Class Summary |
AminoAcids |
implements DataType for amino acids |
Codons |
implements DataType for all Codons (including terminators).
|
CodonTableFactory |
Generates CodonTables |
CodonTableUtils |
Nucleotide Translating Utilities |
DataTypeUtils |
helper class for sequence data types. |
GeneralizedCodons |
Used for mapping an exact codon to an exact state, and vice versa
Can also be used as a DataType (exactly as for Codons, but more versatile). |
IUPACNucleotides |
implements DataType for nucleotides with ambiguous characters |
IUPACPenaltyTable |
Implements a table of transition penalties for a DNA states
and IUPAC ambiguous states. |
Nucleotides |
implements DataType for nucleotides |
NumericDataType |
This datatype stores numeric values. |
SimpleDataType |
interface for sequence data types |
StateRemover |
A standard data type, but with characters removed |
TwoStates |
implements DataType for two-state data |
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)