Package org.biojava.bio.gui.sequence

Class AbstractBeadRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.AbstractBeadRenderer

All Implemented Interfaces:

Serializable, BeadFeatureRenderer, FeatureRenderer, Changeable

Direct Known Subclasses:

EllipticalBeadRenderer, RectangularBeadRenderer, RoundRectangularBeadRenderer

public abstract class AbstractBeadRenderer
extends AbstractChangeable
implements BeadFeatureRenderer, Serializable

AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features. Each subclass of AbstractBeadRenderer should override the abstract method renderBead() and provide the drawing routine for its particular bead type.

A concrete BeadFeatureRenderer may render a series of features in more than one style by delegating to other BeadFeatureRenderers for the additional style(s). This is achieved using the setDelegateRenderer() method which associates an OptimizableFilter with another BeadFeatureRenderer. Any feature accepted by the filter is rendered with that renderer, while the remainder are rendered by the current renderer.

Since:

1.2

Author:

Keith James, Paul Seed

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected double	beadDepth
protected double	beadDisplacement
protected Paint	beadFill
protected Paint	beadOutline
protected Stroke	beadStroke
protected Map	delegates
protected Map	delegationCache
static ChangeType	DEPTH	Constant DEPTH indicating a change to the depth of the renderer.
static ChangeType	DISPLACEMENT	Constant DISPLACEMENT indicating a change to the Y-axis displacement of the features.
static ChangeType	FILL	Constant FILL indicating a change to the fill of the features.
static ChangeType	OUTLINE	Constant OUTLINE indicating a change to the outline paint of the features.
static ChangeType	STROKE	Constant STROKE indicating a change to the outline stroke of the features.

Constructor Summary

Constructors

Constructor	Description
AbstractBeadRenderer()	Creates a new AbstractBeadRenderer with no delegates.
AbstractBeadRenderer(double beadDepth, double beadDisplacement, Paint beadOutline, Paint beadFill, Stroke beadStroke)	Creates a new AbstractBeadRenderer object.

Method Summary

Modifier and Type	Method	Description
double	getBeadDepth()	getBeadDepth returns the depth of a single bead produced by this renderer.
double	getBeadDisplacement()	getBeadDisplacement returns the displacement of beads from the centre line of the renderer.
Paint	getBeadFill()	getBeadFill returns the bead fill paint.
Paint	getBeadOutline()	getBeadOutline returns the bead outline paint.
Stroke	getBeadStroke()	getBeadStroke returns the bead outline stroke.
double	getDepth(SequenceRenderContext context)	getDepth calculates the depth required by this renderer to display its beads.
FeatureHolder	processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)	processMouseEvent defines the behaviour on revieving a mouse event.
void	removeDelegateRenderer(OptimizableFilter filter)	removeDelegateRenderer removes any association of the given OptimizableFilter with a BeadFeatureRenderer.
abstract void	renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)	renderBead should be overridden by the concrete BeadRenderer.
void	renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)	renderFeature draws a feature using the supplied graphics context.
void	setBeadDepth(double depth)	setBeadDepth sets the depth of a single bead produced by this renderer.
void	setBeadDisplacement(double displacement)	setBeadDisplacement sets the displacement of beads from the centre line of the renderer.
void	setBeadFill(Paint fill)	setBeadFill sets the bead fill paint.
void	setBeadOutline(Paint outline)	setBeadOutline sets the bead outline paint.
void	setBeadStroke(Stroke stroke)	setBeadStroke sets the bead outline stroke.
void	setDelegateRenderer(OptimizableFilter filter, BeadFeatureRenderer renderer)	setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Field Detail

DISPLACEMENT

public static final ChangeType DISPLACEMENT

Constant DISPLACEMENT indicating a change to the Y-axis displacement of the features.

DEPTH

public static final ChangeType DEPTH

Constant DEPTH indicating a change to the depth of the renderer.

OUTLINE

public static final ChangeType OUTLINE

Constant OUTLINE indicating a change to the outline paint of the features.

STROKE

public static final ChangeType STROKE

Constant STROKE indicating a change to the outline stroke of the features.

FILL

public static final ChangeType FILL

Constant FILL indicating a change to the fill of the features.

beadDepth

protected double beadDepth

beadDisplacement

protected double beadDisplacement

beadOutline

protected Paint beadOutline

beadFill

protected Paint beadFill

beadStroke

protected Stroke beadStroke

delegates

protected Map delegates

delegationCache

protected Map delegationCache

Constructor Detail

AbstractBeadRenderer

public AbstractBeadRenderer()

Creates a new AbstractBeadRenderer with no delegates. It will render all features itself, using its own style settings.

AbstractBeadRenderer

public AbstractBeadRenderer(double beadDepth,
                            double beadDisplacement,
                            Paint beadOutline,
                            Paint beadFill,
                            Stroke beadStroke)

Creates a new AbstractBeadRenderer object.

