org.biojava.bio.symbol
Class IntegerAlphabet.IntegerSymbol

java.lang.Object
  extended byorg.biojava.utils.Unchangeable
      extended byorg.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
All Implemented Interfaces:
Annotatable, AtomicSymbol, BasisSymbol, Changeable, java.io.Serializable, Symbol
Enclosing class:
IntegerAlphabet

public static class IntegerAlphabet.IntegerSymbol
extends Unchangeable
implements AtomicSymbol, java.io.Serializable

A single int value.

Author:
Matthew Pocock
See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
 
Constructor Summary
protected IntegerAlphabet.IntegerSymbol(int val)
           
 
Method Summary
 boolean equals(java.lang.Object o)
           
 Annotation getAnnotation()
          Should return the associated annotation object.
 java.util.Set getBases()
           
 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.
 int hashCode()
           
 int intValue()
           
 
Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

IntegerAlphabet.IntegerSymbol

protected IntegerAlphabet.IntegerSymbol(int val)
Method Detail

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

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

intValue

public int intValue()

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 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

getBases

public java.util.Set getBases()

hashCode

public int hashCode()

equals

public boolean equals(java.lang.Object o)