Package org.biojava.bio.symbol

Interface FiniteAlphabet

All Superinterfaces:
Alphabet, Annotatable, Changeable
All Known Implementing Classes:
AbstractAlphabet, IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet, SoftMaskedAlphabet
public interface FiniteAlphabet extends Alphabet
An alphabet over a finite set of Symbols.

This interface makes the distinction between an alphabet over a finite (and possibly small) number of symbols and an Alphabet over an infinite (or extremely large) set of symbols. Within a FiniteAlphabet, the == operator should be sufficient to decide upon equality for all AtomicSymbol instances.

The alphabet functions as the repository of objects in the fly-weight design pattern. Only symbols within an alphabet should appear in object that claim to use the alphabet - otherwise something is in error.

Author:
Matthew Pocock

  • Method Details

    • size

      int size()
      The number of symbols in the alphabet.
      Returns:
      the size of the alphabet

    • iterator

      Iterator<Symbol> iterator()
      Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.

      Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.

      Returns:
      an Iterator over the contained AtomicSymbol objects

    • addSymbol

      void addSymbol(Symbol s) throws IllegalSymbolException, ChangeVetoException
      Adds a symbol to this alphabet.

      If the symbol matches more than one AtomicSymbol, then each symbol matching it will be added.

      Parameters:
      s - the Symbol to add
      Throws:
      IllegalSymbolException - if the symbol is null, or if for any reason it can't be added
      ChangeVetoException - if either the alphabet doesn't allow symbols to be added, or the change was vetoed

    • removeSymbol

      void removeSymbol(Symbol s) throws IllegalSymbolException, ChangeVetoException
      Remove a symbol from this alphabet.

      If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.

      Parameters:
      s - the Symbol to removeintGot
      Throws:
      IllegalSymbolException - if the symbol is null, or if for any reason it can't be removed
      ChangeVetoException - if either the alphabet doesn't allow symbols to be added, or the change was vetoed