Package org.biojava.bio.symbol

Class SimpleAlphabet

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractAlphabet

org.biojava.bio.symbol.SimpleAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

public class SimpleAlphabet
extends AbstractAlphabet
implements Serializable

A simple no-frills implementation of the FiniteAlphabet interface.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field	Description
protected ChangeForwarder	annotationForwarder

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

EMPTY_ALPHABET, PARSERS, SYMBOLS

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor	Description
SimpleAlphabet()
SimpleAlphabet(String name)
SimpleAlphabet(Set symbols)
SimpleAlphabet(Set symbols, String name)

Method Summary

Modifier and Type	Method	Description
protected void	addSymbolImpl(AtomicSymbol s)
protected boolean	containsImpl(AtomicSymbol s)
List	getAlphabets()	Return an ordered List of the alphabets which make up a compound alphabet.
Annotation	getAnnotation()	Should return the associated annotation object.
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
String	getName()	Get the name of the alphabet.
protected AtomicSymbol	getSymbolImpl(List symL)
Iterator	iterator()	Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
void	removeSymbol(Symbol s)	Remove a symbol from this alphabet.
void	setName(String name)	Assign a name to the alphabet
int	size()	The number of symbols in the alphabet.

Methods inherited from class org.biojava.bio.symbol.AbstractAlphabet

addSymbol, contains, getAmbiguity, getAmbiguityImpl, getGapSymbol, getSymbol, getTokenization, putTokenization, readResolve, toString, validate

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

Constructor Detail

SimpleAlphabet

public SimpleAlphabet()

SimpleAlphabet

public SimpleAlphabet(Set symbols)

SimpleAlphabet

public SimpleAlphabet(String name)

SimpleAlphabet

public SimpleAlphabet(Set symbols,
                      String name)

Method Detail

iterator

public Iterator iterator()

Description copied from interface: FiniteAlphabet

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.

Specified by:

iterator in interface FiniteAlphabet

Returns:

an Iterator over the contained AtomicSymbol objects

getName

public String getName()

Description copied from interface: Alphabet

Get the name of the alphabet.

Specified by:

getName in interface Alphabet

Returns:

the name as a string.

setName

public void setName(String name)

Assign a name to the alphabet

Parameters:

name - the name you wish to give this alphabet

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

size

public int size()

Description copied from interface: FiniteAlphabet

The number of symbols in the alphabet.

Specified by:

size in interface FiniteAlphabet

Returns:

the size of the alphabet

containsImpl

protected boolean containsImpl(AtomicSymbol s)

Specified by:

containsImpl in class AbstractAlphabet

addSymbolImpl

protected void addSymbolImpl(AtomicSymbol s)
                      throws IllegalSymbolException,
                             ChangeVetoException

Specified by:

addSymbolImpl in class AbstractAlphabet

Throws:

IllegalSymbolException

ChangeVetoException

removeSymbol

public void removeSymbol(Symbol s)
                  throws IllegalSymbolException

Description copied from interface: FiniteAlphabet

Remove a symbol from this alphabet.

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

Specified by:

removeSymbol in interface FiniteAlphabet

Parameters:

s - the Symbol to removeintGot

Throws:

IllegalSymbolException - if the symbol is null, or if for any reason it can't be removed

getAlphabets

public List getAlphabets()

Description copied from interface: Alphabet

Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.

Specified by:

getAlphabets in interface Alphabet

Returns:

a List of alphabets

getSymbolImpl

protected AtomicSymbol getSymbolImpl(List symL)
                              throws IllegalSymbolException

Specified by:

getSymbolImpl in class AbstractAlphabet

Throws:

IllegalSymbolException

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable