info.bioinfweb.libralign.model.implementations

Class AbstractAlignmentModel<T>

java.lang.Object

info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel<T>

Type Parameters:

T - the type of sequence elements (tokens) the implementing provider object works with

All Implemented Interfaces:

AlignmentModel<T>

Direct Known Subclasses:

AbstractAlignmentModelDecorator, AbstractUndecoratedAlignmentModel, SwingUndoAlignmentModel

public abstract class AbstractAlignmentModel<T>
extends java.lang.Object
implements AlignmentModel<T>

This is the base class for all alignment models and alignment model decorators. It implements the common change listener functionality.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AbstractAlignmentModel()

Method Summary

Modifier and Type	Method and Description
protected void	fireAfterSequenceChange(SequenceChangeEvent<T> e) Informs all listeners that a sequence has been inserted, removed or replaced.
protected void	fireAfterSequenceRenamed(SequenceRenamedEvent<T> e) Informs all listeners that a sequence has been renamed.
protected void	fireAfterTokenChange(TokenChangeEvent<T> e) Informs all listeners that a sequence has been inserted, removed or replaced.
java.util.Set<AlignmentModelChangeListener>	getChangeListeners() Returns all change listeners currently attached to this object.
java.lang.String	getID() Some implementations may specify string identifying an alignment, which is then returned by this method.
java.lang.String	getLabel() Returns a string labeling this alignment.
void	setID(java.lang.String id) Allows to specify a new ID for this alignment.
void	setLabel(java.lang.String label) Allows to specify a new label for this alignment.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface info.bioinfweb.libralign.model.AlignmentModel

addSequence, addSequence, appendToken, appendTokens, containsSequence, getMaxSequenceLength, getSequenceCount, getSequenceLength, getTokenAt, getTokenSet, getWriteType, insertTokenAt, insertTokensAt, isSequencesReadOnly, isTokensReadOnly, removeSequence, removeTokenAt, removeTokensAt, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setTokenAt, setTokensAt, setTokenSet

Constructor Detail

AbstractAlignmentModel

public AbstractAlignmentModel()

Method Detail

getID

public java.lang.String getID()

Description copied from interface: AlignmentModel

Some implementations may specify string identifying an alignment, which is then returned by this method. Such string IDs will usually be unique in some context and immutable.

Specified by:

getID in interface AlignmentModel<T>

Returns:

the ID of this alignment or null if none is assigned

setID

public void setID(java.lang.String id)

Description copied from interface: AlignmentModel

Allows to specify a new ID for this alignment.

Specified by:

setID in interface AlignmentModel<T>

Parameters:

id - the new ID

getLabel

public java.lang.String getLabel()

Description copied from interface: AlignmentModel

Returns a string labeling this alignment.

Specified by:

getLabel in interface AlignmentModel<T>

Returns:

the name or title of this alignment

setLabel

public void setLabel(java.lang.String label)

Allows to specify a new label for this alignment. This implementation allows to edit the label and will never throw an UnsupportedOperationException in this method.

Specified by:

setLabel in interface AlignmentModel<T>

Parameters:

label - the new label

getChangeListeners

public java.util.Set<AlignmentModelChangeListener> getChangeListeners()

Description copied from interface: AlignmentModel

Returns all change listeners currently attached to this object. This collection is writable and should also be used to add or remove listeners.

This method returns the same object in every call. Therefore changes made to different references always affect all references.

Specified by:

getChangeListeners in interface AlignmentModel<T>

Returns:

a collection object containing the listeners

fireAfterSequenceChange

protected void fireAfterSequenceChange(SequenceChangeEvent<T> e)

Informs all listeners that a sequence has been inserted, removed or replaced.

fireAfterSequenceRenamed

protected void fireAfterSequenceRenamed(SequenceRenamedEvent<T> e)

Informs all listeners that a sequence has been renamed.

fireAfterTokenChange

protected void fireAfterTokenChange(TokenChangeEvent<T> e)

Informs all listeners that a sequence has been inserted, removed or replaced.