Uses of Class
jebl.evolution.sequences.AminoAcidState
Packages that use AminoAcidState
-
Uses of AminoAcidState in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as AminoAcidStateModifier and TypeFieldDescriptionstatic final AminoAcidStateAminoAcids.A_STATEstatic final AminoAcidStateAminoAcids.B_STATEstatic final AminoAcidStateAminoAcids.C_STATEstatic final AminoAcidState[]AminoAcids.CANONICAL_STATESDeprecated.static final AminoAcidStateAminoAcids.D_STATEstatic final AminoAcidStateAminoAcids.E_STATEstatic final AminoAcidStateAminoAcids.F_STATEstatic final AminoAcidStateAminoAcids.G_STATEstatic final AminoAcidStateAminoAcids.GAP_STATEstatic final AminoAcidStateAminoAcids.H_STATEstatic final AminoAcidStateAminoAcids.I_STATEstatic final AminoAcidStateAminoAcids.J_STATEstatic final AminoAcidStateAminoAcids.K_STATEstatic final AminoAcidStateAminoAcids.L_STATEstatic final AminoAcidStateAminoAcids.M_STATEstatic final AminoAcidStateAminoAcids.N_STATEstatic final AminoAcidStateAminoAcids.O_STATEstatic final AminoAcidStateAminoAcids.P_STATEstatic final AminoAcidStateAminoAcids.Q_STATEstatic final AminoAcidStateAminoAcids.R_STATEstatic final AminoAcidStateAminoAcids.S_STATEstatic final AminoAcidState[]AminoAcids.STATESDeprecated.static final AminoAcidStateAminoAcids.STOP_STATEstatic final AminoAcidStateAminoAcids.T_STATEstatic final AminoAcidStateAminoAcids.U_STATEstatic final AminoAcidStateAminoAcids.UNKNOWN_STATEstatic final AminoAcidStateAminoAcids.V_STATEstatic final AminoAcidStateAminoAcids.W_STATEstatic final AminoAcidStateAminoAcids.X_STATEstatic final AminoAcidStateAminoAcids.Y_STATEstatic final AminoAcidStateAminoAcids.Z_STATEMethods in jebl.evolution.sequences that return AminoAcidStateModifier and TypeMethodDescriptionstatic AminoAcidStateAminoAcids.getGapState()static AminoAcidStateAminoAcids.getState(char code) static AminoAcidStateAminoAcids.getState(int index) static AminoAcidStateGeneticCode.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 AminoAcidStateAminoAcids.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 ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding to it under the given genetic code.static AminoAcidState[]Utils.translate(State[] states, GeneticCode geneticCode, int readingFrame) Translates each of a given sequence ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding 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 StringAminoAcids.getTripletCode(AminoAcidState state) static booleanAminoAcids.isGap(AminoAcidState state) static booleanAminoAcids.isUnknown(AminoAcidState state)