Uses of Class
jebl.evolution.sequences.NucleotideState
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Packages that use NucleotideState Package Description jebl.evolution.sequences -
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Uses of NucleotideState in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as NucleotideState Modifier and Type Field Description static NucleotideState
Nucleotides. A_STATE
static NucleotideState
Nucleotides. B_STATE
static NucleotideState
Nucleotides. C_STATE
static NucleotideState[]
Nucleotides. CANONICAL_STATES
Deprecated.static NucleotideState[]
Nucleotides. COMPLEMENTARY_STATES
Deprecated.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
Deprecated.static NucleotideState
Nucleotides. T_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 Modifier and Type Method Description static NucleotideState[]
Utils. complement(NucleotideState[] sequence)
static NucleotideState
Nucleotides. getComplementaryState(NucleotideState state)
static NucleotideState
Nucleotides. getGapState()
static NucleotideState
Nucleotides. getState(char code)
static NucleotideState
Nucleotides. getState(int index)
static NucleotideState
Nucleotides. getState(java.lang.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(java.lang.String sequenceString)
Methods in jebl.evolution.sequences that return types with arguments of type NucleotideState Modifier and Type Method Description static java.util.List<NucleotideState>
Nucleotides. getCanonicalStates()
Methods in jebl.evolution.sequences with parameters of type NucleotideState Modifier and Type Method Description static NucleotideState[]
Utils. complement(NucleotideState[] sequence)
static NucleotideState
Nucleotides. getComplementaryState(NucleotideState state)
static CodonState
Codons. getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
AminoAcidState
GeneticCode. getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
Returns the state associated with AminoAcid represented by the three nucleotides.static boolean
Nucleotides. isGap(NucleotideState state)
static boolean
Nucleotides. isUnknown(NucleotideState state)
static NucleotideState[]
Utils. reverseComplement(NucleotideState[] sequence)
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