info.bioinfweb.libralign.dataarea

Class DataAreasModel

java.lang.Object

info.bioinfweb.libralign.dataarea.DataAreasModel

public class DataAreasModel
extends java.lang.Object

Manages the data areas attached to an AlignmentArea.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
DataAreasModel(AlignmentArea owner) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
boolean	addListener(DataAreasModelListener listener) Adds a lister to this object that will be informed about future insertions or deletions of data areas.
protected void	finishVisibilityUpdate(boolean eventsFromSingleList, java.util.Collection<? extends DataArea> affectedElements) Enables #fireVisibilityChanged(DataAreaList, Collection) again and makes a call of this method to inform the listeners about previous changes.
protected void	fireInsertedRemoved(ListChangeType type, java.util.Collection<? extends DataArea> affectedElement) Informs all listeners that a data area has been added or removed.
protected void	fireInsertedRemoved(ListChangeType type, DataArea affectedElements) Informs all listeners that a data area has been added or removed.
protected void	fireVisibilityChanged(boolean eventsFromSingleList, java.util.Collection<? extends DataArea> affectedElements) Informs all listeners that the visibility of a set of data areas has changed.
protected void	fireVisibilityChanged(boolean eventsFromSingleList, DataArea affectedElement) Informs all listeners that the visibility of a data area has changed.
DataAreaList	getBottomAreas() Returns a list of data areas to be displayed underneath the alignment.
double	getGlobalMaxLengthBeforeStart() Returns maximum space left of the alignment calculated over all alignment areas in the parent MultipleAlignmentsContainer of the alignment area using this model.
double	getLocalMaxLengthAfterEnd() Returns maximum space right of the alignment end that is needed by any currently visible data area in any list contained in this model.
double	getLocalMaxLengthBeforeStart() Returns maximum space left of the alignment start that is needed by any currently visible data area in any list contained in this model.
AlignmentArea	getOwner() Returns the alignment content area that uses this instance.
DataAreaList	getSequenceAreas(java.lang.String sequenceID) Returns a list of data areas to be displayed underneath the specified sequence.
DataAreaSequenceChangeListener	getSequenceDataChangeListener() Returns the change listener that forwards events from the associated AlignmentModel to all data areas contained in this model.
DataAreaList	getTopAreas() Returns a list of data areas to be displayed on the top of the alignment.
int	getVisibleAreaHeight() Calculates the sum of the heights of all visible data areas contained in this model (above, underneath and attached to any sequence).
int	getVisibleSequenceAreaHeight() Calculates the sum of the heights of all visible data areas contained in this model, that are attached to any sequence.
protected boolean	isVisibilityUpdateInProgress() Returns true if informing listeners about visibility changes of data areas currently disabled.
boolean	removeListener(DataAreasModelListener listener) Removes the specified listener from this objects list.
void	removeSequence(java.lang.String sequenceName) Removes the list of data areas attached to the specified sequence from this model.
void	setLocalMaxLengthBeforeAfterRecalculate() Flags the properties getLocalMaxLengthBeforeStart() and getLocalMaxLengthAfterEnd() to be recalculated when they are accessed the next time.
void	setSequenceDataAreasVisible(boolean visible) Fades all data areas associated with any sequence in or out.
protected void	startVisibilityUpdate() After calling this method #fireVisibilityChanged(DataAreaList, Collection) will have no effect until #finishVisibilityUpdate(DataAreaList, Collection) is called.

Methods inherited from class java.lang.Object

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

Constructor Detail

DataAreasModel

public DataAreasModel(AlignmentArea owner)

Creates a new instance of this class.

Parameters:

owner - the alignment content area that will be using this instance

Method Detail

getOwner

public AlignmentArea getOwner()

Returns the alignment content area that uses this instance.

getTopAreas

public DataAreaList getTopAreas()

Returns a list of data areas to be displayed on the top of the alignment.

Returns:

a modifiable list

getBottomAreas

public DataAreaList getBottomAreas()

Returns a list of data areas to be displayed underneath the alignment.

Returns:

a modifiable list

getSequenceAreas

public DataAreaList getSequenceAreas(java.lang.String sequenceID)

Returns a list of data areas to be displayed underneath the specified sequence.

Parameters:

sequenceName - the unique identifier of the sequence carrying the data areas in the returned list

Returns:

a modifiable list

removeSequence

public void removeSequence(java.lang.String sequenceName)

Removes the list of data areas attached to the specified sequence from this model.

Parameters:

sequenceName - the name of the sequence the data areas to be removed are attached to

setSequenceDataAreasVisible

public void setSequenceDataAreasVisible(boolean visible)

Fades all data areas associated with any sequence in or out.

Parameters:

visible - Specify true here, if you want the elements to be displayed, false otherwise.

