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:
- java.io.Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable
public class SimpleAtomicSymbol
- extends AbstractSymbol
- implements AtomicSymbol, java.io.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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
symbols
protected java.util.List symbols
matches
protected Alphabet matches
SimpleAtomicSymbol
protected SimpleAtomicSymbol(Annotation annotation,
java.util.List syms)
throws IllegalSymbolException
- Throws:
IllegalSymbolException
createMatches
protected Alphabet createMatches()
getSymbols
public final 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
createSymbols
protected java.util.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 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