libSBML C# API  libSBML 5.8.0 C# API
 All Classes Namespaces Files Functions Variables Properties Pages
libsbmlcs.Event Class Reference
Inheritance diagram for libsbmlcs.Event:
[legend]

Detailed Description

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.

Version differences

SBML Level 3

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 attribute 'useValuesFromTriggerTime' on Event is mandatory (it was optional in Level 2);
  • Event's 'listOfEventAssignments' element (of class ListOfEventAssignments) is optional (it was mandatory in Level 2);
  • Event's 'priority' element (of class Priority) is new in Level 3; and
  • The Trigger object gains new mandatory attributes (described as part of the definition of Trigger).

The changes to the attributes of Event are described below; the changes to Trigger and Priority are described in their respective sections.

SBML Level 2

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.

Semantics of events in SBML Level 3 VersionĀ 1

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.

See Also
Trigger
Priority
Delay
EventAssignment

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
 

Constructor & Destructor Documentation

libsbmlcs.Event.Event ( long  level,
long  version 
)

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

Parameters
levela long integer, the SBML Level to assign to this Event
versiona long integer, the SBML Version to assign to this Event
Exceptions
SBMLConstructorExceptionThrown 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.
Note
Upon the addition of an Event object to an SBMLDocument (e.g., using Model::addEvent()), the SBML Level, SBML Version and XML namespace of the document override the values used when creating the Event object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of an Event is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
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.

Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown 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.
Note
Upon the addition of an Event object to an SBMLDocument (e.g., using Model::addEvent()), the SBML XML namespace of the document overrides the value used when creating the Event object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a Event is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
libsbmlcs.Event.Event ( Event  orig)

Copy constructor; creates a copy of this Event.

Parameters
origthe object to copy.
Exceptions
SBMLConstructorExceptionThrown if the argument orig is null.

Member Function Documentation

int libsbmlcs.SBase.addCVTerm ( CVTerm  term,
bool  newBag 
)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.addCVTerm ( CVTerm  term)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.Event.addEventAssignment ( EventAssignment  ea)

Appends a copy of the given EventAssignment to this Event.

Parameters
eathe EventAssignment object to add.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Event. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Event. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Event::createEventAssignment() for a method that does not lead to these issues.
See Also
createEventAssignment()
int libsbmlcs.SBase.appendAnnotation ( XMLNode  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendAnnotation ( string  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendNotes ( XMLNode  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.appendNotes ( string  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.checkCompatibility ( SBase  arg0)
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:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken  elem)
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 ( )

Creates and returns a deep copy of this Event.

Returns
a (deep) copy of this Event.
void libsbmlcs.SBase.connectToParent ( SBase  parent)
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).

Parameters
parentthe SBML object to use
Delay libsbmlcs.Event.createDelay ( )

Creates a new, empty Delay, adds it to this Event and returns the Delay.

Returns
the newly created Delay object instance
EventAssignment libsbmlcs.Event.createEventAssignment ( )

Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.

Returns
the newly created EventAssignment object instance
See Also
addEventAssignment(EventAssignment ea)
Priority libsbmlcs.Event.createPriority ( )

(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority.

Returns
the newly created Priority object instance
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
Trigger libsbmlcs.Event.createTrigger ( )

Creates a new, empty Trigger, adds it to this Event and returns the Trigger.

Returns
the newly created Trigger object instance
int libsbmlcs.SBase.disablePackage ( string  pkgURI,
string  pkgPrefix 
)
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.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override void libsbmlcs.Event.Dispose ( )
virtual

Reimplemented from libsbmlcs.SBase.

void libsbmlcs.SBase.divideAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
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).

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.enablePackage ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)
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.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override bool libsbmlcs.SBase.Equals ( Object  sb)
inherited
SBase libsbmlcs.SBase.getAncestorOfType ( int  type,
string  pkgName 
)
inherited

Returns the first ancestor object that has the given SBML type code.

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.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
SBase libsbmlcs.SBase.getAncestorOfType ( int  type)
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.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
XMLNode libsbmlcs.SBase.getAnnotation ( )
inherited

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.SBase.getAnnotationString ( )
inherited

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
long libsbmlcs.SBase.getColumn ( )
inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getLine()
CVTerm libsbmlcs.SBase.getCVTerm ( long  n)
inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
CVTermList libsbmlcs.SBase.getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
Delay libsbmlcs.Event.getDelay ( )

Get the assignment delay portion of this Event, if there is one.

Returns
the delay of this Event if one is defined, or null if none is defined.
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.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given 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.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string  metaid)
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.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string  id)
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.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
new string libsbmlcs.Event.getElementName ( )

Returns the XML element name of this object, which for Event, is always 'event'.

Returns
the name of this element, i.e., 'event'.
EventAssignment libsbmlcs.Event.getEventAssignment ( long  n)

Return a specific EventAssignment object of this Event.

Parameters
nan integer, the index of the EventAssignment object to return
Returns
the nth EventAssignment of this Event.
EventAssignment libsbmlcs.Event.getEventAssignment ( string  variable)

Return the event assignment indicated by the given variable.

