org.biojava.bio.symbol
Interface Symbol

All Known Subinterfaces:
AtomicSymbol, CrossProductSymbol, DotState, EmissionState, ModelInState, State
All Known Implementing Classes:
SimpleSymbol

public interface Symbol
extends Annotatable

A single symbol.

This is the atomic unit of a SymbolList, or a sequence. It allows for fine-train fly-weighting, so that there can be one instance of each symbol that is referenced multiple times.

Author:
Matthew Pocock

Method Summary
 Alphabet getMatches()
          The alphabet containing the symbols matched by this ambiguity symbol.
 java.lang.String getName()
          The long name for the symbol.
 char getToken()
          The token for the symbol.
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 

Method Detail

getToken

public char getToken()
The token for the symbol.
Returns:
the token

getName

public java.lang.String getName()
The long name for the symbol.
Returns:
the long name

getMatches

public Alphabet getMatches()
The alphabet containing the symbols matched by this ambiguity symbol.

This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

Returns:
the Alphabet of symbols matched by this symbol