| Package | Description |
|---|---|
| jebl.evolution.sequences |
| Modifier and Type | Field | Description |
|---|---|---|
static CodonState[] |
Codons.CANONICAL_STATES |
|
static CodonState |
Codons.GAP_STATE |
|
static CodonState[] |
Codons.STATES |
|
static CodonState |
Codons.UNKNOWN_STATE |
| Modifier and Type | Method | Description |
|---|---|---|
static CodonState |
Codons.getGapState() |
|
static CodonState |
Codons.getState(int index) |
|
static CodonState |
Codons.getState(java.lang.String code) |
Gets the state object for the given code.
|
static CodonState |
Codons.getState(NucleotideState nucleotide1,
NucleotideState nucleotide2,
NucleotideState nucleotide3) |
|
static CodonState |
Codons.getUnknownState() |
|
static CodonState[] |
Codons.toStateArray(byte[] indexArray) |
|
static CodonState[] |
Codons.toStateArray(java.lang.String sequenceString) |
| Modifier and Type | Method | Description |
|---|---|---|
java.util.Set<CodonState> |
GeneticCode.getCodonsForAminoAcid(AminoAcidState aminoAcidState) |
|
java.util.Set<CodonState> |
GeneticCode.getStartCodons() |
|
java.util.Set<CodonState> |
GeneticCode.getStopCodons() |
| Modifier and Type | Method | Description |
|---|---|---|
AminoAcidState |
GeneticCode.getTranslation(CodonState codonState) |
Returns the state associated with AminoAcid represented by codonState.
|
static boolean |
Codons.isGap(CodonState state) |
|
boolean |
GeneticCode.isStartCodon(CodonState codonState) |
Deprecated.
|
boolean |
GeneticCode.isStopCodon(CodonState codonState) |
Deprecated.
|
static boolean |
Codons.isUnknown(CodonState state) |
|
static NucleotideState[] |
Codons.toNucleotides(CodonState state) |
http://code.google.com/p/jebl2/