Uses of Class
jebl.evolution.sequences.CodonState

Packages that use CodonState

jebl.evolution.sequences

Uses of CodonState in jebl.evolution.sequences

Fields in jebl.evolution.sequences declared as CodonState

static CodonState[]	Codons.CANONICAL_STATES
static CodonState	Codons.GAP_STATE
static CodonState[]	Codons.STATES
static CodonState	Codons.UNKNOWN_STATE

Methods in jebl.evolution.sequences that return CodonState

static CodonState	Codons.getGapState()
static CodonState	Codons.getState(int index)
static CodonState	Codons.getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
static CodonState	Codons.getState(String code) Gets the state object for the given code.
static CodonState	Codons.getUnknownState()
static CodonState[]	Codons.toStateArray(byte[] indexArray)
static CodonState[]	Codons.toStateArray(String sequenceString)

Methods in jebl.evolution.sequences that return types with arguments of type CodonState

Set<CodonState>	GeneticCode.getCodonsForAminoAcid(AminoAcidState aminoAcidState)
Set<CodonState>	GeneticCode.getStopCodons()

Methods in jebl.evolution.sequences with parameters of type CodonState

AminoAcidState	GeneticCode.getTranslation(CodonState codonState) Returns the state associated with AminoAcid represented by codonState.
static boolean	Codons.isGap(CodonState state)
boolean	GeneticCode.isStopCodon(CodonState codonState) Note that the state is the canonical state (generated combinatorially)
static boolean	Codons.isUnknown(CodonState state)
static NucleotideState[]	Codons.toNucleotides(CodonState state)