Parameters
variablea string, the identifier of the variable whose EventAssignment is being sought.
Returns
the EventAssignment for the given variable, or null if no such EventAssignment exits.
override int libsbmlcs.SBase.GetHashCode ( )
inherited
new string libsbmlcs.Event.getId ( )

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

Returns
the id of this Event.
long libsbmlcs.SBase.getLevel ( )
inherited

Returns the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
long libsbmlcs.SBase.getLine ( )
inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getColumn()
SBaseList libsbmlcs.SBase.getListOfAllElements ( )
inherited
SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )
inherited
ListOfEventAssignments libsbmlcs.Event.getListOfEventAssignments ( )

Returns the list of event assignments for this Event.

Returns
the list of EventAssignments for this Event.
string libsbmlcs.SBase.getMetaId ( )
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.

Returns
the meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(string metaid)
Model libsbmlcs.SBase.getModel ( )
inherited

Returns the Model object in which the current object is located.

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
ModelHistory libsbmlcs.SBase.getModelHistory ( )
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or null if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new string libsbmlcs.Event.getName ( )

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

Returns
the name of this Event.
XMLNamespaces libsbmlcs.SBase.getNamespaces ( )
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.

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()
XMLNode libsbmlcs.SBase.getNotes ( )
inherited

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, 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().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
string libsbmlcs.SBase.getNotesString ( )
inherited

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, 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.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
long libsbmlcs.SBase.getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
long libsbmlcs.Event.getNumEventAssignments ( )

Returns the number of EventAssignment objects attached to this Event.

Returns
the number of EventAssignments in this Event.
long libsbmlcs.SBase.getNumPlugins ( )
inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
string libsbmlcs.SBase.getPackageName ( )
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
long libsbmlcs.SBase.getPackageVersion ( )
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also
getLevel()
getVersion()
SBase libsbmlcs.SBase.getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See Also
getSBMLDocument()
getModel()
SBasePlugin libsbmlcs.SBase.getPlugin ( string  package)
inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SBasePlugin libsbmlcs.SBase.getPlugin ( long  n)
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
Priority libsbmlcs.Event.getPriority ( )

(SBML Level 3 only) Get the event priority portion of this Event.

Returns
the Priority object of this Event.
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
int libsbmlcs.SBase.getResourceBiologicalQualifier ( string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
int libsbmlcs.SBase.getResourceModelQualifier ( string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
SBMLDocument libsbmlcs.SBase.getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See Also
getParentSBMLObject()
getModel()
SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )
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:

int libsbmlcs.SBase.getSBOTerm ( )
inherited

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 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.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
string libsbmlcs.SBase.getSBOTermAsURL ( )
inherited

Returns the 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.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
string libsbmlcs.SBase.getSBOTermID ( )
inherited

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 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.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
string libsbmlcs.Event.getTimeUnits ( )

Get the value of the 'timeUnits' attribute of this Event, if it has one.

Returns
the value of the attribute 'timeUnits' as a string.
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
Trigger libsbmlcs.Event.getTrigger ( )

Get the event trigger portion of this Event.

Returns
the Trigger object of this Event.
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_.

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()
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.

Returns
the value of the attribute 'useValuesFromTriggerTime' as a bool.
Warning
The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. It is not valid in models defined using SBML Level 2 versions prior to Version 4. If a Level 2 Version 1–3 model sets the attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
long libsbmlcs.SBase.getVersion ( )
inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string  prefix)
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 ( )

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

Note
The required attributes for a Event object are:
  • 'useValuesfromTriggerTime' (required in SBML Level 3)
new bool libsbmlcs.Event.hasRequiredElements ( )

Predicate returning true if all the required elements for this Event object have been set.

Note
The required elements for a Event object are:
  • 'trigger'
  • 'listOfEventAssignments' (required in SBML Level 2, optional in Level 3)
bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
bool libsbmlcs.SBase.isPackageEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
bool libsbmlcs.SBase.isPackageURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
bool libsbmlcs.SBase.isPkgEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgURIEnabled()
bool libsbmlcs.SBase.isPkgURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
bool libsbmlcs.SBase.isSetAnnotation ( )
inherited

Predicate returning true if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
true if a 'annotation' subelement exists, false otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
bool libsbmlcs.Event.isSetDelay ( )

Predicate for testing whether the delay for this Event is set.

Returns
true if the delay of this Event is set, false otherwise.
new bool libsbmlcs.Event.isSetId ( )

Predicate returning true if this Event's 'id' attribute is set.

Returns
true if the 'id' attribute of this Event is set, false otherwise.
bool libsbmlcs.SBase.isSetMetaId ( )
inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (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.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new bool libsbmlcs.Event.isSetName ( )

Predicate returning true if this Event's 'name' attribute is set.

