Uses of Class
jebl.evolution.sequences.GeneticCode
Packages that use GeneticCode
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Uses of GeneticCode in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as GeneticCodeModifier and TypeFieldDescriptionstatic final GeneticCode
GeneticCode.ALT_YEAST
static final GeneticCode
GeneticCode.ASCIDIAN_MT
static final GeneticCode
GeneticCode.BACTERIAL
static final GeneticCode
GeneticCode.BLEPHARISMA_NUC
static final GeneticCode
GeneticCode.CILIATE
static final GeneticCode
GeneticCode.ECHINODERM_MT
static final GeneticCode
GeneticCode.EUPLOTID_NUC
static final GeneticCode
GeneticCode.FLATWORM_MT
static final GeneticCode[]
GeneticCode.GENETIC_CODES
Deprecated.static final GeneticCode
GeneticCode.INVERTEBRATE_MT
static final GeneticCode
GeneticCode.MOLD_PROTOZOAN_MT
static final GeneticCode
GeneticCode.MYCOPLASMA
static final GeneticCode
GeneticCode.UNIVERSAL
static final GeneticCode
GeneticCode.VERTEBRATE_MT
static final GeneticCode
GeneticCode.YEAST
Methods in jebl.evolution.sequences that return GeneticCodeModifier and TypeMethodDescriptionstatic GeneticCode[]
GeneticCode.getGeneticCodesArray()
static GeneticCode
GeneticCode.valueOf
(int NCBITranslationTableNumber) static GeneticCode
Methods in jebl.evolution.sequences that return types with arguments of type GeneticCodeModifier and TypeMethodDescriptionstatic Iterable
<GeneticCode> GeneticCode.getGeneticCodes()
Returns an iterable that allows you to iterate over all the standard genetic codesMethods in jebl.evolution.sequences with parameters of type GeneticCodeModifier and TypeMethodDescriptionstatic String
Utils.translate
(String nucleotideSequence, GeneticCode geneticCode) A wrapper forUtils.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 ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.static AminoAcidState[]
Utils.translate
(State[] states, GeneticCode geneticCode, int readingFrame) Translates each of a given sequence ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.static String
Utils.translateCharSequence
(CharSequence nucleotideSequence, GeneticCode geneticCode) Translates the given nucleotideSequence into an amino acid sequence string, using the given geneticCode.Constructors in jebl.evolution.sequences with parameters of type GeneticCodeModifierConstructorDescriptionTranslatedSequence
(Sequence source, GeneticCode geneticCode) Create a TranslatedSequence from a source codon or nucleotide sequenceTranslatedSequence
(Sequence source, GeneticCode geneticCode, int frame) Create a TranslatedSequence from a source codon or nucleotide sequence
getGeneticCodes()
instead