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See:
Description
Interface Summary | |
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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 | |
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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 |
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
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