Package | Description |
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jebl.evolution.sequences |
Modifier and Type | Method | 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(java.lang.String nucleotides) |
Returns the state associated with AminoAcid represented by the three nucleotides.
|
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.
|
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. |
static AminoAcidState[] |
Utils.translate(State[] states,
GeneticCode geneticCode,
int readingFrame) |
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 | Description |
---|---|---|
static java.util.List<AminoAcidState> |
AminoAcids.getStates() |
Modifier and Type | Method | 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/