Package org.biojava.bio.symbol

Class DoubleAlphabet.DoubleSymbol

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol

All Implemented Interfaces:

Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable

Enclosing class:

DoubleAlphabet

public static class DoubleAlphabet.DoubleSymbol
extends Unchangeable
implements AtomicSymbol, Serializable

A single double value. Get these via DoubleAlphabet.getSymbol(double).

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method	Description
double	doubleValue()
Annotation	getAnnotation()	Should return the associated annotation object.
Set	getBases()
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.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

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

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

doubleValue

public double doubleValue()

Returns:

the double value associated with this double symbol

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 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

getBases

public Set getBases()