Package pal.datatype
package pal.datatype
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
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ClassDescriptionAdditional interface information for data types which represent ambiguity in sub types.implements DataType for amino acidsimplements DataType for all Codons (including terminators).Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.Generates CodonTablesNucleotide Translating Utilitiesinterface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.Some useful methods for implmenting classes and for DataType usersSimple access for data type functions.implements a ResidueDataType for GapBalanced notation.implements DataType for nucleotides with ambiguous charactersImplements a table of transition penalties for a DNA states and IUPAC ambiguous states.An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).Utilities relating to MolecularDataType stuffimplements DataType for nucleotidesThis datatype stores numeric values.interface for sequence data typesimplements 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.A standard data type, but with characters removedImplements a table of transition penalties for a particular datatype.implements DataType for two-state data