Uses of Class
jebl.evolution.sequences.AminoAcidState
Packages that use AminoAcidState
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Uses of AminoAcidState in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as AminoAcidStateModifier and TypeFieldDescriptionstatic final AminoAcidState
AminoAcids.A_STATE
static final AminoAcidState
AminoAcids.B_STATE
static final AminoAcidState
AminoAcids.C_STATE
static final AminoAcidState[]
AminoAcids.CANONICAL_STATES
Deprecated.static final AminoAcidState
AminoAcids.D_STATE
static final AminoAcidState
AminoAcids.E_STATE
static final AminoAcidState
AminoAcids.F_STATE
static final AminoAcidState
AminoAcids.G_STATE
static final AminoAcidState
AminoAcids.GAP_STATE
static final AminoAcidState
AminoAcids.H_STATE
static final AminoAcidState
AminoAcids.I_STATE
static final AminoAcidState
AminoAcids.J_STATE
static final AminoAcidState
AminoAcids.K_STATE
static final AminoAcidState
AminoAcids.L_STATE
static final AminoAcidState
AminoAcids.M_STATE
static final AminoAcidState
AminoAcids.N_STATE
static final AminoAcidState
AminoAcids.O_STATE
static final AminoAcidState
AminoAcids.P_STATE
static final AminoAcidState
AminoAcids.Q_STATE
static final AminoAcidState
AminoAcids.R_STATE
static final AminoAcidState
AminoAcids.S_STATE
static final AminoAcidState[]
AminoAcids.STATES
Deprecated.static final AminoAcidState
AminoAcids.STOP_STATE
static final AminoAcidState
AminoAcids.T_STATE
static final AminoAcidState
AminoAcids.U_STATE
static final AminoAcidState
AminoAcids.UNKNOWN_STATE
static final AminoAcidState
AminoAcids.V_STATE
static final AminoAcidState
AminoAcids.W_STATE
static final AminoAcidState
AminoAcids.X_STATE
static final AminoAcidState
AminoAcids.Y_STATE
static final AminoAcidState
AminoAcids.Z_STATE
Methods in jebl.evolution.sequences that return AminoAcidStateModifier and TypeMethodDescriptionstatic AminoAcidState
AminoAcids.getGapState()
static AminoAcidState
AminoAcids.getState
(char code) static AminoAcidState
AminoAcids.getState
(int index) static AminoAcidState
GeneticCode.getTranslation
(String nucleotides) Returns the state associated with AminoAcid represented by the three nucleotides.GeneticCode.getTranslation
(CodonState codonState) Returns the state associated with AminoAcid represented by codonState.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
(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 AminoAcidStateMethods in jebl.evolution.sequences with parameters of type AminoAcidStateModifier and TypeMethodDescriptionGeneticCode.getCodonsForAminoAcid
(AminoAcidState aminoAcidState) static String
AminoAcids.getTripletCode
(AminoAcidState state) static boolean
AminoAcids.isGap
(AminoAcidState state) static boolean
AminoAcids.isUnknown
(AminoAcidState state)