getAlphabets.Sequence: Get the list of the Alphabet objects attached to the Site...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object.

Usage

## S3 method for class 'Sequence'
getAlphabets(this, index, ...)

Arguments

this	A Sequence object.
index	An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.
...	Not used.

Value

A list of Alphabet objects.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see Sequence.

Examples

	# create a Sequence object with NucleotideAlphabet
	#and BinaryAlphabet objects attached
	s<-Sequence(alphabets=list(NucleotideAlphabet(),BinaryAlphabet()),length=5)
	setStates(s,c("A","0"))
	# get the list of attached Alphabet objects
	getAlphabets(s)
	# get Alphabets from a range
	getAlphabets(s,c(2:3,5))
	# get alphabets via virtual field
	s$alphabets
 

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