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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractAlphabet
org.biojava.bio.symbol.SimpleAlphabet
public class SimpleAlphabet
A simple no-frills implementation of the FiniteAlphabet interface.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary | |
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protected ChangeForwarder |
annotationForwarder
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Fields inherited from interface org.biojava.bio.symbol.Alphabet |
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EMPTY_ALPHABET, PARSERS, SYMBOLS |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Constructor Summary | |
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SimpleAlphabet()
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SimpleAlphabet(Set symbols)
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SimpleAlphabet(Set symbols,
String name)
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SimpleAlphabet(String name)
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Method Summary | |
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protected void |
addSymbolImpl(AtomicSymbol s)
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protected boolean |
containsImpl(AtomicSymbol s)
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List |
getAlphabets()
Return an ordered List of the alphabets which make up a compound alphabet. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
protected ChangeSupport |
getChangeSupport(ChangeType ct)
Called to retrieve the ChangeSupport for this object. |
String |
getName()
Get the name of the alphabet. |
protected AtomicSymbol |
getSymbolImpl(List symL)
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Iterator |
iterator()
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet. |
void |
removeSymbol(Symbol s)
Remove a symbol from this alphabet. |
void |
setName(String name)
Assign a name to the alphabet |
int |
size()
The number of symbols in the alphabet. |
Methods inherited from class org.biojava.bio.symbol.AbstractAlphabet |
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addSymbol, contains, getAmbiguity, getAmbiguityImpl, getGapSymbol, getSymbol, getTokenization, putTokenization, readResolve, toString, validate |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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protected transient ChangeForwarder annotationForwarder
Constructor Detail |
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public SimpleAlphabet()
public SimpleAlphabet(Set symbols)
public SimpleAlphabet(String name)
public SimpleAlphabet(Set symbols, String name)
Method Detail |
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public Iterator iterator()
FiniteAlphabet
Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.
iterator
in interface FiniteAlphabet
public String getName()
Alphabet
getName
in interface Alphabet
public void setName(String name)
name
- the name you wish to give this alphabetpublic Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public int size()
FiniteAlphabet
size
in interface FiniteAlphabet
protected boolean containsImpl(AtomicSymbol s)
containsImpl
in class AbstractAlphabet
protected void addSymbolImpl(AtomicSymbol s) throws IllegalSymbolException, ChangeVetoException
addSymbolImpl
in class AbstractAlphabet
IllegalSymbolException
ChangeVetoException
public void removeSymbol(Symbol s) throws IllegalSymbolException
FiniteAlphabet
If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.
removeSymbol
in interface FiniteAlphabet
s
- the Symbol to removeintGot
IllegalSymbolException
- if the symbol is null, or if for any reason
it can't be removedpublic List getAlphabets()
Alphabet
getAlphabets
in interface Alphabet
protected AtomicSymbol getSymbolImpl(List symL) throws IllegalSymbolException
getSymbolImpl
in class AbstractAlphabet
IllegalSymbolException
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
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 & unregister the
forwarder in the code that does the ChangeEvent handling in setter methods.
ChangeSupport cs = super.getChangeSupport(ct);
if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
someForwarder = new ChangeForwarder(...
this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
}
return cs;
getChangeSupport
in class AbstractChangeable
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