org.biojava.bio.symbol

Class SimpleAtomicSymbol

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbol

org.biojava.bio.symbol.SimpleAtomicSymbol

All Implemented Interfaces:

java.io.Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable

public class SimpleAtomicSymbol
extends AbstractSymbol
implements AtomicSymbol, java.io.Serializable

A basic implementation of AtomicSymbol. If you wish to construct new Symbols, you should normally do so via utility methods on AlphabetManager. This may be a useful base class for custom implementations.

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 and Description
protected Alphabet	matches
protected java.util.List	symbols

Fields inherited from class org.biojava.bio.symbol.AbstractSymbol

annotationForwarder

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleAtomicSymbol(Annotation annotation, java.util.List syms)

Method Summary

Methods

Modifier and Type	Method and Description
protected Alphabet	createMatches()
protected java.util.List	createSymbols()
Annotation	getAnnotation() Should return the associated annotation object.
Alphabet	getMatches() The alphabet containing the symbols matched by this ambiguity symbol.
java.lang.String	getName() The long name for the symbol.
java.util.List	getSymbols() The list of symbols that this symbol is composed from.

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

getChangeSupport, toString

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.bio.symbol.BasisSymbol

getSymbols

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

getMatches, getName

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

symbols

protected java.util.List symbols

matches

protected Alphabet matches

Constructor Detail

SimpleAtomicSymbol

protected SimpleAtomicSymbol(Annotation annotation,
                  java.util.List syms)
                      throws IllegalSymbolException

Throws:

IllegalSymbolException

Method Detail

createMatches

protected Alphabet createMatches()

getSymbols

public final java.util.List getSymbols()

Description copied from interface: BasisSymbol

The list of symbols that this symbol is composed from.

In the usual case, this list will contain just this single symbol. In the case where a symbol represents an ordered combination of other symbols, the list will contain each of these BasisSymbols.

Specified by:

getSymbols in interface BasisSymbol

Returns:

the List of Symbols that this Symbol is built from

createSymbols

protected java.util.List createSymbols()

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

getMatches

public Alphabet getMatches()

Description copied from interface: Symbol

The alphabet containing the symbols matched by this ambiguity symbol.

This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

Specified by:

getMatches in interface Symbol

Returns:

the Alphabet of symbols matched by this symbol

getName

public java.lang.String getName()

Description copied from interface: Symbol

The long name for the symbol.

Specified by:

getName in interface Symbol

Returns:

the long name