Package | Description |
---|---|
jebl.evolution.sequences |
Modifier and Type | Field and Description |
---|---|
static AminoAcidState |
AminoAcids.A_STATE |
static AminoAcidState |
AminoAcids.B_STATE |
static AminoAcidState |
AminoAcids.C_STATE |
static AminoAcidState[] |
AminoAcids.CANONICAL_STATES
Deprecated.
|
static AminoAcidState |
AminoAcids.D_STATE |
static AminoAcidState |
AminoAcids.E_STATE |
static AminoAcidState |
AminoAcids.F_STATE |
static AminoAcidState |
AminoAcids.G_STATE |
static AminoAcidState |
AminoAcids.GAP_STATE |
static AminoAcidState |
AminoAcids.H_STATE |
static AminoAcidState |
AminoAcids.I_STATE |
static AminoAcidState |
AminoAcids.J_STATE |
static AminoAcidState |
AminoAcids.K_STATE |
static AminoAcidState |
AminoAcids.L_STATE |
static AminoAcidState |
AminoAcids.M_STATE |
static AminoAcidState |
AminoAcids.N_STATE |
static AminoAcidState |
AminoAcids.O_STATE |
static AminoAcidState |
AminoAcids.P_STATE |
static AminoAcidState |
AminoAcids.Q_STATE |
static AminoAcidState |
AminoAcids.R_STATE |
static AminoAcidState |
AminoAcids.S_STATE |
static AminoAcidState[] |
AminoAcids.STATES
Deprecated.
|
static AminoAcidState |
AminoAcids.STOP_STATE |
static AminoAcidState |
AminoAcids.T_STATE |
static AminoAcidState |
AminoAcids.U_STATE |
static AminoAcidState |
AminoAcids.UNKNOWN_STATE |
static AminoAcidState |
AminoAcids.V_STATE |
static AminoAcidState |
AminoAcids.W_STATE |
static AminoAcidState |
AminoAcids.X_STATE |
static AminoAcidState |
AminoAcids.Y_STATE |
static AminoAcidState |
AminoAcids.Z_STATE |
Modifier and Type | Method and Description |
---|---|
static AminoAcidState |
AminoAcids.getGapState() |
static AminoAcidState |
AminoAcids.getState(char code) |
static AminoAcidState |
AminoAcids.getState(int index) |
static AminoAcidState |
AminoAcids.getState(java.lang.String code) |
AminoAcidState |
GeneticCode.getTranslation(CodonState codonState)
Returns the state associated with AminoAcid represented by codonState.
|
AminoAcidState |
GeneticCode.getTranslation(NucleotideState nucleotide1,
NucleotideState nucleotide2,
NucleotideState nucleotide3)
Returns the state associated with AminoAcid represented by the three nucleotides.
|
AminoAcidState |
GeneticCode.getTranslation(java.lang.String nucleotides)
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(java.lang.String sequenceString) |
static AminoAcidState[] |
Utils.translate(State[] states,
GeneticCode geneticCode)
Translates each of a given sequence of
NucleotideState s or CodonState s
to the AminoAcidState corresponding to it under the given genetic code. |
Modifier and Type | Method and Description |
---|---|
static java.util.List<AminoAcidState> |
AminoAcids.getStates() |
Modifier and Type | Method and Description |
---|---|
java.util.Set<CodonState> |
GeneticCode.getCodonsForAminoAcid(AminoAcidState aminoAcidState) |
static java.lang.String |
AminoAcids.getTripletCode(AminoAcidState state) |
static boolean |
AminoAcids.isGap(AminoAcidState state) |
static boolean |
AminoAcids.isUnknown(AminoAcidState state) |
http://code.google.com/p/jebl2/