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

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

Modifier and Type	Method	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