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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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An SBML Event object defines when the event can occur, the variables that are affected by it, how the variables are affected, and the event's relationship to other events. The effect of the event can optionally be delayed after the occurrence of the condition which invokes it.
The operation of Event is divided into two phases (even when the event is not delayed): one when the event is triggered, and the other when the event is executed. Trigger objects define the conditions for triggering an event, Delay objects define when the event is actually executed, EventAssignment objects define the effects of executing the event, and (in SBML Level 3) Priority objects influence the order of EventAssignment performance in cases of simultaneous events. Please consult the descriptions of Trigger, Delay, EventAssignment and Priority for more information.
In SBML Level 2 versions before Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element, or after any other simultaneous event may have been executed and changed the model state). In SBML Level 2 Version 4 and in Level 3, the attribute 'useValuesFromTriggerTime' on Event was added to allow a model to indicate the time at which the event's assignments are to be calculated, whether at the moment the event is triggered (if the value of the attribute is True), or at the moment of execution (if 'useValuesFromTriggerTime'=False). If the event has a delay, the 'useValuesFromTriggerTime' is likely to make a significant difference in the values used in the assignment, but the possibility of simultaneous events mean that even zero-delay events can have different results depending on the value of this attribute.
The definition of Event in SBML Level 2 Versions 1 and 2 includes an additional attribute called 'timeUnits', which allowed the time units of the Delay to be set explicitly. Later Versions of SBML Level 2 as well as SBML Level 3 do not define this attribute. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2; however, if a model in SBML Level 3 or Level 2 Versions 3–4 format sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. Models defined in prior Versions of SBML Level 2 cannot use this attribute, and SBMLDocument.checkConsistency() will report an error if they do.
SBML Level 3 introduces several changes to the structure and components of Events compared to SBML Level 2. These changes fall into two main categories: changes to what is optional or required, and additions of new attributes and elements.
True); The changes to the attributes of Event are described below; the changes to Trigger and Priority are described in their respective sections.
The detailed semantics of events are described in the specification documents for each SBML Level/Version. Here we include the description from the SBML Level 1 Version 1. Any transition of a Trigger object's 'math' formula from the value False to True will cause the enclosing Event object to trigger. Such a transition is not possible at the very start of a simulation (i.e., at time t = 0) unless the Trigger object's 'initialValue' attribute has a value of False; this defines the value of the trigger formula to be False immediately prior to the start of simulation, thereby giving it the potential to change in value from False to True when the formula is evaluated at t = 0. If 'initialValue'=True, then the trigger expression cannot transition from False to True at t = 0 but may do so at some time t > 0.
Consider an Event object definition E with delay d in which the Trigger object's 'math' formula makes a transition in value from False to True at times t1 and t2. The EventAssignment within the Event object will have effect at t1 + d and t2 + d irrespective of the relative times of t1 and t2. For example, events can 'overlap' so that t1 < t2 < t1 + d still causes an event assignments to occur at t1 + d and t2 + d.
It is entirely possible for two events to be executed simultaneously, and it is possible for events to trigger other events (i.e., an event assignment can cause an event to trigger). This leads to several points:
A software package should retest all event triggers after executing an event assignment in order to account for the possibility that the assignment causes another event trigger to transition from False to True. This check should be made after each individual Event object's execution, even when several events are to be executed simultaneously.
Any Event object whose Trigger 'persistent' attribute has the value False must have its trigger expression reevaluated continuously between when the event is triggered and when it is executed. If its trigger expression ever evaluates to False, it must be removed from the queue of events pending execution and treated as any other event whose trigger expression evaluates to False.
Although the precise time at which events are executed is not resolved beyond the given execution point in simulated time, it is assumed that the order in which the events occur is resolved. This order can be significant in determining the overall outcome of a given simulation. When an event X triggers another event Y and event Y has zero delay, then event Y is added to the existing set of simultaneous events that are pending execution. Events X and Y form a cascade of events at the same point in simulation time. An event such as Y may have a special priority if it contains a Priority subobject.
All events in a model are open to being in a cascade. The position of an event in the event queue does not affect whether it can be in the cascade: event Y can be triggered whether it is before or after X in the queue of events pending execution. A cascade of events can be potentially infinite (never terminate); when this occurs a simulator should indicate this has occurred—it is incorrect for a simulator to break a cascade arbitrarily and continue the simulation without at least indicating that the infinite cascade occurred.
