AnyAlphabet: The AnyAlphabet class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This is a special Alphabet class which matches any alphabet. The '=='.Alphabet method always returns TRUE when one of the compared objects inherits from AnyAlphabet. This behaviour is handy when creating processes that have no alphabet preference (like a deletion process).

Package:
Class AnyAlphabet

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

Directly known subclasses:

public static class AnyAlphabet
extends Alphabet

Usage

AnyAlphabet(...)

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

	# create some alphabet objects
	a<-BinaryAlphabet()
	b<-NucleotideAlphabet()
	any<-AnyAlphabet()
	# compare objects
	a == b
	any == a
	any == b
 

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