All Superinterfaces:

Alphabet, Annotatable, Changeable

All Known Implementing Classes:

AbstractAlphabet, IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet, SoftMaskedAlphabet

public interface FiniteAlphabet
extends Alphabet 

Author:

Matthew Pocock

• Nested Class Summary

  • Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

    Annotatable.AnnotationForwarder

• Field Summary

  • Fields inherited from interface org.biojava.bio.symbol.Alphabet

    EMPTY_ALPHABET, PARSERS, SYMBOLS

  • Fields inherited from interface org.biojava.bio.Annotatable

    ANNOTATION

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  void	addSymbol (Symbol s) Adds a symbol to this alphabet.
  Iterator<Symbol>	iterator () Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
  void	removeSymbol (Symbol s) Remove a symbol from this alphabet.
  int	size () The number of symbols in the alphabet.

  • Methods inherited from interface org.biojava.bio.symbol.Alphabet

    contains, getAlphabets, getAmbiguity, getGapSymbol, getName, getSymbol, getTokenization, validate

  • Methods inherited from interface org.biojava.bio.Annotatable

    getAnnotation

  • Methods inherited from interface org.biojava.utils.Changeable

    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

• Method Detail

  • 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