libSBML C# API
libSBML 5.8.0 C# API
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Implementation of SBML's Event construct.
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.
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.
The changes to the attributes of Event are described below; the changes to Trigger and Priority are described in their respective sections.
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). In SBML Level 2 Version 4 and in Level 3, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended 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.
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.
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.
Public Member Functions | |
int | addCVTerm (CVTerm term, bool newBag) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addCVTerm (CVTerm term) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addEventAssignment (EventAssignment ea) |
Appends a copy of the given EventAssignment to this Event. More... | |
int | appendAnnotation (XMLNode annotation) |
Appends the given annotation to the 'annotation' subelement of this object. More... | |
int | appendAnnotation (string annotation) |
Appends the given annotation to the 'annotation' subelement of this object. More... | |
int | appendNotes (XMLNode notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
int | appendNotes (string notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
int | checkCompatibility (SBase arg0) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
string | checkMathMLNamespace (XMLToken elem) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
new Event | clone () |
Creates and returns a deep copy of this Event. More... | |
void | connectToParent (SBase parent) |
Sets the parent SBML object of this SBML object. More... | |
Delay | createDelay () |
Creates a new, empty Delay, adds it to this Event and returns the Delay. More... | |
EventAssignment | createEventAssignment () |
Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment. More... | |
Priority | createPriority () |
(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority. More... | |
Trigger | createTrigger () |
Creates a new, empty Trigger, adds it to this Event and returns the Trigger. More... | |
int | disablePackage (string pkgURI, string pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
override void | Dispose () |
void | divideAssignmentsToSIdByFunction (string id, ASTNode function) |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More... | |
int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
override bool | Equals (Object sb) |
Event (long level, long version) | |
Creates a new Event using the given SBML level and version values. More... | |
Event (SBMLNamespaces sbmlns) | |
Creates a new Event using the given SBMLNamespaces object sbmlns . More... | |
Event (Event orig) | |
Copy constructor; creates a copy of this Event. More... | |
SBase | getAncestorOfType (int type, string pkgName) |
Returns the first ancestor object that has the given SBML type code. More... | |
SBase | getAncestorOfType (int type) |
Returns the first ancestor object that has the given SBML type code. More... | |
XMLNode | getAnnotation () |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
string | getAnnotationString () |
Returns the content of the 'annotation' subelement of this object as a character string. More... | |
long | getColumn () |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
CVTerm | getCVTerm (long n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
CVTermList | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
Delay | getDelay () |
Get the assignment delay portion of this Event, if there is one. More... | |
SBase | getElementByMetaId (string metaid) |
Returns the first child element it can find with the given metaid , or null if no such object is found. More... | |
SBase | getElementBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found. More... | |
SBase | getElementFromPluginsByMetaId (string metaid) |
Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More... | |
SBase | getElementFromPluginsBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More... | |
new string | getElementName () |
Returns the XML element name of this object, which for Event, is always 'event' . More... | |
EventAssignment | getEventAssignment (long n) |
Return a specific EventAssignment object of this Event. More... | |
EventAssignment | getEventAssignment (string variable) |
Return the event assignment indicated by the given variable . More... | |
override int | GetHashCode () |
new string | getId () |
Returns the value of the 'id' attribute of this Event. More... | |
long | getLevel () |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
long | getLine () |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
SBaseList | getListOfAllElements () |
SBaseList | getListOfAllElementsFromPlugins () |
ListOfEventAssignments | getListOfEventAssignments () |
Returns the list of event assignments for this Event. More... | |
string | getMetaId () |
Returns the value of the 'metaid' attribute of this object. More... | |
Model | getModel () |
Returns the Model object in which the current object is located. More... | |
ModelHistory | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
new string | getName () |
Returns the value of the 'name' attribute of this Event. More... | |
XMLNamespaces | getNamespaces () |
Returns a list of the XML Namespaces declared on this SBML document. More... | |
XMLNode | getNotes () |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
string | getNotesString () |
Returns the content of the 'notes' subelement of this object as a string. More... | |
long | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
long | getNumEventAssignments () |
Returns the number of EventAssignment objects attached to this Event. More... | |
long | getNumPlugins () |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
string | getPackageName () |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
long | getPackageVersion () |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
SBase | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
SBasePlugin | getPlugin (string package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin | getPlugin (long n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
Priority | getPriority () |
(SBML Level 3 only) Get the event priority portion of this Event. More... | |
int | getResourceBiologicalQualifier (string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
int | getResourceModelQualifier (string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
SBMLDocument | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLNamespaces | getSBMLNamespaces () |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | getSBOTerm () |
Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermAsURL () |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermID () |
Returns the string representation of the 'sboTerm' attribute of this object. More... | |
string | getTimeUnits () |
Get the value of the 'timeUnits' attribute of this Event, if it has one. More... | |
Trigger | getTrigger () |
Get the event trigger portion of this Event. More... | |
new int | getTypeCode () |
