getTemplateSeq.GeneralInsertor: Get the template sequence object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the template sequence object. The template sequence object is used by the default generateBy function to generate insert sequences.

Usage

## S3 method for class 'GeneralInsertor'
getTemplateSeq(this, ...)

Arguments

this	A GeneralInsertor object.
...	Not used.

Value

A Sequence object or NA.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see GeneralInsertor.

Examples

	# create a GeneralInsertor object
	i<-GeneralInsertor(
		rate=0.5,
		propose.by=function(process){sample(c(5:10),1)}, # inserts between 5 and 10
		template.seq=NucleotideSequence(string="AAAAAAA")
	)
	# get template sequence
	getTemplateSeq(i)
	# get template sequence via virtual field
	i$templateSeq
	# set template sequence
	setTemplateSeq(i, NucleotideSequence(string="C"));
	# generate insert
	generateInsert(i)
	# set template sequence via virtual field
	i$templateSeq<-NucleotideSequence(string="G")
	# generate insert
	generateInsert(i)
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.