Package pal.datatype
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
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Interface Summary 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 Summary Class Description AminoAcids implements DataType for amino acidsCodons implements DataType for all Codons (including terminators).CodonTableFactory Generates CodonTablesCodonTableUtils Nucleotide Translating UtilitiesDataType.Utils Some useful methods for implmenting classes and for DataType usersDataTypeTool Simple access for data type functions.GapBalanced implements a ResidueDataType for GapBalanced notation.IUPACNucleotides implements DataType for nucleotides with ambiguous charactersIUPACPenaltyTable Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.MolecularDataType.Utils Utilities relating to MolecularDataType stuffNucleotides implements DataType for nucleotidesNumericDataType This datatype stores numeric values.SimpleDataType interface for sequence data typesSpecificAminoAcids 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 removedTwoStates implements DataType for two-state data