Returns the libSBML type code of this object instance. More... | |
bool | getUseValuesFromTriggerTime () |
Get the value of the 'useValuesFromTriggerTime' attribute of this Event. More... | |
long | getVersion () |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
bool | hasNonstandardIdentifierBeginningWith (string prefix) |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More... | |
new bool | hasRequiredAttributes () |
Predicate returning true if all the required attributes for this Event object have been set. More... | |
new bool | hasRequiredElements () |
Predicate returning true if all the required elements for this Event object have been set. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
bool | isPackageEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPkgEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isSetAnnotation () |
Predicate returning true if this object's 'annotation' subelement exists and has content. More... | |
bool | isSetDelay () |
Predicate for testing whether the delay for this Event is set. More... | |
new bool | isSetId () |
Predicate returning true if this Event's 'id' attribute is set. More... | |
bool | isSetMetaId () |
Predicate returning true if this object's 'metaid' attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
new bool | isSetName () |
Predicate returning true if this Event's 'name' attribute is set. More... | |
bool | isSetNotes () |
Predicate returning true if this object's 'notes' subelement exists and has content. More... | |
bool | isSetPriority () |
(SBML Level 3 only) Predicate for testing whether the priority for this Event is set. More... | |
bool | isSetSBOTerm () |
Predicate returning true if this object's 'sboTerm' attribute is set. More... | |
bool | isSetTimeUnits () |
Predicate for testing whether the 'timeUnits' attribute of this Event is set. More... | |
bool | isSetTrigger () |
Predicate for testing whether the trigger for this Event is set. More... | |
bool | isSetUseValuesFromTriggerTime () |
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (SBase sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (SBase sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
void | multiplyAssignmentsToSIdByFunction (string id, ASTNode function) |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More... | |
int | prependStringToAllIdentifiers (string prefix) |
Add the given string to all identifiers in the object. More... | |
EventAssignment | removeEventAssignment (long n) |
Removes the nth EventAssignment object from this Event object and returns a pointer to it. More... | |
EventAssignment | removeEventAssignment (string variable) |
Removes the EventAssignment object with the given 'variable' attribute from this Event object and returns a pointer to it. More... | |
int | removeFromParentAndDelete () |
Removes itself from its parent. More... | |
int | removeTopLevelAnnotationElement (string elementName, string elementURI) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
int | removeTopLevelAnnotationElement (string elementName) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
void | renameMetaIdRefs (string oldid, string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
void | renameSIdRefs (string oldid, string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists). More... | |
void | renameUnitSIdRefs (string oldid, string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
void | replaceSIDWithFunction (string id, ASTNode function) |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More... | |
int | replaceTopLevelAnnotationElement (XMLNode annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
int | replaceTopLevelAnnotationElement (string annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
int | setAnnotation (XMLNode annotation) |
Sets the value of the 'annotation' subelement of this SBML object. More... | |
int | setAnnotation (string annotation) |
Sets the value of the 'annotation' subelement of this SBML object. More... | |
int | setDelay (Delay delay) |
Sets the delay definition of this Event to a copy of the given Delay object instance. More... | |
new int | setId (string sid) |
Sets the value of the 'id' attribute of this Event. More... | |
int | setMetaId (string metaid) |
Sets the value of the 'metaid' attribute of this object. More... | |
int | setModelHistory (ModelHistory history) |
Sets the ModelHistory of this object. More... | |
new int | setName (string name) |
Sets the value of the 'name' attribute of this Event. More... | |
int | setNamespaces (XMLNamespaces xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (XMLNode notes) |
Sets the value of the 'notes' subelement of this SBML object. More... | |
int | setNotes (string notes, bool addXHTMLMarkup) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
int | setNotes (string notes) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
int | setPriority (Priority priority) |
(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance. More... | |
void | setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | setSBOTerm (int value) |
Sets the value of the 'sboTerm' attribute. More... | |
int | setSBOTerm (string sboid) |
Sets the value of the 'sboTerm' attribute by string. More... | |
int | setTimeUnits (string sid) |
Sets the 'timeUnits' attribute of this Event to a copy of sid . More... | |
int | setTrigger (Trigger trigger) |
Sets the trigger definition of this Event to a copy of the given Trigger object instance. More... | |
int | setUseValuesFromTriggerTime (bool value) |
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value . More... | |
string | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
int | unsetAnnotation () |
Unsets the value of the 'annotation' subelement of this SBML object. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
int | unsetDelay () |
Unsets the Delay of this Event. More... | |
new int | unsetId () |
Unsets the value of the 'id' attribute of this Event. More... | |
int | unsetMetaId () |
Unsets the value of the 'metaid' attribute of this SBML object. More... | |
int | unsetModelHistory () |
Unsets the ModelHistory object attached to this object. More... | |
new int | unsetName () |
Unsets the value of the 'name' attribute of this Event. More... | |
int | unsetNotes () |
Unsets the value of the 'notes' subelement of this SBML object. More... | |
int | unsetPriority () |
(SBML Level 3 only) Unsets the Priority of this Event. More... | |
int | unsetSBOTerm () |
Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
int | unsetTimeUnits () |
Unsets the 'timeUnits' attribute of this Event. More... | |
int | unsetTrigger () |
Unsets the Trigger of this Event. More... | |
void | writeExtensionElements (XMLOutputStream stream) |
Writes out contained SBML objects of package extensions (if any) as XML elements. More... | |
Static Public Member Functions | |
static bool | operator!= (SBase lhs, SBase rhs) |
static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
bool | swigCMemOwn |
libsbmlcs.Event.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 |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Event.Event | ( | SBMLNamespaces | sbmlns | ) |
Creates a new Event using the given SBMLNamespaces object sbmlns
.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.
