org.biojava.bio.symbol

Class FundamentalAtomicSymbol

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbol

org.biojava.bio.symbol.FundamentalAtomicSymbol

All Implemented Interfaces:

Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable

Direct Known Subclasses:

SimpleDotState, SimpleModelInState

public class FundamentalAtomicSymbol
extends AbstractSymbol
implements AtomicSymbol, Serializable

An atomic symbol consisting only of itself. This is the fundamental type of symbol, and needs a special implementation. If you wish to construct new Symbols, you should normally do so via utility methods on AlphabetManager. This may be useful as a base-class for other Symbol implementations.

Since:

1.1

Author:

Thomas Down

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.AbstractSymbol

annotationForwarder

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
FundamentalAtomicSymbol(String name, Annotation annotation)

Method Summary

Methods

Modifier and Type	Method and Description
Annotation	getAnnotation() Should return the associated annotation object.
Alphabet	getMatches() The alphabet containing the symbols matched by this ambiguity symbol.
String	getName() The long name for the symbol.
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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

FundamentalAtomicSymbol

public FundamentalAtomicSymbol(String name,
                       Annotation annotation)

Method Detail

getName

public String getName()

Description copied from interface: Symbol

The long name for the symbol.

Specified by:

getName in interface Symbol

Returns:

the long name

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

getSymbols

public 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

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