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:
- java.io.Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable
- Direct Known Subclasses:
- SimpleDotState, SimpleModelInState
public class FundamentalAtomicSymbol
- extends AbstractSymbol
- implements AtomicSymbol, java.io.Serializable
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:
- Serialized Form
Method Summary |
Annotation |
getAnnotation()
Should return the associated annotation object. |
Alphabet |
getMatches()
The alphabet containing the symbols matched by this ambiguity symbol. |
java.lang.String |
getName()
The long name for the symbol. |
java.util.List |
getSymbols()
The list of symbols that this symbol is composed from. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
FundamentalAtomicSymbol
public FundamentalAtomicSymbol(java.lang.String name,
Annotation annotation)
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
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
getSymbols
public 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
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