Class SimpleAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,FiniteAlphabet
,Changeable
- 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 interface org.biojava.bio.symbol.Alphabet
EMPTY_ALPHABET, PARSERS, SYMBOLS
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Constructor Summary
ConstructorsConstructorDescriptionSimpleAlphabet
(String name) SimpleAlphabet
(Set symbols) SimpleAlphabet
(Set symbols, String name) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
protected boolean
Return an ordered List of the alphabets which make up a compound alphabet.Should return the associated annotation object.protected ChangeSupport
Called to retrieve the ChangeSupport for this object.getName()
Get the name of the alphabet.protected AtomicSymbol
getSymbolImpl
(List symL) iterator()
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.void
Remove a symbol from this alphabet.void
Assign a name to the alphabetint
size()
The number of symbols in the alphabet.Methods inherited from class org.biojava.bio.symbol.AbstractAlphabet
addSymbol, contains, getAmbiguity, getAmbiguityImpl, getGapSymbol, getSymbol, getTokenization, putTokenization, readResolve, toString, validate
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.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Field Details
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annotationForwarder
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Constructor Details
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SimpleAlphabet
public SimpleAlphabet() -
SimpleAlphabet
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SimpleAlphabet
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SimpleAlphabet
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Method Details
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iterator
Description copied from interface:FiniteAlphabet
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.
- Specified by:
iterator
in interfaceFiniteAlphabet
- Returns:
- an Iterator over the contained AtomicSymbol objects
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getName
Description copied from interface:Alphabet
Get the name of the alphabet. -
setName
Assign a name to the alphabet- Parameters:
name
- the name you wish to give this alphabet
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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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size
Description copied from interface:FiniteAlphabet
The number of symbols in the alphabet.- Specified by:
size
in interfaceFiniteAlphabet
- Returns:
- the size of the alphabet
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containsImpl
- Specified by:
containsImpl
in classAbstractAlphabet
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addSymbolImpl
- Specified by:
addSymbolImpl
in classAbstractAlphabet
- Throws:
IllegalSymbolException
ChangeVetoException
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removeSymbol
Description copied from interface:FiniteAlphabet
Remove a symbol from this alphabet.If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.
- Specified by:
removeSymbol
in interfaceFiniteAlphabet
- Parameters:
s
- the Symbol to removeintGot- Throws:
IllegalSymbolException
- if the symbol is null, or if for any reason it can't be removed
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getAlphabets
Description copied from interface:Alphabet
Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.- Specified by:
getAlphabets
in interfaceAlphabet
- Returns:
- a List of alphabets
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getSymbolImpl
- Specified by:
getSymbolImpl
in classAbstractAlphabet
- Throws:
IllegalSymbolException
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getChangeSupport
Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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