jebl.evolution.sequences
Class GeneticCode

java.lang.Object
  jebl.evolution.sequences.GeneticCode

public final class GeneticCode
extends Object

A set of standard genetic codes.

Author:

Andrew Rambaut, Alexei Drummond

Field Summary

static GeneticCode	ALT_YEAST
static GeneticCode	ASCIDIAN_MT
static GeneticCode	BACTERIAL
static GeneticCode	BLEPHARISMA_NUC
static GeneticCode	CILIATE
static GeneticCode	ECHINODERM_MT
static GeneticCode	EUPLOTID_NUC
static GeneticCode	FLATWORM_MT
static GeneticCode[]	GENETIC_CODES
static GeneticCode	INVERTEBRATE_MT
static GeneticCode	MOLD_PROTOZOAN_MT
static GeneticCode	MYCOPLASMA
static GeneticCode	UNIVERSAL
static GeneticCode	VERTEBRATE_MT
static GeneticCode	YEAST

Method Summary

String	getCodeTable() Returns the description of the genetic code
Set<CodonState>	getCodonsForAminoAcid(AminoAcidState aminoAcidState)
String	getDescription() Returns the description of the genetic code
String	getName() Returns the name of the genetic code
int	getStopCodonCount() Returns the number of terminator amino acids.
Set<CodonState>	getStopCodons()
AminoAcidState	getTranslation(CodonState codonState) Returns the state associated with AminoAcid represented by codonState.
boolean	isStopCodon(CodonState codonState) Note that the state is the canonical state (generated combinatorially)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

UNIVERSAL

public static final GeneticCode UNIVERSAL

VERTEBRATE_MT

public static final GeneticCode VERTEBRATE_MT

YEAST

public static final GeneticCode YEAST

MOLD_PROTOZOAN_MT

public static final GeneticCode MOLD_PROTOZOAN_MT

MYCOPLASMA

public static final GeneticCode MYCOPLASMA

INVERTEBRATE_MT

public static final GeneticCode INVERTEBRATE_MT

CILIATE

public static final GeneticCode CILIATE

ECHINODERM_MT

public static final GeneticCode ECHINODERM_MT

EUPLOTID_NUC

public static final GeneticCode EUPLOTID_NUC

BACTERIAL

public static final GeneticCode BACTERIAL

ALT_YEAST

public static final GeneticCode ALT_YEAST

ASCIDIAN_MT

public static final GeneticCode ASCIDIAN_MT

FLATWORM_MT

public static final GeneticCode FLATWORM_MT

BLEPHARISMA_NUC

public static final GeneticCode BLEPHARISMA_NUC

GENETIC_CODES

public static final GeneticCode[] GENETIC_CODES

Method Detail

getName

public String getName()

Returns the name of the genetic code

getDescription

public String getDescription()

Returns the description of the genetic code

getCodeTable

public String getCodeTable()

Returns the description of the genetic code

getTranslation

public AminoAcidState getTranslation(CodonState codonState)

Returns the state associated with AminoAcid represented by codonState. Note that the state is the canonical state (generated combinatorially)

Returns:

'?' if codon unknown

See Also:

AminoAcids, Codons

isStopCodon

public boolean isStopCodon(CodonState codonState)

Note that the state is the canonical state (generated combinatorially)

Returns:

whether the codonState is a stop codon

getCodonsForAminoAcid

public Set<CodonState> getCodonsForAminoAcid(AminoAcidState aminoAcidState)

Returns:

all the possible codons for a given amino acid

getStopCodons

public Set<CodonState> getStopCodons()

Returns:

the codon states of stops.

getStopCodonCount

public int getStopCodonCount()

Returns the number of terminator amino acids.

toString

public String toString()

Overrides:

toString in class Object