Uses of Class
jebl.evolution.sequences.AminoAcidState
-
Packages that use AminoAcidState Package Description jebl.evolution.sequences -
-
Uses of AminoAcidState in jebl.evolution.sequences
Methods in jebl.evolution.sequences that return AminoAcidState Modifier and Type Method Description static AminoAcidState
AminoAcids. getGapState()
static AminoAcidState
AminoAcids. getState(char code)
static AminoAcidState
AminoAcids. getState(int index)
static AminoAcidState
AminoAcids. getState(java.lang.String code)
AminoAcidState
GeneticCode. getTranslation(java.lang.String nucleotides)
Returns the state associated with AminoAcid represented by the three nucleotides.AminoAcidState
GeneticCode. getTranslation(CodonState codonState)
Returns the state associated with AminoAcid represented by codonState.AminoAcidState
GeneticCode. getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
Returns the state associated with AminoAcid represented by the three nucleotides.static AminoAcidState
AminoAcids. getUnknownState()
static AminoAcidState[]
AminoAcids. toStateArray(byte[] indexArray)
static AminoAcidState[]
AminoAcids. toStateArray(java.lang.String sequenceString)
static AminoAcidState[]
Utils. translate(State[] states, GeneticCode geneticCode)
Translates each of a given sequence ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.static AminoAcidState[]
Utils. translate(State[] states, GeneticCode geneticCode, int readingFrame)
Translates each of a given sequence ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.Methods in jebl.evolution.sequences that return types with arguments of type AminoAcidState Modifier and Type Method Description static java.util.List<AminoAcidState>
AminoAcids. getStates()
Methods in jebl.evolution.sequences with parameters of type AminoAcidState Modifier and Type Method Description java.util.Set<CodonState>
GeneticCode. getCodonsForAminoAcid(AminoAcidState aminoAcidState)
static java.lang.String
AminoAcids. getTripletCode(AminoAcidState state)
static boolean
AminoAcids. isGap(AminoAcidState state)
static boolean
AminoAcids. isUnknown(AminoAcidState state)
-