info.bioinfweb.libralign.dataarea.implementations.charset

Class CharSetArea

java.lang.Object

info.bioinfweb.tic.TICComponent

info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

info.bioinfweb.libralign.dataarea.DataArea

info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea

All Implemented Interfaces:

AlignmentModelChangeListener

public class CharSetArea
extends DataArea

A data area displaying different character sets associated with the current alignment, as they are e.g. defined in Nexus files.

Since:

0.2.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static double	BORDER_FRACTION

Fields inherited from class info.bioinfweb.tic.TICComponent

DISPATCHER_MAP, repaintRequested

Constructor Summary

Constructors

Constructor and Description
CharSetArea(AlignmentContentArea owner, AlignmentArea labeledAlignmentArea) Creates a new instance of this class with an empty data model.
CharSetArea(AlignmentContentArea owner, AlignmentArea labeledAlignmentArea, CharSetDataModel model) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
<T,U> void	afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current) Called if this listener was moved to another instance of AlignmentModel.
<T> void	afterSequenceChange(SequenceChangeEvent<T> e) Called after a sequence has been inserted, removed or replaced.
<T> void	afterSequenceRenamed(SequenceRenamedEvent<T> e) Called after a sequence was renamed.
<T> void	afterTokenChange(TokenChangeEvent<T> e) Called after a single token or a set of tokens has been inserted, removed or replaced.
protected AlignmentLabelSubArea	createLabelSubArea(AlignmentLabelArea owner) This method can be overwritten to provide a specific implementation for labeling the implementing data area.
protected void	fireSelectionChanged()
double	getHeight() Returns the height in pixels considering the current zoom factor this component needs.
CharSetDataModel	getModel() Returns the underlying model providing character set data.
int	getSelectedIndex()
java.util.Set<SelectionListener<info.bioinfweb.commons.events.GenericEventObject<CharSetArea>>>	getSelectionListeners()
void	paintPart(AlignmentPaintEvent event) Implementations of this method perform the painting of a part of the component.
CharSetDataModel	setModel(CharSetDataModel model, boolean moveListeners) Changes the model instance that is displayed by this area.
void	setSelectedIndex(int selectedIndex)
java.util.Set<DataAreaListType>	validLocations() This data area is allowed to attached at the top and bottom of an alignment area as well as to each sequence.

Methods inherited from class info.bioinfweb.libralign.dataarea.DataArea

getLabeledAlignmentArea, getLabeledAlignmentModel, getLengthAfterEnd, getLengthBeforeStart, getList, isVisible, setList, setVisible

Methods inherited from class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

getLabelSubArea, getOwner, getSize, paint, repaint

Methods inherited from class info.bioinfweb.tic.TICComponent

addKeyListener, addMouseListener, addMouseWheelListener, assignSize, dispatchEvent, getCurrentToolkit, getKeyListenersSet, getMouseListenersSet, getMouseWheelListenersSet, getSwingComponentClassName, getSwingComponentConstructorParameters, getSWTComponentClassName, getSWTComponentConstructorParameters, getToolkitComponent, hasDefinedSize, hasToolkitComponent, isUpdateOngoing, removeKeyListener, removeMouseListener, removeWheelMouseListener, setToolkitComponent, setUpdateOngoing

Methods inherited from class java.lang.Object

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

Field Detail

BORDER_FRACTION

public static final double BORDER_FRACTION

See Also:

Constant Field Values

Constructor Detail

CharSetArea

public CharSetArea(AlignmentContentArea owner,
                   AlignmentArea labeledAlignmentArea,
                   CharSetDataModel model)

Creates a new instance of this class.

Parameters:

owner - the alignment area that will be containing the returned data area instance

labeledAlignmentArea - the alignment area that shall determine the token widths considered when painting the character sets (Should only be different from owner.getOwner() if the new instance will be placed in a different alignment area than the sequence data in a scenario with a MultipleAlignmentsContainer.)

model - the model providing the character set data

Throws:

java.lang.IllegalArgumentException - if model is null

CharSetArea

public CharSetArea(AlignmentContentArea owner,
                   AlignmentArea labeledAlignmentArea)

Creates a new instance of this class with an empty data model.