Returns
true if the 'name' attribute of this Event is set, false otherwise.
bool libsbmlcs.SBase.isSetNotes ( )
inherited

Predicate returning true if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
true if a 'notes' subelement exists, false otherwise.
See Also
getNotes()
getNotesString()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool libsbmlcs.Event.isSetPriority ( )

(SBML Level 3 only) Predicate for testing whether the priority for this Event is set.

Returns
true if the priority of this Event is set, false otherwise.
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
bool libsbmlcs.SBase.isSetSBOTerm ( )
inherited

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

Returns
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
bool libsbmlcs.Event.isSetTimeUnits ( )

Predicate for testing whether the 'timeUnits' attribute of this Event is set.

Returns
true if the 'timeUnits' attribute of this Event is set, false otherwise.
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
bool libsbmlcs.Event.isSetTrigger ( )

Predicate for testing whether the trigger for this Event is set.

Returns
true if the trigger of this Event is set, false otherwise.
bool libsbmlcs.Event.isSetUseValuesFromTriggerTime ( )

Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.

Returns
true if the 'useValuesFromTriggerTime' attribute of this Event is set, false otherwise.
Note
In SBML Level 2, this attribute is optional and has a default value of true, whereas in Level 3 Version 1, this optional is mandatory and has no default value.
bool libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool libsbmlcs.SBase.matchesSBMLNamespaces ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is the same as sb's, false otherwise.
void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

static bool libsbmlcs.SBase.operator!= ( SBase  lhs,
SBase  rhs 
)
staticinherited
static bool libsbmlcs.SBase.operator== ( SBase  lhs,
SBase  rhs 
)
staticinherited
int libsbmlcs.SBase.prependStringToAllIdentifiers ( string  prefix)
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.

Parameters
nthe index of the EventAssignment object to remove
Returns
the EventAssignment object removed. As mentioned above, the caller owns the returned item. 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.

Parameters
variablethe 'variable' attribute of the EventAssignment object to remove
Returns
the EventAssignment object removed. As mentioned above, the caller owns the returned object. null is returned if no EventAssignment object with the 'variable' attribute exists in this Event object.
int libsbmlcs.SBase.removeFromParentAndDelete ( )
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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName,
string  elementURI 
)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
void libsbmlcs.SBase.renameMetaIdRefs ( string  oldid,
string  newid 
)
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.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.renameSIdRefs ( string  oldid,
string  newid 
)
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.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.renameUnitSIdRefs ( string  oldid,
string  newid 
)
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.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.replaceSIDWithFunction ( string  id,
ASTNode  function 
)
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.

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(XMLNode)
int libsbmlcs.SBase.setAnnotation ( XMLNode  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.setAnnotation ( string  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.Event.setDelay ( Delay  delay)

Sets the delay definition of this Event to a copy of the given Delay object instance.

Parameters
delaythe Delay object instance to use
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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.

Parameters
sidthe string to use as the identifier of this Event
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setMetaId ( string  metaid)
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.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
int libsbmlcs.SBase.setModelHistory ( ModelHistory  history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Event.setName ( string  name)

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

The string in name is copied.

Parameters
namethe new name for the Event
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNamespaces ( XMLNamespaces  xmlns)
inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNotes ( XMLNode  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes,
bool  addXHTMLMarkup 
)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa 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.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.Event.setPriority ( Priority  priority)

(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance.

Parameters
prioritythe Priority object instance to use
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces  sbmlns)
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:

int libsbmlcs.SBase.setSBOTerm ( int  value)
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.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(string sboid)
int libsbmlcs.SBase.setSBOTerm ( string  sboid)
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.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(int value)
int libsbmlcs.Event.setTimeUnits ( string  sid)

Sets the 'timeUnits' attribute of this Event to a copy of sid.

Parameters
sidthe identifier of the time units to use.
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Event.setTrigger ( Trigger  trigger)

Sets the trigger definition of this Event to a copy of the given Trigger object instance.

Parameters
triggerthe Trigger object instance to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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.

Parameters
valuethe value of useValuesFromTriggerTime to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. It is not valid in models defined using SBML Level 2 versions prior to Version 4. If a Version 1– 3 model sets the attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
string libsbmlcs.SBase.toSBML ( )
inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
int libsbmlcs.SBase.unsetAnnotation ( )
inherited

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
int libsbmlcs.SBase.unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Event.unsetDelay ( )

Unsets the Delay of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
new int libsbmlcs.Event.unsetId ( )

Unsets the value of the 'id' attribute of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetMetaId ( )
inherited

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Event.unsetName ( )

Unsets the value of the 'name' attribute of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetNotes ( )
inherited

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.Event.unsetPriority ( )

(SBML Level 3 only) Unsets the Priority of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
int libsbmlcs.SBase.unsetSBOTerm ( )
inherited

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Event.unsetTimeUnits ( )

Unsets the 'timeUnits' attribute of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Version 3 and Version 4 cannot contain it. If a Version 3 or 4 model sets this attribute, the consistency-checking method SBMLDocument::checkConsistency() will report an error.
int libsbmlcs.Event.unsetTrigger ( )

Unsets the Trigger of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream  stream)
inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn
protectedinherited