Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## 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:
  Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable

    public class SimpleAtomicSymbol

extends AbstractSymbol
implements AtomicSymbol, 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
`protected Alphabet` | `matches`
`protected List` | `symbols`

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

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

Constructor Summary
`protected` | `SimpleAtomicSymbol(Annotation annotation, List syms)`

Method Summary
`protected Alphabet` | `createMatches()`
`protected List` | `createSymbols()`
`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.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 List symbols

### matches

    protected Alphabet matches

Constructor Detail

### SimpleAtomicSymbol

    protected SimpleAtomicSymbol(Annotation annotation,
                                 List syms)
                          throws IllegalSymbolException

Throws:
  `IllegalSymbolException`

Method Detail

### createMatches

    protected Alphabet createMatches()

### getSymbols

    public final 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 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 String getName()

  Description copied from interface: `Symbol`
  The long name for the symbol.

  Specified by:
    `getName` in interface `Symbol`
  Returns:
    the long name

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD