Package 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
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsFields inherited from class org.biojava.bio.symbol.AbstractSymbol
annotationForwarder
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Constructor Summary
Constructors -
Method Summary
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.Annotatable
getAnnotation
Methods inherited from interface org.biojava.bio.symbol.BasisSymbol
getSymbols
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.symbol.Symbol
getMatches, getName
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Field Details
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symbols
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matches
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Constructor Details
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SimpleAtomicSymbol
- Throws:
IllegalSymbolException
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Method Details
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createMatches
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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
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createSymbols
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getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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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
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getName
Description copied from interface:Symbol
The long name for the symbol.
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