Parameters:

owner - the alignment area that will be containing the returned data area instance

labeledAlignmentArea - the alignment area that shall determine the token widths considered when painting the character sets (Should only be different from owner.getOwner() if the new instance will be placed in a different alignment area than the sequence data in a scenario with a MultipleAlignmentsContainer.)

Method Detail

getModel

public CharSetDataModel getModel()

Returns the underlying model providing character set data.

Returns:

the instance of the underlying model

setModel

public CharSetDataModel setModel(CharSetDataModel model,
                                 boolean moveListeners)

Changes the model instance that is displayed by this area.

Parameters:

model - the new model

moveListeners - Specify true here if all listers registered to the current model should be moved to the new model or false otherwise

Returns:

the previous model

Throws:

java.lang.IllegalArgumentException - if model is null

getSelectedIndex

public int getSelectedIndex()

setSelectedIndex

public void setSelectedIndex(int selectedIndex)

getHeight

public double getHeight()

Description copied from class: AlignmentSubArea

Returns the height in pixels considering the current zoom factor this component needs.

Specified by:

getHeight in class AlignmentSubArea

Returns:

a double value > 0

paintPart

public void paintPart(AlignmentPaintEvent event)

Description copied from class: AlignmentSubArea

Implementations of this method perform the painting of a part of the component. It is used when an AlignmentArea is set to contain no subcomponents but to paint its contents directly.

This default implementation always throws an UnsupportedOperationException. Note that therefore inherited classes must either overwrite this method or #createComponent() in order to return an instance there that does not delegate to this method.

Note that the aim of this method is to allow painting very wide components, which may have a width larger than Integer.MAX_VALUE. Therefore painting coordinates are stored as double values (using Graphics2D and Rectangle2D.Double). Implementations should not calculate pixel coordinates as ints at any time to avoid overflows, but only use double (or possibly long if necessary).

Overrides:

paintPart in class AlignmentSubArea

Parameters:

event - the paint event providing information on the area to be painted, the graphics context and tool methods.

validLocations

public java.util.Set<DataAreaListType> validLocations()

This data area is allowed to attached at the top and bottom of an alignment area as well as to each sequence. (You would usually attach this area to an alignment area as a whole, but anyway it is still allowed to attach it to a single sequence.)

Specified by:

validLocations in class DataArea

Returns:

a non-empty set of locations

See Also:

DataArea.validLocations()

afterSequenceChange

public <T> void afterSequenceChange(SequenceChangeEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a sequence has been inserted, removed or replaced.

Parameters:

e - the event object containing information on the change

afterSequenceRenamed

public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a sequence was renamed.

Parameters:

e - the event object containing information on the change

afterTokenChange

public <T> void afterTokenChange(TokenChangeEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a single token or a set of tokens has been inserted, removed or replaced.

Parameters:

e - the event object containing information on the change

afterModelChanged

public <T,U> void afterModelChanged(AlignmentModel<T> previous,
                                    AlignmentModel<U> current)

Description copied from interface: AlignmentModelChangeListener

Called if this listener was moved to another instance of AlignmentModel.

This happens if the alignment model of an AlignmentArea was changed.

Parameters:

previous - the alignment model this listener was attached to before the event happened

current - the new alignment model this listener is attached to now

createLabelSubArea

protected AlignmentLabelSubArea createLabelSubArea(AlignmentLabelArea owner)

Description copied from class: AlignmentSubArea

This method can be overwritten to provide a specific implementation for labeling the implementing data area.

This default implementation always returns an instance of DefaultLabelSubArea.

Overrides:

createLabelSubArea in class AlignmentSubArea

Parameters:

owner - the alignment label area that can be set as the owner of the returned component.

Returns:

a new instance of DefaultLabelSubArea linked to this instance

fireSelectionChanged

protected void fireSelectionChanged()

getSelectionListeners

public java.util.Set<SelectionListener<info.bioinfweb.commons.events.GenericEventObject<CharSetArea>>> getSelectionListeners()