Package pal.datatype

Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)

See:
          Description

Interface Summary
CodonTable Describes a device for translating Nucleotide triplets or codon indices into amino acid codes
DataType interface for sequence data types
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
DataTypeUtils helper class for sequence data types.
GeneralizedCodons Used for mapping an exact codon to an exact state, and vice versa Can also be used as a DataType (exactly as for Codons, but more versatile).
IUPACNucleotides implements DataType for nucleotides with ambiguous characters
IUPACPenaltyTable Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.
Nucleotides implements DataType for nucleotides
NumericDataType This datatype stores numeric values.
SimpleDataType interface for sequence data types
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.)