Simultaneous events having no defined priorities are executed in an undefined order. This does not mean that the behavior of the simulation is completely undefined; merely that the order of execution of these particular events is undefined. A given simulator may use any algorithm to choose an order as long as every event is executed exactly once.
Events with defined priorities are executed in the order implied by their Priority 'math' formula values, with events having higher priorities being executed ahead of events with lower priorities, and events with identical priorities being executed in a random order with respect to one another (as determined at run-time by some random algorithm equivalent to coin-flipping). Newly-triggered events that are to be executed immediately (i.e., if they define no delays) should be inserted into the queue of events pending execution according to their priorities: events with higher priority values value must be inserted ahead of events with lower priority values and after any pending events with even higher priorities, and inserted randomly among pending events with the same priority values. Events without Priority objects must be inserted into the queue in some fashion, but the algorithm used to place it in the queue is undefined. Similarly, there is no restriction on the order of a newly-inserted event with a defined Priority with respect to any other pending Event without a defined Priority.
A model variable that is the target of one or more event assignments can change more than once when simultaneous events are processed at some time point t. The model's behavior (output) for such a variable is the value of the variable at the end of processing all the simultaneous events at time t.
In SBML Level 3 Version 2, several restrictions were lifted that have the potential to affect the semantics of an Event:
The Trigger subobject of an Event is optional. If missing, an Event is never triggered, unless an alternate triggering scheme is introduced by an SBML Level 3 package.
The 'math' subelements of an Event Trigger, Delay, Priority, and EventAssignment are all optional. If any of these elements lack a 'math' subelement, and that information is not supplied in an SBML Level 3 package, it is mathematically equivalent to the Trigger, Delay, Priority, or EventAssignment not being present at all.
The ListOfEventAssignments may be empty, which is mathematically equivalent to the Event not having a ListOfEventAssignments at all.
False, and all other values are interpreted as True. If a Boolean value is used in a numeric context, a True is interpreted as a 1, and a False is interpreted as a 0. This means (for example) that a Trigger value that changes from 0.0 to anything else is equivalent to changing from False to True. 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 | addEventAssignment (self, ea) |
| Appends a copy of the given EventAssignment to this Event. 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 Event object. More... | |
| def | connectToChild (self) |
| def | createDelay (self) |
| Creates a new, empty Delay, adds it to this Event and returns the Delay. More... | |
| def | createEventAssignment (self) |
| Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment. More... | |
| def | createPriority (self) |
| def | createTrigger (self) |
| Creates a new, empty Trigger, adds it to this Event and returns the Trigger. 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 | getDelay (self, args) |
| Get the assignment delay portion of this Event, if there is one. 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, metaid) |
Returns the first child element it can find with the given metaid, or None if no such object is found. More... | |
| def | getElementBySId (self, id) |
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 Event, is always 'event'. More... | |
| def | getEventAssignment (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getId (self) |
| Returns the value of the 'id' attribute of this Event. 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 | getListOfEventAssignments (self, args) |
| Returns the list of event assignments for this Event. 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 Event. 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 | getNumEventAssignments (self) |
| Returns the number of EventAssignment objects attached to this Event. 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 | getPriority (self, args) |
| 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 | getTimeUnits (self) |
| Get the value of the 'timeUnits' attribute of this Event, if it has one. More... | |
| def | getTrigger (self, args) |
| Get the event trigger portion of this Event. More... | |
| def | getTypeCode (self) |
| Returns the libSBML type code of this object instance. More... | |
| def | getURI (self) |
| Gets the namespace URI to which this element belongs to. More... | |
| def | getUseValuesFromTriggerTime (self) |
| Get the value of the 'useValuesFromTriggerTime' attribute of this Event. 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 Event object have been set. More... | |
| def | hasRequiredElements (self) |
Predicate returning True if all the required elements for this Event 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 | initDefaults (self) |
| Initializes the fields of this Event object to 'typical' default values. 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 | isSetDelay (self) |
