AminoAcidAlphabet: The AminoAcidAlphabet class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Class of Alphabet objects representing amino acids, using the one-letter IUPAC amino acid codes as symbol set:

	IUPAC code	Amino acid

	A		Alanine
	C		Cysteine
	D		Aspartic Acid
	E		Glutamic Acid
	F		Phenylalanine
	G		Glycine
	H		Histidine
	I		Isoleucine
	K		Lysine
	L		Leucine
	M		Methionine
	N		Asparagine
	P		Proline
	Q		Glutamine
	R		Arginine
	S		Serine
	T		Threonine
	V		Valine
	W		Tryptophan
	Y		Tyrosine

Package:
Class AminoAcidAlphabet

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Alphabet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AminoAcidAlphabet

Directly known subclasses:

public static class AminoAcidAlphabet
extends Alphabet

Usage

AminoAcidAlphabet(...)

Arguments

...

Not used.

Fields and Methods

Methods:
No methods defined.

Methods inherited from Alphabet:
!=, ==, as.character, checkConsistency, getSize, getSymbolLength, getSymbols, getType, getWriteProtected, hasSymbols, is, isEmpty, setSize, setSymbolLength, setSymbols, setType, 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

Author(s)

Botond Sipos, Gregory Jordan

See Also

Alphabet

Examples

	a<-AminoAcidAlphabet();
	# get object summary
	summary(a)
 

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