Uses of Class
jebl.evolution.sequences.NucleotideState

Packages that use NucleotideState

jebl.evolution.sequences

Uses of NucleotideState in jebl.evolution.sequences

Fields in jebl.evolution.sequences declared as NucleotideState

static NucleotideState	Nucleotides.A_STATE
static NucleotideState	Nucleotides.B_STATE
static NucleotideState	Nucleotides.C_STATE
static NucleotideState[]	Nucleotides.CANONICAL_STATES
static NucleotideState[]	Nucleotides.COMPLEMENTARY_STATES
static NucleotideState	Nucleotides.D_STATE
static NucleotideState	Nucleotides.G_STATE
static NucleotideState	Nucleotides.GAP_STATE
static NucleotideState	Nucleotides.H_STATE
static NucleotideState	Nucleotides.K_STATE
static NucleotideState	Nucleotides.M_STATE
static NucleotideState	Nucleotides.N_STATE
static NucleotideState	Nucleotides.R_STATE
static NucleotideState	Nucleotides.S_STATE
static NucleotideState[]	Nucleotides.STATES
static NucleotideState	Nucleotides.T_STATE
static NucleotideState	Nucleotides.U_STATE
static NucleotideState	Nucleotides.UNKNOWN_STATE
static NucleotideState	Nucleotides.V_STATE
static NucleotideState	Nucleotides.W_STATE
static NucleotideState	Nucleotides.Y_STATE

Methods in jebl.evolution.sequences that return NucleotideState

static NucleotideState[]	Utils.complement(NucleotideState[] sequence)
static NucleotideState	Nucleotides.getGapState()
static NucleotideState	Nucleotides.getState(char code)
static NucleotideState	Nucleotides.getState(int index)
static NucleotideState	Nucleotides.getState(String code)
static NucleotideState	Nucleotides.getUnknownState()
static NucleotideState[]	Utils.reverseComplement(NucleotideState[] sequence)
static NucleotideState[]	Codons.toNucleotides(CodonState state)
static NucleotideState[]	Nucleotides.toStateArray(byte[] indexArray)
static NucleotideState[]	Nucleotides.toStateArray(String sequenceString)

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

static List<NucleotideState>

Nucleotides.getCanonicalStates()

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

static NucleotideState[]	Utils.complement(NucleotideState[] sequence)
static CodonState	Codons.getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
static boolean	Nucleotides.isGap(NucleotideState state)
static boolean	Nucleotides.isUnknown(NucleotideState state)
static NucleotideState[]	Utils.reverseComplement(NucleotideState[] sequence)