Package pal.datatype


package pal.datatype
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
  • Class
    Description
    Additional interface information for data types which represent ambiguity in sub types.
    implements DataType for amino acids
    implements DataType for all Codons (including terminators).
    Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.
    Generates CodonTables
    Nucleotide Translating Utilities
    interface 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 users
    Simple access for data type functions.
    implements a ResidueDataType for GapBalanced notation.
    implements DataType for nucleotides with ambiguous characters
    Implements 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 stuff
    implements DataType for nucleotides
    This datatype stores numeric values.
    interface for sequence data types
    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.
    A standard data type, but with characters removed
    Implements a table of transition penalties for a particular datatype.
    implements DataType for two-state data