (self) |
| Returns the libSBML type code for this SBML object. More... | |
| def | getURI (self) |
| Gets the namespace URI to which this element belongs to. More... | |
| def | getVersion (self) |
| Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
| def | hasRequiredAttributes (self) |
Predicate returning True if all the required attributes for this InitialAssignment object have been set. More... | |
| def | hasRequiredElements (self) |
Predicate returning True if all the required elements for this InitialAssignment object have been set. More... | |
| def | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| def | isPackageEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
| def | isPackageURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| def | isPkgEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
| def | isPkgURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| def | isSetAnnotation (self) |
Predicate returning True if this object's 'annotation' subelement exists and has content. More... | |
| def | isSetId (self) |
Predicate returning True if a call to getId() returns a non-empty string. More... | |
| def | isSetIdAttribute (self) |
Predicate returning True if this object's 'id' attribute is set. More... | |
| def | isSetMath (self) |
Predicate returning True if this InitialAssignment's 'math' subelement contains a value. More... | |
| def | isSetMetaId (self) |
Predicate returning True if this object's 'metaid' attribute is set. More... | |
| def | isSetModelHistory (self) |
Predicate returning True if this object has a ModelHistory object attached to it. More... | |
| def | isSetName (self) |
Predicate returning True if this object's 'name' attribute is set. More... | |
| def | isSetNotes (self) |
Predicate returning True if this object's 'notes' subelement exists and has content. More... | |
| def | isSetSBOTerm (self) |
Predicate returning True if this object's 'sboTerm' attribute is set. More... | |
| def | isSetSymbol (self) |
Predicate returning True if this InitialAssignment's 'symbol' attribute is set. More... | |
| def | isSetUserData (self) |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| def | matchesRequiredSBMLNamespacesForAddition (self, args) |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| def | matchesSBMLNamespaces (self, args) |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| def | removeFromParentAndDelete (self) |
| Removes this object from its parent. More... | |
| def | removeTopLevelAnnotationElement (self, args) |
| Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
| def | renameMetaIdRefs (self, oldid, newid) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| def | renameSIdRefs (self, oldid, newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| def | renameUnitSIdRefs (self, oldid, newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
| def | replaceTopLevelAnnotationElement (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setAnnotation (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setId (self, sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| def | setIdAttribute (self, sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| def | setMath (self, math) |
| Sets the 'math' subelement of this InitialAssignment. More... | |
| def | setMetaId (self, metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| def | setModelHistory (self, history) |
| Sets the ModelHistory of this object. More... | |
| def | setName (self, name) |
| Sets the value of the 'name' attribute of this SBML object. More... | |
| def | setNamespaces (self, xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| def | setNotes (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setSBOTerm (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setSymbol (self, sid) |
| Sets the 'symbol' attribute value of this InitialAssignment. More... | |
| def | toSBML (self) |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| def | toXMLNode (self) |
| Returns this element as an XMLNode. More... | |
| def | unsetAnnotation (self) |
| Unsets the value of the 'annotation' subelement of this SBML object. More... | |
| def | unsetCVTerms (self) |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| def | unsetId (self) |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| def | unsetIdAttribute (self) |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| def | unsetMetaId (self) |
| Unsets the value of the 'metaid' attribute of this SBML object. More... | |
| def | unsetModelHistory (self) |
| Unsets the ModelHistory object attached to this object. More... | |
| def | unsetName (self) |
| Unsets the value of the 'name' attribute of this SBML object. More... | |
| def | unsetNotes (self) |
| Unsets the value of the 'notes' subelement of this SBML object. More... | |
| def | unsetSBOTerm (self) |
| Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
| def | unsetSymbol (self) |
| Unsets the 'symbol' attribute value of this InitialAssignment. More... | |
| def | unsetUserData (self) |
| Unsets the user data of this element. More... | |
| def libsbml.InitialAssignment.__init__ | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
__init__(long level, long version) InitialAssignment __init__(SBMLNamespaces sbmlns) InitialAssignment __init__(InitialAssignment orig) InitialAssignment
Each variant is described separately below.