sbmlns | an SBMLNamespaces object. |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Event.Event | ( | Event | orig | ) |
Copy constructor; creates a copy of this Event.
orig | the object to copy. |
SBMLConstructorException | Thrown if the argument orig is null . |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
int libsbmlcs.Event.addEventAssignment | ( | EventAssignment | ea | ) |
Appends a copy of the given EventAssignment to this Event.
ea | the EventAssignment object to add. |
|
inherited |
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
|
inherited |
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
new Event libsbmlcs.Event.clone | ( | ) |
|
inherited |
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).
parent | the SBML object to use |
Delay libsbmlcs.Event.createDelay | ( | ) |
EventAssignment libsbmlcs.Event.createEventAssignment | ( | ) |
Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.
Priority libsbmlcs.Event.createPriority | ( | ) |
Trigger libsbmlcs.Event.createTrigger | ( | ) |
|
inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
virtual |
Reimplemented from libsbmlcs.SBase.
|
inherited |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).
|
inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
|
inherited |
|
inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
Delay libsbmlcs.Event.getDelay | ( | ) |
SBase libsbmlcs.Event.getElementByMetaId | ( | string | metaid | ) |
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. SBase libsbmlcs.Event.getElementBySId | ( | string | id | ) |
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
id | string representing the id of objects to find |
id
.
|
inherited |
Returns the first child element it can find with the given metaid
from all plug-ins associated with this element, or null
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
|
inherited |
Returns the first child element found that has the given id
in the model-wide SId namespace from all plug-ins associated with this element, or null
if no such object is found.
id | string representing the id of objects to find |
id
. new string libsbmlcs.Event.getElementName | ( | ) |
Returns the XML element name of this object, which for Event, is always 'event'
.
'event'
. EventAssignment libsbmlcs.Event.getEventAssignment | ( | long | n | ) |
Return a specific EventAssignment object of this Event.
n | an integer, the index of the EventAssignment object to return |
n
th EventAssignment of this Event. EventAssignment libsbmlcs.Event.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 null
if no such EventAssignment exits.
|
inherited |
new string libsbmlcs.Event.getId | ( | ) |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
ListOfEventAssignments libsbmlcs.Event.getListOfEventAssignments | ( | ) |
|
inherited |
Returns the value of the 'metaid' attribute of this object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null
if none exist.new string libsbmlcs.Event.getName | ( | ) |
|
inherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
|
inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type, 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 '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().
|
inherited |
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type, 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.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
long libsbmlcs.Event.getNumEventAssignments | ( | ) |
Returns the number of EventAssignment objects attached to this Event.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
Priority libsbmlcs.Event.getPriority | ( | ) |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
|
inherited |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
string libsbmlcs.Event.getTimeUnits | ( | ) |
Get the value of the 'timeUnits' attribute of this Event, if it has one.
Trigger libsbmlcs.Event.getTrigger | ( | ) |
new int libsbmlcs.Event.getTypeCode | ( | ) |
Returns the libSBML type code of this object instance.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_
.
bool libsbmlcs.Event.getUseValuesFromTriggerTime | ( | ) |
Get the value of the 'useValuesFromTriggerTime' attribute of this Event.
The optional Delay on Event means there are two times to consider when computing the results of an event: the time at which the event is triggered, and the time at which assignments are executed. It is also possible to distinguish between the time at which the EventAssignment's expression is calculated, and the time at which the assignment is made: the expression could be evaluated at the same time the assignments are performed, i.e., when the event is executed, but it could also be defined to be evaluated at the time the event is triggered.
