org.biojava.bio.symbol

Class SingletonAlphabet

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractAlphabet

org.biojava.bio.symbol.SingletonAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

public class SingletonAlphabet
extends AbstractAlphabet
implements FiniteAlphabet, Serializable

An alphabet that contains a single atomic symbol.

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

serialVersionUID

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 and Description
SingletonAlphabet(AtomicSymbol sym)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSymbolImpl(AtomicSymbol sym)
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.
String	getName() Get the name of the alphabet.
protected AtomicSymbol	getSymbolImpl(List symList)
SymbolTokenization	getTokenization(String name) Get a SymbolTokenization by name.
Iterator	iterator() Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
void	removeSymbol(Symbol sym) Remove a symbol from this 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, putTokenization, readResolve, toString, validate

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, 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.bio.symbol.FiniteAlphabet

addSymbol

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

contains, getAmbiguity, getGapSymbol, getSymbol, validate

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SingletonAlphabet

public SingletonAlphabet(AtomicSymbol sym)

Method Detail

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

containsImpl

protected boolean containsImpl(AtomicSymbol s)

Specified by:

containsImpl in class AbstractAlphabet

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.

getTokenization

public SymbolTokenization getTokenization(String name)
                                   throws NoSuchElementException

Description copied from interface: Alphabet

Get a SymbolTokenization by name.

The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.

Every alphabet should have a SymbolTokenzation under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolTokenization under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behavior of the returned SymbolTokenization is not defined here.

A SymbolTokenization under the name 'default' should be defined for all sequences, that determines the behavior when printing out a sequence. Standard behavior is to define the 'token' SymbolTokenization as default if it exists, else to define the 'name' SymbolTokenization as the default, but others are possible.

Specified by:

getTokenization in interface Alphabet

Overrides:

getTokenization in class AbstractAlphabet

Parameters:

name - the name of the parser

Returns:

a parser for that name

Throws:

NoSuchElementException - if the name is unknown

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

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

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

addSymbolImpl

public void addSymbolImpl(AtomicSymbol sym)
                   throws IllegalSymbolException

Specified by:

addSymbolImpl in class AbstractAlphabet

Throws:

IllegalSymbolException

removeSymbol

public void removeSymbol(Symbol sym)
                  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:

sym - the Symbol to removeintGot

Throws:

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

getSymbolImpl

protected AtomicSymbol getSymbolImpl(List symList)
                              throws IllegalSymbolException

Specified by:

getSymbolImpl in class AbstractAlphabet

Throws:

IllegalSymbolException