InitialAssignment(SBMLNamespaces sbmlns)
Creates a new InitialAssignment using the given SBMLNamespaces object sbmlns.
| sbmlns | an SBMLNamespaces object. |
| ValueError | Thrown if the given sbmlns is inconsistent or incompatible with this object. |
InitialAssignment(long level, long version)
Creates a new InitialAssignment using the given SBML level and version values.
| level | a long integer, the SBML Level to assign to this InitialAssignment. |
| version | a long integer, the SBML Version to assign to this InitialAssignment. |
| ValueError | Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version. |
InitialAssignment(InitialAssignment orig)
Copy constructor; creates a copy of this InitialAssignment.
| orig | the object to copy. |
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inherited |
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm term, bool newBag) int addCVTerm(CVTerm term) int
| 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.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendAnnotation(XMLNode annotation) int appendAnnotation(string annotation) int
Each variant is described separately below.
appendAnnotation(XMLNode annotation)
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() or SBase.setAnnotation(), 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. |
appendAnnotation(string annotation)
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() or SBase.setAnnotation(), 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 |
This method has multiple variants; they differ in the arguments they accept.
appendNotes(XMLNode notes) int appendNotes(string notes) int
Each variant is described separately below.
appendNotes(string notes)
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. |
appendNotes(XMLNode notes)
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. |
| def libsbml.InitialAssignment.clone | ( | self | ) |
Creates and returns a deep copy of this InitialAssignment object.
clone() InitialAssignment
|
inherited |
connectToChild()
| def libsbml.InitialAssignment.containsUndeclaredUnits | ( | self, | |
| args | |||
| ) |
Predicate returning True if the math expression of this InitialAssignment contains parameters/numbers with undeclared units.
containsUndeclaredUnits() boolTrue if the math expression of this InitialAssignment includes parameters/numbers with undeclared units, False otherwise.True indicates that the UnitDefinition returned by InitialAssignment::getDerivedUnitDefinition may not accurately represent the units of the expression.
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inherited |
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(bool recursive) deleteDisabledPlugins()
If the plugin is re-enabled later, it will then not have any previously-stored information.
| recursive | if True, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
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inherited |
Disables the given SBML Level 3 package on this object.
disablePackage(string pkgURI, string pkgPrefix) intThis 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. |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
enablePackage(string pkgURI, string pkgPrefix, bool flag) intThis 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().
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (True) or disable (False) the package. |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
getAncestorOfType(int type, string pkgName) SBase getAncestorOfType(int type) SBase
Each variant is described separately below.
getAncestorOfType(int type, string pkgName = 'core')
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 Python 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. |
None 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 None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.getAncestorOfType(int type, string pkgName = 'core')
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 Python 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. |
None 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 None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotation() XMLNode
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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Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() stringSBML 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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Returns the column number where this object first appears in the XML representation of the SBML document.
getColumn() long0.
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Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *| def libsbml.InitialAssignment.getDerivedUnitDefinition | ( | self, | |
| args | |||
| ) |
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this InitialAssignment.
getDerivedUnitDefinition() UnitDefinition
<ci> elements used within that expression. The method InitialAssignment.getDerivedUnitDefinition() returns the calculated units, to the extent that libSBML can compute them.None.None if one cannot be constructed.
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Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
getDisabledPlugin(long n) SBasePlugin
If no such plugin exists, None is returned.
| n | the index of the disabled plug-in to return. |
n is invalid, None is returned.
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Returns the first child element it can find with a specific 'metaid' attribute value, or None if no such object is found.
getElementByMetaId(string metaid) SBase
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. |
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Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.
getElementBySId(string id) SBase
| id | string representing the 'id' attribute value of the object to find. |
| def libsbml.InitialAssignment.getElementName | ( | self | ) |
Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'.
getElementName() string'initialAssignment'. | def libsbml.InitialAssignment.getId | ( | self | ) |
Returns the value of the 'symbol' attribute of this InitialAssignment (NOT the 'id').
getId() stringThe 'symbol' attribute of an InitialAssignment indicates the element which the results of the 'math' are to be applied.
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Returns the value of the 'id' attribute of this SBML object.
getIdAttribute() stringSId 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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Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
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Returns the line number where this object first appears in the XML representation of the SBML document.
getLine() long0.
