| Package | Description | 
|---|---|
| org.biojava.bio | 
 The core classes that will be used throughout the bio packages. 
 | 
| org.biojava.bio.dist | 
 
Probability distributions over Alphabets. 
 | 
| org.biojava.bio.gui.sequence | 
 
Graphical displays of biological sequences and associated annotations. 
 | 
| org.biojava.bio.seq.db | 
 
Collections of biological sequence data. 
 | 
| org.biojava.bio.seq.projection | 
 Code for projecting Feature objects and systematically altering their
properties. 
 | 
| org.biojava.bio.symbol | 
 Representation of the Symbols that make up a sequence, and locations within
them. 
 | 
| org.biojava.utils | 
 
Miscellaneous utility classes used by other BioJava components. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
OverlayAnnotation.PropertyForwarder.generateEvent(ChangeEvent ce)  | 
protected ChangeEvent | 
Annotatable.AnnotationForwarder.generateEvent(ChangeEvent ce)
Deprecated.  
  | 
ChangeEvent | 
MergeAnnotation.PropertyForwarder.generateEvent(ChangeEvent ce)  | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
OverlayAnnotation.PropertyForwarder.generateEvent(ChangeEvent ce)  | 
protected ChangeEvent | 
Annotatable.AnnotationForwarder.generateEvent(ChangeEvent ce)
Deprecated.  
  | 
ChangeEvent | 
MergeAnnotation.PropertyForwarder.generateEvent(ChangeEvent ce)  | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
Distribution.NullModelForwarder.generateEvent(ChangeEvent ce)
Deprecated.  
  | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
Distribution.NullModelForwarder.generateEvent(ChangeEvent ce)
Deprecated.  
  | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
SequenceRenderer.RendererForwarder.generateEvent(ChangeEvent ce)  | 
ChangeEvent | 
PairwiseSequenceRenderer.PairwiseRendererForwarder.generateEvent(ChangeEvent ce)
generateEvent generates events in response to
 layout change and repaint requests. | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
SequenceRenderer.RendererForwarder.generateEvent(ChangeEvent ce)  | 
ChangeEvent | 
PairwiseSequenceRenderer.PairwiseRendererForwarder.generateEvent(ChangeEvent ce)
generateEvent generates events in response to
 layout change and repaint requests. | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
SequenceDBWrapper.SequencesForwarder.generateEvent(ChangeEvent ce)  | 
| Modifier and Type | Method and Description | 
|---|---|
ChangeEvent | 
SequenceDBWrapper.SequencesForwarder.generateEvent(ChangeEvent ce)  | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
ProjectedFeatureHolder.forwardChangeEvent(ChangeEvent cev)
Called internally to generate a forwarded version of a ChangeEvent from our
 underlying FeatureHolder 
 | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
ProjectedFeatureHolder.forwardChangeEvent(ChangeEvent cev)
Called internally to generate a forwarded version of a ChangeEvent from our
 underlying FeatureHolder 
 | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
AbstractSymbolList.EditScreener.generateEvent(ChangeEvent ce)  | 
protected ChangeEvent | 
AbstractSymbolList.EditTranslater.generateEvent(ChangeEvent ce)  | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
AbstractSymbolList.EditScreener.generateEvent(ChangeEvent ce)  | 
protected ChangeEvent | 
AbstractSymbolList.EditTranslater.generateEvent(ChangeEvent ce)  | 
void | 
SimpleSymbolList.postChange(ChangeEvent cev)  | 
void | 
SimpleSymbolList.preChange(ChangeEvent cev)
On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols 
 | 
| Modifier and Type | Method and Description | 
|---|---|
protected ChangeEvent | 
ChangeForwarder.generateEvent(ChangeEvent ce)
 Return the new event to represent the originating event ce. 
 | 
protected ChangeEvent | 
ChangeForwarder.Retyper.generateEvent(ChangeEvent ce)  | 
ChangeEvent | 
ChangeEvent.getChainedEvent()
Return the event which caused this to be fired, or  
null
 if this change was not caused by another event. | 
ChangeEvent | 
ChangeVetoException.getChangeEvent()
Return the ChangeEvent which is being vetoed. 
 | 
ChangeEvent | 
ChangeListener.ChangeEventRecorder.getEvent()  | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
IndexedChangeHub.firePostChange(Object key,
              ChangeEvent cev)  | 
void | 
ChangeHub.firePostChange(Object key,
              ChangeEvent cev)
invoke the firePostChangeEvent on all ChangeListeners associated with
 a specific key. 
 | 
void | 
ChangeSupport.firePostChangeEvent(ChangeEvent ce)
 Inform the listeners that a change has taken place using their
 firePostChangeEvent methods. 
 | 
void | 
IndexedChangeHub.firePreChange(Object key,
             ChangeEvent cev)  | 
void | 
ChangeHub.firePreChange(Object key,
             ChangeEvent cev)
invoke the firePreChangeEvent on all ChangeListeners associated with
 a specific key. 
 | 
void | 
ChangeSupport.firePreChangeEvent(ChangeEvent ce)
 Inform the listeners that a change is about to take place using their
 firePreChangeEvent methods. 
 | 
protected ChangeEvent | 
ChangeForwarder.generateEvent(ChangeEvent ce)
 Return the new event to represent the originating event ce. 
 | 
protected ChangeEvent | 
ChangeForwarder.Retyper.generateEvent(ChangeEvent ce)  | 
protected abstract boolean | 
IndexedChangeHub.isMyChangeEvent(ChangeEvent cev,
               IndexedChangeHub.ListenerMemento lm)  | 
void | 
ChangeListener.postChange(ChangeEvent cev)
 Called when a change has just taken place. 
 | 
void | 
ChangeListener.AlwaysVetoListener.postChange(ChangeEvent cev)  | 
void | 
ChangeListener.LoggingListener.postChange(ChangeEvent cev)  | 
void | 
ChangeAdapter.postChange(ChangeEvent ce)  | 
void | 
ChangeForwarder.postChange(ChangeEvent ce)  | 
void | 
ChangeListener.preChange(ChangeEvent cev)
 Called before a change takes place. 
 | 
void | 
ChangeListener.AlwaysVetoListener.preChange(ChangeEvent cev)  | 
void | 
ChangeListener.ChangeEventRecorder.preChange(ChangeEvent cev)  | 
void | 
ChangeListener.LoggingListener.preChange(ChangeEvent cev)  | 
void | 
ChangeAdapter.preChange(ChangeEvent ce)  | 
void | 
ChangeForwarder.preChange(ChangeEvent ce)  | 
| Constructor and Description | 
|---|
ChangeEvent(Object source,
           ChangeType type,
           Object change,
           Object previous,
           ChangeEvent chain)
Construct a ChangeEvent to be fired because another ChangeEvent has
 been received from a property object. 
 | 
ChangeVetoException(ChangeEvent change)
Construct an exception to veto a change without explanation. 
 | 
ChangeVetoException(ChangeEvent change,
                   String reason)
Construct an exception to veto a change for a specified reason. 
 | 
ChangeVetoException(Throwable ex,
                   ChangeEvent change)
Propogate an exception without (additional) explanation. 
 | 
ChangeVetoException(Throwable ex,
                   ChangeEvent change,
                   String reason)
Propogate an exception, giving a detail message 
 | 
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