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.)