Representation of the Symbols that make up a sequence, and locations within them.

This package is not intended to have strong biological ties. It is here to make programming things like dynamic-programming much easier. It also handles serialization of well-known alphabets so that applicable singleton properties of alphabets and Symbols are maintained.

All coordinates are in 'bio-coordinates' - that is - legal indexes start from 1 and a range is inclusive (4 to 7 includes 4, 5, 6 and 7).

A Symbol is a single token. The Symbol maintains a name, a token (char), and an Annotation bundle. A set of Symbols is represented by an Alphabet instance. If the Alphabet can guarantee that there are only ever a finite number of Symbols contained with in it, then it must implement FiniteAlphabet. The Symbol objects within a FiniteAlphabet can be tested for equality by comparing their references directly. A SymbolList is a string over the Symbols from a single Alphabet instance. This allows you to represent a sequence of tokens, such as DNA nucleotides, or stock-market prices.

CrossProductAlphabet and CrossProductSymbol allow alphabets and symbols to be represented that are the combination of two or more alphabets and symbols under cross-product. For example, the CrossProduct alphabet DNA x DNA would contain all di-nucleotides. DNA x DNA x DNA x Protein would contain all combinations of three nucleotides and a single amino-acid. Dice x Coin would contain every possible combination of dice roles (1..6) and of coin flips (Heads, Tails) as the Symbol objects (1, Heads), (1, Tails), (2, Heads) ... (6, Tails). If any one of the Alphabets that make up the source of a CrossProductAlphabet is not finite, then the resulting CrossProductAlphabet will not be finite either.

Locations within a SymbolList can be represented by a Location object. This interface defines a sub-set of points that are within the Location. This uses bio-coordinates, and defines all the operations that you are likely to need to build your own Locations (union, intersection and the like).