See Also:

DataAreaList.setAllVisible(boolean)

getVisibleSequenceAreaHeight

public int getVisibleSequenceAreaHeight()

Calculates the sum of the heights of all visible data areas contained in this model, that are attached to any sequence.

Returns:

a double value greater of equal to zero

getVisibleAreaHeight

public int getVisibleAreaHeight()

Calculates the sum of the heights of all visible data areas contained in this model (above, underneath and attached to any sequence).

Returns:

a double value greater of equal to zero

getLocalMaxLengthBeforeStart

public double getLocalMaxLengthBeforeStart()

Returns maximum space left of the alignment start that is needed by any currently visible data area in any list contained in this model. Note the space that is actually present will be determined using getGlobalMaxLengthBeforeStart().

Returns:

an integer >= 0

setLocalMaxLengthBeforeAfterRecalculate

public void setLocalMaxLengthBeforeAfterRecalculate()

Flags the properties getLocalMaxLengthBeforeStart() and getLocalMaxLengthAfterEnd() to be recalculated when they are accessed the next time.

LibrAlign does not recalculate these values on every call for performance reasons. Usually application code will not have to call this method directly.

getGlobalMaxLengthBeforeStart

public double getGlobalMaxLengthBeforeStart()

Returns maximum space left of the alignment calculated over all alignment areas in the parent MultipleAlignmentsContainer of the alignment area using this model. If that alignment area is not contained in such a container the return value is equivalent to getLocalMaxLengthBeforeStart().

Returns:

an integer >= 0

getLocalMaxLengthAfterEnd

public double getLocalMaxLengthAfterEnd()

Returns maximum space right of the alignment end that is needed by any currently visible data area in any list contained in this model.

Returns:

an integer >= 0

addListener

public boolean addListener(DataAreasModelListener listener)

Adds a lister to this object that will be informed about future insertions or deletions of data areas.

Parameters:

listener - the listener object to be notified in the future

Returns:

true (as specified by Collection.add(Object))

removeListener

public boolean removeListener(DataAreasModelListener listener)

Removes the specified listener from this objects list.

Parameters:

listener - the listener to be removed

Returns:

true if this list contained the specified element

getSequenceDataChangeListener

public DataAreaSequenceChangeListener getSequenceDataChangeListener()

Returns the change listener that forwards events from the associated AlignmentModel to all data areas contained in this model.

fireInsertedRemoved

protected void fireInsertedRemoved(ListChangeType type,
                                   java.util.Collection<? extends DataArea> affectedElement)

Informs all listeners that a data area has been added or removed.

fireInsertedRemoved

protected void fireInsertedRemoved(ListChangeType type,
                                   DataArea affectedElements)

Informs all listeners that a data area has been added or removed.

startVisibilityUpdate

protected void startVisibilityUpdate()

After calling this method #fireVisibilityChanged(DataAreaList, Collection) will have no effect until #finishVisibilityUpdate(DataAreaList, Collection) is called.

This method can be called before changing the visibility of many data areas in one step. #finishVisibilityUpdate(DataAreaList, Collection) can than be used to inform the listeners about the changed with one single event.

isVisibilityUpdateInProgress

protected boolean isVisibilityUpdateInProgress()

Returns true if informing listeners about visibility changes of data areas currently disabled.

Returns:

true if #fireVisibilityChanged(DataAreaList, Collection) would currently have no effect, false otherwise

finishVisibilityUpdate

protected void finishVisibilityUpdate(boolean eventsFromSingleList,
                                      java.util.Collection<? extends DataArea> affectedElements)

Enables #fireVisibilityChanged(DataAreaList, Collection) again and makes a call of this method to inform the listeners about previous changes.

Parameters:

e - the event describing the changes since the previous call of startVisibilityUpdate() that will be send to all listeners

fireVisibilityChanged

protected void fireVisibilityChanged(boolean eventsFromSingleList,
                                     java.util.Collection<? extends DataArea> affectedElements)

Informs all listeners that the visibility of a set of data areas has changed.

This method will have no effect if isVisibilityUpdateInProgress() return true.

Parameters:

eventsFromSingleList - Specify true here if all elements in affectedElements are contained in the same DataAreaList.

affectedElements - a list of elements that have been changed

fireVisibilityChanged

protected void fireVisibilityChanged(boolean eventsFromSingleList,
                                     DataArea affectedElement)

Informs all listeners that the visibility of a data area has changed. (Convenience method that calls #fireVisibilityChanged(DataAreaList, Collection) internally.)

This method will have no effect if isVisibilityUpdateInProgress() return true.

Parameters:

eventsFromSingleList - Specify true here if all elements in affectedElements are contained in the same DataAreaList.

affectedElements - a list of elements that have been changed