| Predicate for testing whether the delay for this Event is set. More... | |
| def | isSetId (self) |
Predicate returning True if this Event's 'id' attribute is set. More... | |
| def | isSetIdAttribute (self) |
Predicate returning True if this object's 'id' attribute is set. 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 Event's 'name' attribute is set. More... | |
| def | isSetNotes (self) |
Predicate returning True if this object's 'notes' subelement exists and has content. More... | |
| def | isSetPriority (self) |
| def | isSetSBOTerm (self) |
Predicate returning True if this object's 'sboTerm' attribute is set. More... | |
| def | isSetTimeUnits (self) |
| Predicate for testing whether the 'timeUnits' attribute of this Event is set. More... | |
| def | isSetTrigger (self) |
| Predicate for testing whether the trigger for this Event 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 | isSetUseValuesFromTriggerTime (self) |
| Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is 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 | removeEventAssignment (self, args) |
| This method has multiple variants; they differ in the arguments they accept. 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 | setDelay (self, delay) |
| Sets the delay definition of this Event to a copy of the given Delay object instance. More... | |
| def | setId (self, sid) |
| Sets the value of the 'id' attribute of this Event. More... | |
| def | setIdAttribute (self, sid) |
| Sets the value of the 'id' attribute of this SBML object. 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 Event. 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 | setPriority (self, priority) |
| def | setSBOTerm (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setTimeUnits (self, sid) |
Sets the 'timeUnits' attribute of this Event to a copy of sid. More... | |
| def | setTrigger (self, trigger) |
| Sets the trigger definition of this Event to a copy of the given Trigger object instance. More... | |
| def | setUseValuesFromTriggerTime (self, value) |
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value. 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 | unsetDelay (self) |
| Unsets the Delay of this Event. More... | |
| def | unsetId (self) |
| Unsets the value of the 'id' attribute of this Event. 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 Event. More... | |
| def | unsetNotes (self) |
| Unsets the value of the 'notes' subelement of this SBML object. More... | |
| def | unsetPriority (self) |
| def | unsetSBOTerm (self) |
| Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
| def | unsetTimeUnits (self) |
| Unsets the 'timeUnits' attribute of this Event. More... | |
| def | unsetTrigger (self) |
| Unsets the Trigger of this Event. More... | |
| def | unsetUserData (self) |
| Unsets the user data of this element. More... | |
| def | unsetUseValuesFromTriggerTime (self) |
| Unsets the value of the 'useValuesFromTriggerTime' attribute of this Event. More... | |
| def libsbml.Event.__init__ | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
__init__(long level, long version) Event __init__(SBMLNamespaces sbmlns) Event __init__(Event orig) Event
Each variant is described separately below.
Event(SBMLNamespaces sbmlns)
Creates a new Event using the given SBMLNamespaces object sbmlns.
| sbmlns | an SBMLNamespaces object. |
| ValueError | Thrown if the given sbmlns is inconsistent or incompatible with this object. |
Event(long level, long version)
Creates a new Event using the given SBML level and version values.
| level | a long integer, the SBML Level to assign to this Event. |
| version | a long integer, the SBML Version to assign to this Event. |
| ValueError | Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version. |
Event(Event orig)
Copy constructor; creates a copy of this Event.
| orig | the object to copy. |
|
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. | def libsbml.Event.addEventAssignment | ( | self, | |
| ea | |||
| ) |
Appends a copy of the given EventAssignment to this Event.
addEventAssignment(EventAssignment ea) int
| ea | the EventAssignment object to add. |
create) for alternatives that do not lead to these issues.
|
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.Event.clone | ( | self | ) |
| def libsbml.Event.connectToChild | ( | self | ) |
connectToChild()
| def libsbml.Event.createDelay | ( | self | ) |
| def libsbml.Event.createEventAssignment | ( | self | ) |
Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.
createEventAssignment() EventAssignment
| def libsbml.Event.createPriority | ( | self | ) |
createPriority() Priority
(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority.
None if the SBML level and version used for this Event does not define Priority children.| def libsbml.Event.createTrigger | ( | self | ) |
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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. |
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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. |
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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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inherited |
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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inherited |
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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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
getColumn() long0.
