Uses of Class
jebl.evolution.sequences.CodonState
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Packages that use CodonState Package Description jebl.evolution.sequences -
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Uses of CodonState in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as CodonState Modifier and Type Field Description static CodonState[]Codons. CANONICAL_STATESstatic CodonStateCodons. GAP_STATEstatic CodonState[]Codons. STATESstatic CodonStateCodons. UNKNOWN_STATEMethods in jebl.evolution.sequences that return CodonState Modifier and Type Method Description static CodonStateCodons. getGapState()static CodonStateCodons. getState(int index)static CodonStateCodons. getState(java.lang.String code)Gets the state object for the given code.static CodonStateCodons. getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)static CodonStateCodons. getUnknownState()static CodonState[]Nucleotides. toCodons(State[] states, int readingFrame)Convert an array of nucleotide states into an array of codon statesstatic CodonState[]Codons. toStateArray(byte[] indexArray)static CodonState[]Codons. toStateArray(java.lang.String sequenceString)Methods in jebl.evolution.sequences that return types with arguments of type CodonState Modifier and Type Method Description java.util.Set<CodonState>GeneticCode. getCodonsForAminoAcid(AminoAcidState aminoAcidState)java.util.Set<CodonState>GeneticCode. getStartCodons()java.util.Set<CodonState>GeneticCode. getStopCodons()Methods in jebl.evolution.sequences with parameters of type CodonState Modifier and Type Method Description AminoAcidStateGeneticCode. getTranslation(CodonState codonState)Returns the state associated with AminoAcid represented by codonState.static booleanCodons. isGap(CodonState state)booleanGeneticCode. isStartCodon(CodonState codonState)Deprecated.booleanGeneticCode. isStopCodon(CodonState codonState)Deprecated.static booleanCodons. isUnknown(CodonState state)static NucleotideState[]Codons. toNucleotides(CodonState state)
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