In 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). 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.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').
new bool libsbmlcs.Event.hasRequiredAttributes | ( | ) |
new bool libsbmlcs.Event.hasRequiredElements | ( | ) |
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
'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.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'annotation' subelement exists and has content.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true
if a 'annotation' subelement exists, false
otherwise.bool libsbmlcs.Event.isSetDelay | ( | ) |
new bool libsbmlcs.Event.isSetId | ( | ) |
|
inherited |
Predicate returning true
if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
true
if the 'metaid' attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.new bool libsbmlcs.Event.isSetName | ( | ) |
|
inherited |
Predicate returning true
if this object's 'notes' subelement exists and has content.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
true
if a 'notes' subelement exists, false
otherwise.bool libsbmlcs.Event.isSetPriority | ( | ) |
|
inherited |
Predicate returning true
if this object's 'sboTerm' attribute is set.
true
if the 'sboTerm' attribute of this SBML object is set, false
otherwise. bool libsbmlcs.Event.isSetTimeUnits | ( | ) |
Predicate for testing whether the 'timeUnits' attribute of this Event is set.
true
if the 'timeUnits' attribute of this Event is set, false
otherwise.bool libsbmlcs.Event.isSetTrigger | ( | ) |
bool libsbmlcs.Event.isSetUseValuesFromTriggerTime | ( | ) |
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.
true
if the 'useValuesFromTriggerTime' attribute of this Event is set, false
otherwise.true
, whereas in Level 3 Version 1, this optional is mandatory and has no default value.
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
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.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
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.
|
inherited |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).
|
inherited |
Add the given string to all identifiers in the object.
If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.
EventAssignment libsbmlcs.Event.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 |
null
is returned if the given index is out of range. EventAssignment libsbmlcs.Event.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 null
is returned.
variable | the 'variable' attribute of the EventAssignment object to remove |
null
is returned if no EventAssignment object with the 'variable' attribute exists in this Event object.
|
inherited |
Removes itself from its parent.
If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, 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.
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-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 |
|
inherited |
Renames all the SIdRef
attributes on this element, including any found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate) mathematical formulas, 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 |
Renames all the UnitSIdRef
attributes on this element.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit 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 |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.
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inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); 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 |
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inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); 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 |
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
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inherited |
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
int libsbmlcs.Event.setDelay | ( | Delay | delay | ) |
new int libsbmlcs.Event.setId | ( | string | sid | ) |
Sets the value of the 'id' attribute of this Event.
The string sid
is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type
SId
, which defines the permitted syntax of identifiers. We
express the syntax using an extended form of BNF notation:
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. In addition, there are a few
conditions for the uniqueness of identifiers in an SBML model. Please
consult the SBML specifications for the exact formulations.
sid | the string to use as the identifier of this Event |
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inherited |
Sets the value of the 'metaid' attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers 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.
metaid | the identifier string to use as the value of the 'metaid' attribute |
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inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
new int libsbmlcs.Event.setName | ( | string | name | ) |
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inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
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inherited |
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool 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. |
int libsbmlcs.Event.setPriority | ( | Priority | priority | ) |
(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 |
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
|
inherited |
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
int libsbmlcs.Event.setTimeUnits | ( | string | sid | ) |
Sets the 'timeUnits' attribute of this Event to a copy of sid
.
sid | the identifier of the time units to use. |
int libsbmlcs.Event.setTrigger | ( | Trigger | trigger | ) |
int libsbmlcs.Event.setUseValuesFromTriggerTime | ( | bool | value | ) |
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value
.
The optional Delay on Event means there are two times to consider when computing the results of an event: the time at which the event is triggered, and the time at which assignments are executed. It is also possible to distinguish between the time at which the EventAssignment's expression is calculated, and the time at which the assignment is made: the expression could be evaluated at the same time the assignments are performed, i.e., when the event is executed, but it could also be defined to be evaluated at the time the event is triggered.
In 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). 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.
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
int libsbmlcs.Event.unsetDelay | ( | ) |
new int libsbmlcs.Event.unsetId | ( | ) |
Unsets the value of the 'id' attribute of this Event.
|
inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
|
inherited |
Unsets the ModelHistory object attached to this object.
new int libsbmlcs.Event.unsetName | ( | ) |
Unsets the value of the 'name' attribute of this Event.
|
inherited |
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
int libsbmlcs.Event.unsetPriority | ( | ) |
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
int libsbmlcs.Event.unsetTimeUnits | ( | ) |
Unsets the 'timeUnits' attribute of this Event.
int libsbmlcs.Event.unsetTrigger | ( | ) |
|
inherited |
Writes out contained SBML objects of package extensions (if any) as XML elements.
|
protectedinherited |