SimpleAlphabet (BioJava-1.5-beta API)
Keywords: org.biojava.bio.symbol.SimpleAlphabet class

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## org.biojava.bio.symbol
Class SimpleAlphabet

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.symbol.AbstractAlphabet
              org.biojava.bio.symbol.SimpleAlphabet

All Implemented Interfaces:
  Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

    public class SimpleAlphabet

extends AbstractAlphabet
implements Serializable

A simple no-frills implementation of the FiniteAlphabet interface.

Author:
  Matthew Pocock
See Also:
  Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary
`protected ChangeForwarder` | `annotationForwarder`

Fields inherited from interface org.biojava.bio.symbol.Alphabet
`EMPTY_ALPHABET, PARSERS, SYMBOLS`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Constructor Summary
`SimpleAlphabet()`
`SimpleAlphabet(Set symbols)`
`SimpleAlphabet(Set symbols, String name)`
`SimpleAlphabet(String name)`

Method Summary
`protected void` | `addSymbolImpl(AtomicSymbol s)`
`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.
`protected ChangeSupport` | `getChangeSupport(ChangeType ct)` Called to retrieve the ChangeSupport for this object.
`String` | `getName()` Get the name of the alphabet.
`protected AtomicSymbol` | `getSymbolImpl(List symL)`
`Iterator` | `iterator()` Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
`void` | `removeSymbol(Symbol s)` Remove a symbol from this alphabet.
`void` | `setName(String name)` Assign a name to the 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, getTokenization, putTokenization, readResolve, toString, validate`

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`

Field Detail

### annotationForwarder

    protected transient ChangeForwarder annotationForwarder

Constructor Detail

### SimpleAlphabet

    public SimpleAlphabet()

### SimpleAlphabet

    public SimpleAlphabet(Set symbols)

### SimpleAlphabet

    public SimpleAlphabet(String name)

### SimpleAlphabet

    public SimpleAlphabet(Set symbols,
                          String name)

Method Detail

### 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

### 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.

### setName

    public void setName(String name)

  Assign a name to the alphabet

  Parameters:
    `name` - the name you wish to give this 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

### 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

### containsImpl

    protected boolean containsImpl(AtomicSymbol s)

  Specified by:
    `containsImpl` in class `AbstractAlphabet`

### addSymbolImpl

    protected void addSymbolImpl(AtomicSymbol s)
                          throws IllegalSymbolException,
                                 ChangeVetoException

  Specified by:
    `addSymbolImpl` in class `AbstractAlphabet`
  Throws:
    `IllegalSymbolException`
    `ChangeVetoException`

### removeSymbol

    public void removeSymbol(Symbol s)
                      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:
    `s` - the Symbol to removeintGot
  Throws:
    `IllegalSymbolException` - if the symbol is null, or if for any reason it can't be removed

### 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

### getSymbolImpl

    protected AtomicSymbol getSymbolImpl(List symL)
                                  throws IllegalSymbolException

  Specified by:
    `getSymbolImpl` in class `AbstractAlphabet`
  Throws:
    `IllegalSymbolException`

### getChangeSupport

    protected ChangeSupport getChangeSupport(ChangeType ct)

  Description copied from class: `AbstractChangeable`
  Called to retrieve the ChangeSupport for this object.

  Your implementation of this method should have the following structure: ``

       ChangeSupport cs = super.getChangeSupport(ct);

       if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
         someForwarder = new ChangeForwarder(...

         this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
       }

       return cs;

  It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

  Overrides:
    `getChangeSupport` in class `AbstractChangeable`

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