Parameters:

beadDepth - a double.

beadDisplacement - a double.

beadOutline - a Paint.

beadFill - a Paint.

beadStroke - a Stroke.

Method Detail

processMouseEvent

public FeatureHolder processMouseEvent(FeatureHolder holder,
                                       SequenceRenderContext context,
                                       MouseEvent mEvent)

processMouseEvent defines the behaviour on revieving a mouse event.

Specified by:

processMouseEvent in interface FeatureRenderer

Parameters:

holder - a FeatureHolder.

context - a SequenceRenderContext.

mEvent - a MouseEvent.

Returns:

a FeatureHolder.

renderFeature

public void renderFeature(Graphics2D g2,
                          Feature f,
                          SequenceRenderContext context)

renderFeature draws a feature using the supplied graphics context. The rendering may be delegated to another FeatureRenderer instance.

Specified by:

renderFeature in interface FeatureRenderer

Parameters:

g2 - a Graphics2D context.

f - a Feature to render.

context - a SequenceRenderContext context.

setDelegateRenderer

public void setDelegateRenderer(OptimizableFilter filter,
                                BeadFeatureRenderer renderer)
                         throws IllegalArgumentException

setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer. Any feature accepted by the filter will be passed to the associated renderer for drawing. The OptimizableFilters should be disjoint with respect to each other (a feature may not be rendered more than once).

Specified by:

setDelegateRenderer in interface BeadFeatureRenderer

Parameters:

filter - an OptimizableFilter.

renderer - a BeadFeatureRenderer.

Throws:

IllegalArgumentException - if the filter is not disjoint with existing delegate filters.

removeDelegateRenderer

public void removeDelegateRenderer(OptimizableFilter filter)

removeDelegateRenderer removes any association of the given OptimizableFilter with a BeadFeatureRenderer.

Parameters:

filter - an OptimizableFilter.

getDepth

public double getDepth(SequenceRenderContext context)

getDepth calculates the depth required by this renderer to display its beads. It recurses through its delegate renderers and returns the highest value. Concrete renderers should override this method and supply code to calculate their own depth. If a subclass needs to know the depth of its delegates (as is likely if it has any) they can call this method using super.getDepth().

Specified by:

getDepth in interface FeatureRenderer

Parameters:

context - a SequenceRenderContext.

Returns:

a double.

getBeadDepth

public double getBeadDepth()

getBeadDepth returns the depth of a single bead produced by this renderer.

Specified by:

getBeadDepth in interface BeadFeatureRenderer

Returns:

a double.

setBeadDepth

public void setBeadDepth(double depth)
                  throws ChangeVetoException

setBeadDepth sets the depth of a single bead produced by this renderer.

Parameters:

depth - a double.

Throws:

ChangeVetoException - if an error occurs.

getBeadDisplacement

public double getBeadDisplacement()

getBeadDisplacement returns the displacement of beads from the centre line of the renderer. A positive value indicates displacment downwards (for horizontal renderers) or to the right (for vertical renderers).

Specified by:

getBeadDisplacement in interface BeadFeatureRenderer

Returns:

a double.

setBeadDisplacement

public void setBeadDisplacement(double displacement)
                         throws ChangeVetoException

setBeadDisplacement sets the displacement of beads from the centre line of the renderer. A positive value indicates displacment downwards (for horizontal renderers) or to the right (for vertical renderers).

Parameters:

displacement - a double.

Throws:

ChangeVetoException - if an error occurs.

getBeadOutline

public Paint getBeadOutline()

getBeadOutline returns the bead outline paint.

Returns:

a Paint.

setBeadOutline

public void setBeadOutline(Paint outline)
                    throws ChangeVetoException

setBeadOutline sets the bead outline paint.

Parameters:

outline - a Paint.

Throws:

ChangeVetoException - if an error occurs.

getBeadStroke

public Stroke getBeadStroke()

getBeadStroke returns the bead outline stroke.

Returns:

a Stroke.

setBeadStroke

public void setBeadStroke(Stroke stroke)
                   throws ChangeVetoException

setBeadStroke sets the bead outline stroke.

Parameters:

stroke - a Stroke.

Throws:

ChangeVetoException - if an error occurs.

getBeadFill

public Paint getBeadFill()

getBeadFill returns the bead fill paint.

Returns:

a Paint.

setBeadFill

public void setBeadFill(Paint fill)
                 throws ChangeVetoException

setBeadFill sets the bead fill paint.

Parameters:

fill - a Paint.

Throws:

ChangeVetoException - if an error occurs.

renderBead

public abstract void renderBead(Graphics2D g2,
                                Feature f,
                                SequenceRenderContext context)

renderBead should be overridden by the concrete BeadRenderer.

Specified by:

renderBead in interface BeadFeatureRenderer

Parameters:

g2 - a Graphics2D.

f - a Feature to render.

context - a SequenceRenderContext context.