phylosim (version 3.0.5)

GeneralInsertor: The GeneralInsertor class

Description

This is a class implementing a process generating insertion events. The rate of each event is calculated as the product of the general rate of the process and the "rate.multiplier" site-process specific parameter. The simulation code calls the Perform method on the selected insertion event objects, which call their insertion event handler to perform the insertion.

The insert lengths are proposed by the function stored in the proposeBy virtual field. The function must have the following arguments: process (the insertion process object).

The insertion events are accepted or rejected by the function stored in the acceptBy virtual field. The function must have the following arguments: process (the insertion process object), sequence (the target sequence object), window (a vector of positions affecting acceptance). The probability of accepting an insertion is calculated as the product of the site-process-specific "insertion.tolerance" parameters of the sites neighboring the insertion. The number of sites considered is determined by the acceptWin virtual field.

The insert is generated by the generateInsert method by calling the function stored in the generateBy virtual field. The default generator function truncates/duplicates the sequence object stored in the templateSeq virtual field to get a sequence having the sampled length. After constructing the Sequence object, it calls the sampleStates.Sequence method on the resulting object. That means that if we start with a template sequence which has NA states, but has a substitution process attached, then the resulting sequence will be different every time.

Before inserting the sequence returned by generateInsert, the handler function will pass the object through the function stored in the insertHook virtual field. This allows to perform arbitrary modifications on the inserted Sequence object.

The sequence is inserted randomly on the left or the right of the target position.

Package: Class GeneralInsertor

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Process ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GeneralInDel ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--GeneralInsertor

Directly known subclasses: BrownianInsertor, ContinuousInsertor, DiscreteInsertor

public static class GeneralInsertor extends GeneralInDel

Usage

GeneralInsertor(name="Anonymous", rate=NA, propose.by=NA, accept.by=NA, template.seq=NA,
  insert.hook=NA, accept.win=NA, ...)

Arguments

name

The name of the object.

rate

The general rate of the object (no default).

propose.by

A function used to propose events (no default).

accept.by

A function used to accept/reject events (no default).

template.seq

A Sequence object used as a template for generating insertions (no default).

insert.hook

A function object, see setInsertHook (no default).

accept.win

A window of sites affecting the acceptance of insert events.

...

Additional arguments.

Fields and Methods

Methods:

	checkConsistency	-
	generateInsert	-
	getAcceptWin	-
	getEventsAtSite	-
	getGenerateBy	-
	getInsertHook	-
	getTemplateSeq	-
	is	-
	setAcceptWin	-
	setGenerateBy	-
	setInsertHook	-
	setTemplateSeq	-
	summary	-

Methods inherited from GeneralInDel: checkConsistency, getAcceptBy, getProposeBy, getRate, hasUndefinedRate, is, proposeLength, setAcceptBy, setProposeBy, setRate, summary

Methods inherited from Process: !=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, 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

See Also

GeneralInDel DiscreteInsertor ContinuousInsertor BrownianInsertor

Examples

# NOT RUN {
	# create a GeneralInsertor object
	i<-GeneralInsertor(
		name="GIN",
		rate=1,
		propose.by=function(process){4}, # fixed insert length
		acceptBy=function(process,sequence,window){TRUE},# always accept insertions
		template.seq=NucleotideSequence(string="A"),# a boring template sequence
		insert.hook=function(seq){ return(seq)},# a boring insert hook
		accept.win=2 #4 sites affecting acceptance
	)
	i
	# check if object inherits from GeneralInsertor
	is.GeneralInsertor(i)
	# get object summary
	summary(i)
	# set/get general rate
	i$rate<-0.5
	i$rate
	# set/get name
	i$name<-"Ins"
	i$name
	# set/get proposeBy
	# sample insertion length between 1 and 10
	i$proposeBy<-function(process){sample(1:10,1)}
	i$proposeBy
	# set/get acceptBy
	# reject half of the insertions
	i$acceptBy<-function(process, sequence, window){ sample(c(TRUE,FALSE), 1) }
	i$acceptBy
	# get generateBy
	i$generateBy
	# set/get acceptWin
	i$acceptWin<-1;
	# set/get insert hook
	i$insertHook<-function(
                           seq,
                           target.seq,
                           event.pos,
                           insert.pos
                           ){ attachProcess(seq, GTR() );seq}
	i$insertHook
	# set/get template sequence
	i$templateSeq<-NucleotideSequence(
                                       length=5,
                                       processes=list(list(JC69()))
                                   ) # length: 5, states: NA
	i$templateSeq
	# generate an insert sequence
	generateInsert(i)
	# create a sequence object and attach the process i
	s<-NucleotideSequence(string="AAAAA",processes=list(list(i)))
       # set rate multiplier
       setRateMultipliers(s,i,2)
       # get the list of active events from site 2
       events<-getEventsAtSite(i,s$sites[[2]])
       events
       # set postition for event
       e<-events[[1]]
       e$.position<-2
       # print sequence
       s
       # perform event
       Perform(e)
       # check sequence again
       s
 
# }