Process: The Process 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 a generic process acting on Site and Sequence objects. Process objects can be attached to Site objects if the associated Alphabet objects match.

The processes can have site-process-specific parameters. The templates for site-process-specific parameters and their default values are stored in the Process objects and copied into the Site object when the process is attached. See the documentation of the Site class for more details.

The rate multiplier parameter (id="rate.multiplier") is present in the Process class and is inherited by all descendant classes.

Package:
Class Process

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process

Directly known subclasses:
AminoAcidSubst, BinarySubst, BrownianInsertor, CodonSubst, CodonUNREST, ContinuousDeletor, ContinuousInsertor, DiscreteDeletor, DiscreteInsertor, ECMrest, ECMunrest, F81, F84, FastFieldDeletor, GTR, GY94, GeneralDeletor, GeneralInDel, GeneralInsertor, GeneralSubstitution, HKY, JC69, JTT, JTT.dcmut, K80, K81, LG, MtZoa, PAM, PAM.dcmut, T92, TN93, ToleranceSubstitution, UNREST, WAG, cpREV, mtArt, mtMam, mtREV24

public static class Process
extends PSRoot

1	Process(name=NA, alphabet=NA, ...)

`name`	The name of the Process object: a character vector of length one.
`alphabet`	The associated Alphabet object.
`...`	Not used.

Methods:

	`!=`	-
	`==`	-
	`as.character`	-
	`checkConsistency`	-
	`clone`	-
	`getAlphabet`	-
	`getEventsAtSite`	-
	`getId`	-
	`getName`	-
	`getParameterAtSite`	-
	`getSiteSpecificParamIds`	-
	`getSiteSpecificParamList`	-
	`getWriteProtected`	-
	`hasSiteSpecificParameter`	-
	`hasUndefinedRate`	-
	`is`	-
	`setAlphabet`	-
	`setId`	-
	`setName`	-
	`setParameterAtSite`	-
	`setSiteSpecificParamIds`	-
	`setSiteSpecificParamList`	-
	`setWriteProtected`	-
	`summary`	-

Botond Sipos, Gregory Jordan

For more information see Process.

	# create a Process object
	p<-Process(name="MyProc",alphabet=AminoAcidAlphabet())
	# check if it's a Process object
	is.Process(p)
	# check object consistency
	checkConsistency(p)
	# set process name
	p$name<-"Ppppproccc"
	# get process name
	p$name
	# get unique process identifier
	p$id
	# get the list of site specific paramters and paramter IDs
	p$siteSpecificParamList
	p$siteSpecificParamIds
	# get Process object summary
	summary(p)
	# clone process object
	pp<-clone(p)
	# test object identity
	p == p
	p == pp
	# create a site object
	s<-Site(alphabet=AminoAcidAlphabet())
	# attach process to Site object
	attachProcess(s,p)
	# get events at specified site
	getEventsAtSite(p,s)	# empty list
	# detach process via virtual field
	s$processes<-list()
	# attach processes via virtual field
	s$processes<-list(p,pp)
	# set the value of the rate multiplier for Site s
	setParameterAtSite(p,s,id="rate.multiplier",value=2)
	# get the value of the rate multiplier for Site s
	getParameterAtSite(p,s,id="rate.multiplier")