Interface | Description |
---|---|
AmbiguousDataType |
Additional interface information for data types which represent ambiguity in
sub types.
|
CodonTable |
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|
MolecularDataType |
An extension to the generic DataType class for DataTypes
related to genetic residues (by this it is meant Nucleotides,
AminoAcids, and Codons).
|
TransitionPenaltyTable |
Implements a table of transition penalties for a particular datatype.
|
Class | Description |
---|---|
AminoAcids |
implements DataType for amino acids
|
Codons |
implements DataType for all Codons (including terminators).
|
CodonTableFactory |
Generates CodonTables
|
CodonTableUtils |
Nucleotide Translating Utilities
|
DataType.Utils |
Some useful methods for implmenting classes and for DataType users
|
DataTypeTool |
Simple access for data type functions.
|
GapBalanced |
implements a ResidueDataType for GapBalanced notation.
|
IUPACNucleotides |
implements DataType for nucleotides with ambiguous characters
|
IUPACPenaltyTable |
Implements a table of transition penalties for a DNA states
and IUPAC ambiguous states.
|
MolecularDataType.Utils |
Utilities relating to MolecularDataType stuff
|
Nucleotides |
implements DataType for nucleotides
|
NumericDataType |
This datatype stores numeric values.
|
SimpleDataType |
interface for sequence data types
|
SpecificAminoAcids |
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by
supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.
|
StateRemover |
A standard data type, but with characters removed
|
TwoStates |
implements DataType for two-state data
|