Package 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
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:
-
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 -
Method Summary
Modifier and TypeMethodDescriptionShould return the associated annotation object.The alphabet containing the symbols matched by this ambiguity symbol.getName()
The long name for the symbol.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 Details
-
FundamentalAtomicSymbol
-
-
Method Details
-
getName
Description copied from interface:Symbol
The long name for the symbol. -
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 interfaceSymbol
- Returns:
- the Alphabet of symbols matched by this symbol
-
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 interfaceBasisSymbol
- Returns:
- the List of Symbols that this Symbol is built from
-
getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
-