Package | Description |
---|---|
jebl.evolution.sequences |
Modifier and Type | Field | Description |
---|---|---|
static GeneticCode |
GeneticCode.ALT_YEAST |
|
static GeneticCode |
GeneticCode.ASCIDIAN_MT |
|
static GeneticCode |
GeneticCode.BACTERIAL |
|
static GeneticCode |
GeneticCode.BLEPHARISMA_NUC |
|
static GeneticCode |
GeneticCode.CILIATE |
|
static GeneticCode |
GeneticCode.ECHINODERM_MT |
|
static GeneticCode |
GeneticCode.EUPLOTID_NUC |
|
static GeneticCode |
GeneticCode.FLATWORM_MT |
|
static GeneticCode[] |
GeneticCode.GENETIC_CODES |
Deprecated.
use
getGeneticCodes() instead |
static GeneticCode |
GeneticCode.INVERTEBRATE_MT |
|
static GeneticCode |
GeneticCode.MOLD_PROTOZOAN_MT |
|
static GeneticCode |
GeneticCode.MYCOPLASMA |
|
static GeneticCode |
GeneticCode.UNIVERSAL |
|
static GeneticCode |
GeneticCode.VERTEBRATE_MT |
|
static GeneticCode |
GeneticCode.YEAST |
Modifier and Type | Method | Description |
---|---|---|
static GeneticCode[] |
GeneticCode.getGeneticCodesArray() |
|
static GeneticCode |
GeneticCode.valueOf(int NCBITranslationTableNumber) |
|
static GeneticCode |
GeneticCode.valueOf(java.lang.String name) |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.Iterable<GeneticCode> |
GeneticCode.getGeneticCodes() |
Returns an iterable that allows you to iterate over all the standard genetic codes
|
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
Utils.translate(java.lang.String nucleotideSequence,
GeneticCode geneticCode) |
A wrapper for
Utils.translateCharSequence(CharSequence,GeneticCode)
that takes a nucleotide sequence as a String only rather than a
CharSequence. |
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode) |
|
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode,
int readingFrame) |
|
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. |
static java.lang.String |
Utils.translateCharSequence(java.lang.CharSequence nucleotideSequence,
GeneticCode geneticCode) |
Translates the given nucleotideSequence into an amino acid sequence
string, using the given geneticCode.
|
Constructor | Description |
---|---|
TranslatedSequence(Sequence source,
GeneticCode geneticCode) |
Create a TranslatedSequence from a source codon or nucleotide sequence
|
TranslatedSequence(Sequence source,
GeneticCode geneticCode,
int frame) |
Create a TranslatedSequence from a source codon or nucleotide sequence
|
http://code.google.com/p/jebl2/