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Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter) SBaseList getListOfAllElements() SBaseList
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Returns a List of all child SBase objects contained in SBML package plug-ins.
getListOfAllElementsFromPlugins(ElementFilter filter) SBaseList getListOfAllElementsFromPlugins() SBaseList
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
| def libsbml.InitialAssignment.getMath | ( | self | ) |
Get the mathematical formula of this InitialAssignment.
getMath() ASTNode
None if the math is not set.
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Returns the value of the 'metaid' attribute of this SBML object.
getMetaId() stringID, 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.
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Returns the ModelHistory object, if any, attached to this object.
getModelHistory() ModelHistory
None if none exist.
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Returns the value of the 'name' attribute of this SBML object.
getName() stringThe '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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Returns a list of the XML Namespaces declared on the SBML document owning this object.
getNamespaces() XMLNamespaces
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.
None in certain very usual circumstances where a namespace is not set.
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Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
getNotes() XMLNode
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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Returns the content of the 'notes' subelement of this object as a string.
getNotesString() stringThe 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.
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Returns the number of CVTerm objects in the annotations of this SBML object.
getNumCVTerms() long
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Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long
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Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() long
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Returns the SBML Core Version within the SBML Level of the actual object.
getPackageCoreVersion() long
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Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() string"core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
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Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() long0 will be returned if this element belongs to the SBML Level 3 Core package.
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Returns the parent SBML object containing this object.
getParentSBMLObject() SBase
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
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This method has multiple variants; they differ in the arguments they accept.
getPlugin(string package) SBasePlugin getPlugin(long n) SBasePlugin
Each variant is described separately below.
getPlugin(long n)
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() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| n | the index of the plug-in to return. |
n is invalid, None is returned.getPlugin(string package)
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() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| package | the name or URI of the package. |
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Returns the XML namespace prefix of this element.
getPrefix() stringThis 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.
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Returns the MIRIAM biological qualifier associated with the given resource.
getResourceBiologicalQualifier(string resource) longIn 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 name begins with BQB_ from 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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Returns the MIRIAM model qualifier associated with the given resource.
getResourceModelQualifier(string resource) longIn 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 BQM_ 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 name begins with BQM_ from 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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Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
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.
getSBOTerm() intint, and SBO identifiers are stored simply as integers. -1 if the value is not set.
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Returns the URL representation of the 'sboTerm' attribute of this object.
getSBOTermAsURL() stringThis method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
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Returns the string representation of the 'sboTerm' attribute of this object.
getSBOTermID() stringint, and SBO identifiers are stored simply as integers. | def libsbml.InitialAssignment.getSymbol | ( | self | ) |
Get the value of the 'symbol' attribute of this InitialAssignment.
getSymbol() string| def libsbml.InitialAssignment.getTypeCode | ( | self | ) |
Returns the libSBML type code for this SBML object.
getTypeCode() intSBML_. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class 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.
getURI() stringFor 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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Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long| def libsbml.InitialAssignment.hasRequiredAttributes | ( | self | ) |
Predicate returning True if all the required attributes for this InitialAssignment object have been set.
hasRequiredAttributes() boolThe required attributes for an InitialAssignment object are:
True if the required attributes have been set, False otherwise. | def libsbml.InitialAssignment.hasRequiredElements | ( | self | ) |
Predicate returning True if all the required elements for this InitialAssignment object have been set.
hasRequiredElements() bool
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Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
hasValidLevelVersionNamespaceCombination() boolThe 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/level3/version1/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 the given SBML Level 3 package is enabled with this object.
isPackageEnabled(string pkgName) boolThe 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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Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.
isPackageURIEnabled(string pkgURI) bool| 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 the given SBML Level 3 package is enabled with this object.
isPkgEnabled(string pkgName) boolThe 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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Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.
isPkgURIEnabled(string pkgURI) bool| 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 object's 'annotation' subelement exists and has content.
isSetAnnotation() boolWhereas 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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Predicate returning True if a call to getId() returns a non-empty string.
isSetId() boolFor 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.
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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Predicate returning True if this object's 'id' attribute is set.
isSetIdAttribute() boolSId 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.| def libsbml.InitialAssignment.isSetMath | ( | self | ) |
Predicate returning True if this InitialAssignment's 'math' subelement contains a value.
isSetMath() boolTrue if the 'math' for this InitialAssignment is set, False otherwise.
