Package org.biojava.bio.symbol

Class IntegerAlphabet.IntegerSymbol

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol

All Implemented Interfaces:

Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable

Enclosing class:

IntegerAlphabet

public static class IntegerAlphabet.IntegerSymbol
extends Unchangeable
implements AtomicSymbol, Serializable

A single int value.

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

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	IntegerSymbol(int val)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
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.
int	hashCode()
int	intValue()

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, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

IntegerSymbol

protected IntegerSymbol(int val)

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

intValue

public int intValue()

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()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object