Package | Description |
---|---|
jebl.evolution.sequences |
Modifier and Type | Field and 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 and Description |
---|---|
static GeneticCode[] |
GeneticCode.getGeneticCodesArray() |
static GeneticCode |
GeneticCode.valueOf(int NCBITranslationTableNumber) |
static GeneticCode |
GeneticCode.valueOf(java.lang.String name) |
Modifier and Type | Method and 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 and Description |
---|---|
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.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 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 and Description |
---|
TranslatedSequence(Sequence source,
GeneticCode geneticCode) |
http://code.google.com/p/jebl2/