Package | Description |
---|---|
jebl.evolution.sequences |
Modifier and Type | Field and 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 |
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
static java.util.List<NucleotideState> |
Nucleotides.getCanonicalStates() |
Modifier and Type | Method and 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) |
http://code.google.com/p/jebl2/