Package pal.datatype

Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)

See:
Description

Interface Summary

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 Summary

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

Package pal.datatype Description

Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)