Uses of Class
jebl.evolution.sequences.GeneticCode
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Packages that use GeneticCode Package Description jebl.evolution.sequences -
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Uses of GeneticCode in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as GeneticCode Modifier and Type Field Description static GeneticCodeGeneticCode. ALT_YEASTstatic GeneticCodeGeneticCode. ASCIDIAN_MTstatic GeneticCodeGeneticCode. BACTERIALstatic GeneticCodeGeneticCode. BLEPHARISMA_NUCstatic GeneticCodeGeneticCode. CILIATEstatic GeneticCodeGeneticCode. ECHINODERM_MTstatic GeneticCodeGeneticCode. EUPLOTID_NUCstatic GeneticCodeGeneticCode. FLATWORM_MTstatic GeneticCode[]GeneticCode. GENETIC_CODESDeprecated.usegetGeneticCodes()insteadstatic GeneticCodeGeneticCode. INVERTEBRATE_MTstatic GeneticCodeGeneticCode. MOLD_PROTOZOAN_MTstatic GeneticCodeGeneticCode. MYCOPLASMAstatic GeneticCodeGeneticCode. UNIVERSALstatic GeneticCodeGeneticCode. VERTEBRATE_MTstatic GeneticCodeGeneticCode. YEASTMethods in jebl.evolution.sequences that return GeneticCode Modifier and Type Method Description static GeneticCode[]GeneticCode. getGeneticCodesArray()static GeneticCodeGeneticCode. valueOf(int NCBITranslationTableNumber)static GeneticCodeGeneticCode. valueOf(java.lang.String name)Methods in jebl.evolution.sequences that return types with arguments of type GeneticCode 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 codesMethods in jebl.evolution.sequences with parameters of type GeneticCode Modifier and Type Method Description static java.lang.StringUtils. translate(java.lang.String nucleotideSequence, GeneticCode geneticCode)A wrapper forUtils.translateCharSequence(CharSequence,GeneticCode)that takes a nucleotide sequence as a String only rather than a CharSequence.static SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode)static SequenceUtils. translate(Sequence sequence, GeneticCode geneticCode, int readingFrame)static AminoAcidState[]Utils. translate(State[] states, GeneticCode geneticCode)Translates each of a given sequence ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding to it under the given genetic code.static AminoAcidState[]Utils. translate(State[] states, GeneticCode geneticCode, int readingFrame)Translates each of a given sequence ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding to it under the given genetic code.static java.lang.StringUtils. translateCharSequence(java.lang.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 GeneticCode Constructor Description TranslatedSequence(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
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