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inherited |
Predicate returning True if this object's 'metaid' attribute is set.
isSetMetaId() boolID, 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.
isSetModelHistory() boolTrue 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.
isSetName() boolThe '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.
isSetNotes() boolThe 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.
isSetSBOTerm() boolTrue if the 'sboTerm' attribute of this SBML object is set, False otherwise. | def libsbml.InitialAssignment.isSetSymbol | ( | self | ) |
Predicate returning True if this InitialAssignment's 'symbol' attribute is set.
isSetSymbol() boolTrue if the 'symbol' attribute of this InitialAssignment is set, False otherwise.
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inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
isSetUserData() boolTrue if this object's user data has been set, 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.
matchesRequiredSBMLNamespacesForAddition(SBase sb) bool
| 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.
matchesSBMLNamespaces(SBase sb) bool
| 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.
removeFromParentAndDelete() intIf 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.
removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty) int removeTopLevelAnnotationElement(string elementName, string elementURI) int removeTopLevelAnnotationElement(string elementName) int
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). |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
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. |
| def libsbml.InitialAssignment.renameSIdRefs | ( | self, | |
| oldid, | |||
| newid | |||
| ) |
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(string oldid, string newid)
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. |
| def libsbml.InitialAssignment.renameUnitSIdRefs | ( | self, | |
| oldid, | |||
| newid | |||
| ) |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
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. |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
replaceTopLevelAnnotationElement(XMLNode annotation) int replaceTopLevelAnnotationElement(string annotation) int
Each variant is described separately below.
replaceTopLevelAnnotationElement(XMLNode annotation)
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. |
replaceTopLevelAnnotationElement(string annotation)
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. |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
setAnnotation(XMLNode annotation) int setAnnotation(string annotation) int
Each variant is described separately below.
setAnnotation(XMLNode annotation)
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() or SBase.appendAnnotation().
| annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object. |
setAnnotation(string annotation)
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() or SBase.appendAnnotation().
| annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object. |
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inherited |
Sets the value of the 'id' attribute of this SBML object.
setId(string sid) intsid is copied.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. |
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inherited |
Sets the value of the 'id' attribute of this SBML object.
setIdAttribute(string sid) intsid is copied.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. |
| def libsbml.InitialAssignment.setMath | ( | self, | |
| math | |||
| ) |
Sets the 'math' subelement of this InitialAssignment.
setMath(ASTNode math) int
The AST passed in math is copied.
| math | an AST containing the mathematical expression to be used as the formula for this InitialAssignment. |
|
inherited |
Sets the value of the meta-identifier attribute of this SBML object.
setMetaId(string metaid) intID, 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.
setModelHistory(ModelHistory history) int
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.
setName(string name) intThe string in name is copied.
| name | the new name for the SBML object. |
|
inherited |
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces xmlns) int
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 |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup) int setNotes(string notes) int
Each variant is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
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. |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.setNotes(XMLNode notes)
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 |
This method has multiple variants; they differ in the arguments they accept.
setSBOTerm(int value) int setSBOTerm(string sboid) int
Each variant is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
int, and SBO identifiers are stored simply as integers. | value | the NNNNNNN integer portion of the SBO identifier. |
setSBOTerm(string sboid)
Sets the value of the 'sboTerm' attribute by string.
int, and SBO identifiers are stored simply as integers. | def libsbml.InitialAssignment.setSymbol | ( | self, | |
| sid | |||
| ) |
Sets the 'symbol' attribute value of this InitialAssignment.
setSymbol(string sid) int| sid | the identifier of an element defined in this model whose value can be set. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
|
inherited |
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAnnotation() intWhereas 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.
unsetCVTerms() int
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
unsetId() intSId 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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Unsets the value of the 'id' attribute of this SBML object.
unsetIdAttribute() intMost (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.
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Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaId() intID, 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.
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Unsets the ModelHistory object attached to this object.
unsetModelHistory() int
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Unsets the value of the 'name' attribute of this SBML object.
unsetName() intThe '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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Unsets the value of the 'notes' subelement of this SBML object.
unsetNotes() intThe 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.
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Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSBOTerm() int| def libsbml.InitialAssignment.unsetSymbol | ( | self | ) |
Unsets the 'symbol' attribute value of this InitialAssignment.
unsetSymbol() int
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Unsets the user data of this element.
unsetUserData() int