org.biojava.bio.gui.sequence

Class AlignmentRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.SequenceRendererWrapper

org.biojava.bio.gui.sequence.AlignmentRenderer

All Implemented Interfaces:

Serializable, SequenceRenderer, Changeable

public class AlignmentRenderer
extends SequenceRendererWrapper

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer

SequenceRenderer.RendererForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	LABEL

Fields inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

RENDERER

Constructor Summary

Constructors

Constructor and Description
AlignmentRenderer()

Method Summary

Methods

Modifier and Type	Method and Description
SequenceRenderContext	contextForLabel(SequenceRenderContext src, String label)
double	getDepth(SequenceRenderContext ctx) Retrieve the depth of this renderer when rendering src.
String	getLabel()
double	getMinimumLeader(SequenceRenderContext ctx) Retrieve the minimum leading distance for this renderer when rendering src.
double	getMinimumTrailer(SequenceRenderContext ctx) Retrieve the minimum trailing distance for this renderer when rendering src.
void	paint(Graphics2D g, SequenceRenderContext ctx) Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
void	setLabel(String label)

Methods inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getChangeSupport, getRenderer, processMouseEvent, setRenderer

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

LABEL

public static ChangeType LABEL

Constructor Detail

AlignmentRenderer

public AlignmentRenderer()

Method Detail

setLabel

public void setLabel(String label)
              throws ChangeVetoException

Throws:

ChangeVetoException

getLabel

public String getLabel()

getDepth

public double getDepth(SequenceRenderContext ctx)

Description copied from interface: SequenceRenderer

Retrieve the depth of this renderer when rendering src.

The depth may vary between sequence panels - for example based upon sequence length. Each line of information in the SequenceRendererContext only renders a region of the sequence. The depth for one complete line may be different from that for another due to the sequence having more or less information in that region to show. For example, a feature renderer implementation may chose to collapse down to a depth of zero pixels if there are no features to render within a region.

Specified by:

getDepth in interface SequenceRenderer

Overrides:

getDepth in class SequenceRendererWrapper

Parameters:

ctx - the SequenceRenderContext to return info for

Returns:

the depth of the renderer for that sequence panel

getMinimumLeader

public double getMinimumLeader(SequenceRenderContext ctx)

Description copied from interface: SequenceRenderer

Retrieve the minimum leading distance for this renderer when rendering src.

The leading distance may vary between sequence panels - for example based upon sequence length.

Specified by:

getMinimumLeader in interface SequenceRenderer

Overrides:

getMinimumLeader in class SequenceRendererWrapper

Parameters:

ctx - the SequenceRenderContext to return info for

Returns:

the leading distance of the renderer for that sequence panel

getMinimumTrailer

public double getMinimumTrailer(SequenceRenderContext ctx)

Description copied from interface: SequenceRenderer

Retrieve the minimum trailing distance for this renderer when rendering src.

The trailing distance may vary between sequence panels - for example based upon sequence length.

Specified by:

getMinimumTrailer in interface SequenceRenderer

Overrides:

getMinimumTrailer in class SequenceRendererWrapper

Parameters:

ctx - the SequenceRenderContext to return info for

Returns:

the trailing distance of the renderer for that sequence panel

paint

public void paint(Graphics2D g,
         SequenceRenderContext ctx)

Description copied from interface: SequenceRenderer

Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.

Specified by:

paint in interface SequenceRenderer

Overrides:

paint in class SequenceRendererWrapper

Parameters:

g - the Graphics2D to render to

ctx - the SequenceRenderContext that encapsulates the information to render

contextForLabel

public SequenceRenderContext contextForLabel(SequenceRenderContext src,
                                    String label)