Uses of Class
org.mathIT.genes.Codon

Packages that use Codon

Package	Description
org.mathIT.genes	Provides classes to simulate biological amino acid sequences and to use the genetic code

Uses of Codon in org.mathIT.genes

Methods in org.mathIT.genes that return Codon

Modifier and Type	Method and Description
static Codon	Codon.decode(AminoAcid aminoAcid) Returns the codon which is related to the specified amino acid by the genetic code.
static Codon	Codon.fromBitmaskCode(byte bitmaskCode) Returns the DNA codon which is represented by the specified bitmask code, an integer x satisfying 0 ≤ x < 64.
static Codon	Codon.fromString(CharSequence triplet) Returns the DNA codon which is represented by the specified three-letter string, a triplet, consisting of the DNA letters T, C, A, G.
static Codon	Codon.fromTriplet(char x, char y, char z) Returns the DNA codon which is represented by the specified three nucleobases, a triplet, consisting of the DNA letters T, C, A, G.
static Codon	Codon.valueOf(String name) Returns the enum constant of this type with the specified name.
static Codon[]	Codon.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.mathIT.genes that return types with arguments of type Codon

Modifier and Type	Method and Description
ArrayList<Codon>	ORF.getSequence() Returns the codon sequence of this gene.

Constructors in org.mathIT.genes with parameters of type Codon

Constructor and Description
ORF(Codon[] sequence) Constructor of this gene.

Constructor parameters in org.mathIT.genes with type arguments of type Codon

Constructor and Description
ORF(ArrayList<Codon> sequence) Constructor of this gene.
ORF(String info, ArrayList<Codon> sequence) Constructor of this gene.
ORF(TreeMap<Codon,Double> frequency) Constructor of this gene.