org.biojava.bio.symbol
Class FundamentalAtomicSymbol

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.symbol.AbstractSymbol
          extended by 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
FundamentalAtomicSymbol(String name, Annotation annotation)
           
 
Method Summary
 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


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