Alphabet: The Alphabet class
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Fields and Methods Author(s) See Also Examples

Class representing an alphabet (a set of symbols). Package:
Class Alphabet

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

Directly known subclasses:
AminoAcidAlphabet, AnyAlphabet, BinaryAlphabet, CodonAlphabet, NucleotideAlphabet

public static class Alphabet
extends PSRoot

1	Alphabet(symbols=NA, type="Generic", ...)

`symbols`	A character vector containing the symbols for the alphabet. All elements must have the same length and no duplicates are allowed. No element of the vector may contain the dash symbol, which is reserved for gaps.
`type`	An identifier for the Alphabet object.
`...`	Not used.

Methods:

	`!=`	-
	`==`	-
	`as.character`	-
	`checkConsistency`	-
	`getSize`	-
	`getSymbolLength`	-
	`getSymbols`	-
	`getType`	-
	`getWriteProtected`	-
	`hasSymbols`	-
	`is`	-
	`isEmpty`	-
	`setSize`	-
	`setSymbolLength`	-
	`setSymbols`	-
	`setType`	-
	`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

Botond Sipos, Gregory Jordan

Site Process Event BinaryAlphabet NucleotideAlphabet AminoAcidAlphabet

		# create an alphabet object
		a<-Alphabet(type="Binary",symbols=c("0","1"));
		# print summary
		summary(a);
		# change the identifier
		a$type<-"Nucleotide";
		# change the symbol set
		a$symbols<-c("A","T","G","C");
		# print summary again
		summary(a);
		# clone the alphabet object
		b<-clone(a);
		# test the equality of the symbol sets
		a == b;