Package | Description |
---|---|
jebl.evolution.sequences |
Modifier and Type | Field and Description |
---|---|
static CodonState[] |
Codons.CANONICAL_STATES |
static CodonState |
Codons.GAP_STATE |
static CodonState[] |
Codons.STATES |
static CodonState |
Codons.UNKNOWN_STATE |
Modifier and Type | Method and Description |
---|---|
static CodonState |
Codons.getGapState() |
static CodonState |
Codons.getState(int index) |
static CodonState |
Codons.getState(NucleotideState nucleotide1,
NucleotideState nucleotide2,
NucleotideState nucleotide3) |
static CodonState |
Codons.getState(java.lang.String code)
Gets the state object for the given code.
|
static CodonState |
Codons.getUnknownState() |
static CodonState[] |
Codons.toStateArray(byte[] indexArray) |
static CodonState[] |
Codons.toStateArray(java.lang.String sequenceString) |
Modifier and Type | Method and 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 and 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/