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inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *| def libsbml.Event.getDelay | ( | self, | |
| args | |||
| ) |
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inherited |
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.| def libsbml.Event.getElementByMetaId | ( | self, | |
| metaid | |||
| ) |
Returns the first child element it can find with the given metaid, or None if no such object is found.
getElementByMetaId(string metaid) SBase
| metaid | string representing the metaid of the object to find. |
metaid. | def libsbml.Event.getElementBySId | ( | self, | |
| id | |||
| ) |
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 of the object to find. |
id. | def libsbml.Event.getElementName | ( | self | ) |
Returns the XML element name of this object, which for Event, is always 'event'.
getElementName() string'event'. | def libsbml.Event.getEventAssignment | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
getEventAssignment(long n) EventAssignment getEventAssignment(string variable) EventAssignment
Each variant is described separately below.
getEventAssignment(string variable)
Return the event assignment indicated by the given variable.
| variable | a string, the identifier of the variable whose EventAssignment is being sought. |
variable, or None if no such EventAssignment exists.getEventAssignment(long n)
Return a specific EventAssignment object of this Event.
| n | an integer, the index of the EventAssignment object to return. |
nth EventAssignment of this Event. | def libsbml.Event.getId | ( | self | ) |
Returns the value of the 'id' attribute of this Event.
getId() 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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inherited |
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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inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
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inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
getLine() long0.
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inherited |
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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inherited |
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.Event.getListOfEventAssignments | ( | self, | |
| args | |||
| ) |
Returns the list of event assignments for this Event.
getListOfEventAssignments() ListOfEventAssignments
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inherited |
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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inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
getModelHistory() ModelHistory
None if none exist.| def libsbml.Event.getName | ( | self | ) |
Returns the value of the 'name' attribute of this Event.
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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inherited |
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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inherited |
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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inherited |
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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inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumCVTerms() long
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inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long| def libsbml.Event.getNumEventAssignments | ( | self | ) |
Returns the number of EventAssignment objects attached to this Event.
getNumEventAssignments() long
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inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() long
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inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
getPackageCoreVersion() long
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inherited |
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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inherited |
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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inherited |
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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inherited |
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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inherited |
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.
| def libsbml.Event.getPriority | ( | self, | |
| args | |||
| ) |
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inherited |
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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inherited |
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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inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
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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inherited |
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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inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
getSBOTermID() stringint, and SBO identifiers are stored simply as integers. | def libsbml.Event.getTimeUnits | ( | self | ) |
Get the value of the 'timeUnits' attribute of this Event, if it has one.
getTimeUnits() string| def libsbml.Event.getTrigger | ( | self, | |
| args | |||
| ) |
| def libsbml.Event.getTypeCode | ( | self | ) |
Returns the libSBML type code of this object instance.
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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inherited |
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.
| def libsbml.Event.getUseValuesFromTriggerTime | ( | self | ) |
Get the value of the 'useValuesFromTriggerTime' attribute of this Event.
getUseValuesFromTriggerTime() boolIn SBML Level 2 versions prior to Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element, or after any other simultaneous event may have been executed and changed the model state). In SBML Level 2 Version 4, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended to be evaluated. In SBML Level 2, the attribute has a default value of True, which corresponds to the interpretation of event assignments prior to Version 4: the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed. In SBML Level 3, the attribute is mandatory, not optional, and all events must specify a value for it.
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inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long| def libsbml.Event.hasRequiredAttributes | ( | self | ) |
| def libsbml.Event.hasRequiredElements | ( | self | ) |
Predicate returning True if all the required elements for this Event object have been set.
hasRequiredElements() bool
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inherited |
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. | def libsbml.Event.initDefaults | ( | self | ) |
Initializes the fields of this Event object to 'typical' default values.
initDefaults()
The SBML Event component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:
True
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inherited |
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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inherited |
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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inherited |
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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inherited |
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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inherited |
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.| def libsbml.Event.isSetDelay | ( | self | ) |
| def libsbml.Event.isSetId | ( | self | ) |
Predicate returning True if this Event's 'id' attribute is set.
isSetId() 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.
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inherited |
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.
