CodonAlphabet: The CodonAlphabet class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This class implements codon alphabets and handles the translation of codons to their corresponding amino acids. Stop codons are excluded from the symbol set, thus the symbol set depends on the genetic code table. The genetic code table can be specified through the table.id constructor parameter.

The available genetic code tables:

	1	Standard
	2	Vertebrate Mitochondrial
	3	Yeast Mitochondrial
	4	Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma
	5	Invertebrate Mitochondrial
	6	Ciliate, Dasycladacean and Hexamita Nuclear
	9	Echinoderm Mitochondrial
	10	Euplotid Nuclear
	11	Bacterial
	12	Alternative Yeast Nuclear
	13	Ascidian Mitochondrial
	14	Flatworm Mitochondrial
	15	Blepharisma Nuclear
	16	Chlorophycean Mitochondrial
	21	Trematode Mitochondrial
	22	Scenedesmus obliquus Mitochondrial
	23	Thraustochytrium Mitochondrial
	

Package:
Class CodonAlphabet

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

Directly known subclasses:

public static class CodonAlphabet
extends Alphabet

Usage

CodonAlphabet(table.id=1, ...)

Arguments

table.id	The identifier of the genetic code table.
...	Not used.

Fields and Methods

Methods:

	areSynonymous	-
	checkConsistency	-
	getTableId	-
	getTransTable	-
	is	-
	isStartCodon	-
	isStopCodon	-
	setTableId	-
	setTransTable	-
	summary	-
	translateCodon	-

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

For more information see CodonAlphabet.

Examples

	# create a CodonAlphabet object
	a<-CodonAlphabet(table.id=2)
	# get object summary
	summary(a)
 

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