Event: The Event class
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Fields and Methods Author(s) See Also Examples

This is the class representing an event. Event objects usually are generated by the getEventsAtSite.* methods based on the state of attached Site object and the properties of the generating Process object.

The Perform method will refuse to modify target objects if the position field is not set. The Perform method can be called only once for any Event object.

Package:
Class Event

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Event

Directly known subclasses:

public static class Event
extends PSRoot

1	Event(name=NA, rate=NA, site=NA, position=NA, process=NA, handler=NA, ...)

`name`	The name of the Event object. Often stores useful information.
`rate`	The rate of the event.
`site`	The associated Site object.
`position`	The position of associated Site object in the enclosing Sequence object (if any).
`process`	The generator Process object.
`handler`	The handler function for the Event object. It will be called by `Perform.Event` with the Event object as an argument to make the changes corresponding to the event.
`...`	Not used.

Methods:

	`Perform`	-
	`as.character`	-
	`checkConsistency`	-
	`getHandler`	-
	`getName`	-
	`getPosition`	-
	`getProcess`	-
	`getRate`	-
	`getSite`	-
	`getWriteProtected`	-
	`is`	-
	`setHandler`	-
	`setName`	-
	`setPosition`	-
	`setProcess`	-
	`setRate`	-
	`setSite`	-
	`setWriteProtected`	-
	`summary`	-

Methods inherited from PSRoot:
checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Botond Sipos, Gregory Jordan

Site Process Sequence getEventsAtSite.GeneralSubstitution

	# Note: the following examples are not very useful
	# unless you want to implement your own process.

	# create a Sequence object and a Process object
	seq<-NucleotideSequence(string="A");
	p<-Process(alphabet=NucleotideAlphabet())
	# get the Site object from the Sequence object
	s<-seq$sites[[1]]
	# attach p to s
	attachProcess(s,p)
	# create an Event object
	e<-Event(name="A->G",rate=0.1,site=s,process=p,position=1)
	# get object summary
	summary(e)
	# get event name
	e$name
	# set/get event rate
	e$rate<-0.2
	e$rate
	# get site
	e$site
	# set/get event handler
	e$.handler<-function(this){this$.site$state<-"G"}
	e$handler
	# perform the event
	Perform(e)
	# check the state of the target site
	s$state