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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.| def libsbml.Event.isSetName | ( | self | ) |
Predicate returning True if this Event'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.| def libsbml.Event.isSetPriority | ( | self | ) |
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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.Event.isSetTimeUnits | ( | self | ) |
Predicate for testing whether the 'timeUnits' attribute of this Event is set.
isSetTimeUnits() boolTrue if the 'timeUnits' attribute of this Event is set, False otherwise.| def libsbml.Event.isSetTrigger | ( | self | ) |
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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. | def libsbml.Event.isSetUseValuesFromTriggerTime | ( | self | ) |
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.
isSetUseValuesFromTriggerTime() boolTrue if the 'useValuesFromTriggerTime' attribute of this Event is set, False otherwise.True, whereas in Level 3, this optional is mandatory and has no default value.
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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. | def libsbml.Event.removeEventAssignment | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
removeEventAssignment(long n) EventAssignment removeEventAssignment(string variable) EventAssignment
Each variant is described separately below.
removeEventAssignment(string variable)
Removes the EventAssignment object with the given 'variable' attribute from this Event object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the EventAssignment objects in this Event object have the 'variable' attribute variable, then None is returned.
| variable | the 'variable' attribute of the EventAssignment object to remove. |
None is returned if no EventAssignment object with the 'variable' attribute exists in this Event object.removeEventAssignment(long n)
Removes the nth EventAssignment object from this Event object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| n | the index of the EventAssignment object to remove. |
None is returned if the given index is out of range.
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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. |
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inherited |
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. |
|
inherited |
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. |
| def libsbml.Event.setDelay | ( | self, | |
| delay | |||
| ) |
| def libsbml.Event.setId | ( | self, | |
| sid | |||
| ) |
Sets the value of the 'id' attribute of this Event.
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. |
|
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. |
|
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. |
| def libsbml.Event.setName | ( | self, | |
| name | |||
| ) |
Sets the value of the 'name' attribute of this Event.
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. |
| def libsbml.Event.setPriority | ( | self, | |
| priority | |||
| ) |
setPriority(Priority priority) int
(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance.
| priority | the Priority object instance to use. |
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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.Event.setTimeUnits | ( | self, | |
| sid | |||
| ) |
Sets the 'timeUnits' attribute of this Event to a copy of sid.
setTimeUnits(string sid) int| sid | the identifier of the time units to use. |
| def libsbml.Event.setTrigger | ( | self, | |
| trigger | |||
| ) |
| def libsbml.Event.setUseValuesFromTriggerTime | ( | self, | |
| value | |||
| ) |
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value.
setUseValuesFromTriggerTime(bool value) intIn SBML Level 2 versions prior to Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element, or after any other simultaneous event may have been executed and changed the model state). In SBML Level 2 Version 4, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended to be evaluated. In SBML Level 2, the attribute has a default value of True, which corresponds to the interpretation of event assignments prior to Version 4: the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed. In SBML Level 3, the attribute is mandatory, not optional, and all events must specify a value for it.
| value | the value of useValuesFromTriggerTime to use. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
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inherited |
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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| def libsbml.Event.unsetDelay | ( | self | ) |
| def libsbml.Event.unsetId | ( | self | ) |
Unsets the value of the 'id' attribute of this Event.
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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inherited |
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.
|
inherited |
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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inherited |
Unsets the ModelHistory object attached to this object.
unsetModelHistory() int| def libsbml.Event.unsetName | ( | self | ) |
Unsets the value of the 'name' attribute of this Event.
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.
|
inherited |
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.
| def libsbml.Event.unsetPriority | ( | self | ) |
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSBOTerm() int| def libsbml.Event.unsetTimeUnits | ( | self | ) |
Unsets the 'timeUnits' attribute of this Event.
unsetTimeUnits() int| def libsbml.Event.unsetTrigger | ( | self | ) |
|
inherited |
Unsets the user data of this element.
unsetUserData() int| def libsbml.Event.unsetUseValuesFromTriggerTime | ( | self | ) |
Unsets the value of the 'useValuesFromTriggerTime' attribute of this Event.
unsetUseValuesFromTriggerTime() intIn SBML Level 2 versions prior to Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element, or after any other simultaneous event may have been executed and changed the model state). In SBML Level 2 Version 4, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended to be evaluated. In SBML Level 2, the attribute has a default value of True, which corresponds to the interpretation of event assignments prior to Version 4: the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed. In SBML Level 3, the attribute is mandatory, not optional, and all events must specify a value for it.