phylosim (version 3.0.5)

AminoAcidAlphabet: The AminoAcidAlphabet class

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

See Also

Alphabet

Examples

# NOT RUN {
	a<-AminoAcidAlphabet();
	# get object summary
	summary(a)
 
# }