| Package | Description |
|---|---|
| info.bioinfweb.libralign.alignmentarea |
Contains basic implementations for displaying an alignment area.
|
| info.bioinfweb.libralign.dataarea |
Contains
DataArea from which all data areas used in LibrAlign
must be inherited as well as related classes and a set of general data area implementations provided with
LibrAlign which are located in the subpackage implementations. |
| info.bioinfweb.libralign.dataarea.implementations |
Contains classes that implement a concrete data area.
|
| info.bioinfweb.libralign.dataarea.implementations.charset |
Contains data area related classes to display character sets of an alignment.
|
| info.bioinfweb.libralign.dataarea.implementations.pherogram |
Contains
PherogramArea and other classes used in its
implementation. |
| info.bioinfweb.libralign.dataarea.implementations.sequenceindex | |
| info.bioinfweb.libralign.model |
Contains the
AlignmentModel interface which
is the bridge between LibrAlign and any source of alignment data that is displayed with it as well as
related classes and a set of implementations of this interface provided with LibrAlign. |
| info.bioinfweb.libralign.model.events |
Contains the event objects used by implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.implementations |
Contains common implementations of
AlignmentModel
which are part of LibrAlign. |
| info.bioinfweb.libralign.model.implementations.decorate | |
| info.bioinfweb.libralign.multiplealignments |
Contains classes used in the implementation of
MultipleAlignmentsContainer
which allow to combine several AlignmentAreas. |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
AlignmentArea.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
DataAreaSequenceChangeListener.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
void |
ConsensusSequenceArea.afterTokenChange(TokenChangeEvent e) |
<T> void |
LabelDataArea.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
CharSetArea.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
PherogramArea.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
SequenceIndexArea.afterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
AlignmentModelChangeAdapter.afterTokenChange(TokenChangeEvent<T> e) |
<T> void |
AlignmentModelChangeListener.afterTokenChange(TokenChangeEvent<T> e)
Called after a single token or a set of tokens has been inserted, removed or replaced.
|
| Modifier and Type | Method and Description |
|---|---|
TokenChangeEvent<T> |
TokenChangeEvent.clone() |
TokenChangeEvent<T> |
TokenChangeEvent.cloneWithNewSource(AlignmentModel<T> source) |
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newInsertInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int startIndex,
java.util.Collection<? extends T> newTokens)
Creates a new instance of this class that represents an insertion of a list of tokens.
|
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newInsertInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int index,
T newToken)
Creates a new instance of this class that represents an insertion of a single token.
|
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newRemoveInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int startIndex,
java.util.Collection<? extends T> removedTokens)
Creates a new instance of this class that represents a deletion of a list of tokens.
|
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newRemoveInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int index,
T removedToken)
Creates a new instance of this class that represents a deletion of a single token.
|
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newReplaceInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int startIndex,
java.util.Collection<? extends T> replacedTokens)
Creates a new instance of this class that represents a replacement of a list of tokens.
|
static <T> TokenChangeEvent<T> |
TokenChangeEvent.newReplaceInstance(AlignmentModel<T> source,
java.lang.String sequenceID,
int index,
T replacedToken)
Creates a new instance of this class that represents a replacement of a single token.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
AbstractAlignmentModel.fireAfterTokenChange(TokenChangeEvent<T> e)
Informs all listeners that a sequence has been inserted, removed or replaced.
|
protected void |
AbstractUndecoratedAlignmentModel.fireAfterTokenChange(TokenChangeEvent<T> e) |
| Modifier and Type | Method and Description |
|---|---|
protected abstract java.lang.Iterable<TokenChangeEvent<T>> |
AbstractAlignmentModelDecorator.convertTokenChangeEvent(TokenChangeEvent<U> event)
Converts a token change event from the underlying (decorated) model to a collection of according change
events to be used with this decorator.
|
protected java.lang.Iterable<TokenChangeEvent<T>> |
AbstractTokenReplacementAlignmentModelDecorator.convertTokenChangeEvent(TokenChangeEvent<U> event) |
| Modifier and Type | Method and Description |
|---|---|
protected abstract java.lang.Iterable<TokenChangeEvent<T>> |
AbstractAlignmentModelDecorator.convertTokenChangeEvent(TokenChangeEvent<U> event)
Converts a token change event from the underlying (decorated) model to a collection of according change
events to be used with this decorator.
|
protected java.lang.Iterable<TokenChangeEvent<T>> |
AbstractTokenReplacementAlignmentModelDecorator.convertTokenChangeEvent(TokenChangeEvent<U> event) |
| Modifier and Type | Method and Description |
|---|---|
<T> void |
MultipleAlignmentsModelEventForwarder.afterTokenChange(TokenChangeEvent<T> e) |