Package org.biojava.bio.gui.sequence

Class GappedRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.SequenceRendererWrapper

org.biojava.bio.gui.sequence.GappedRenderer

All Implemented Interfaces:

Serializable, SequenceRenderer, Changeable

public class GappedRenderer
extends SequenceRendererWrapper

A renderer that will display a gapped sequence as a discontinuous series of regions.

Each ungapped block in the gapped symbol list will be displayed as a contiguous region by this renderer. Where there are gaps, this renderer will display nothing. Then, when the gaps are over, it will continue to render the ungapped sequence. This has the effect of snapping the image of the ungapped sequence where there are gaps, so as to allow it to be viewed in the gapped co-ordinate system.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

SequenceRenderer.RendererForwarder

Field Summary

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

RENDERER

Constructor Summary

Constructors

Constructor	Description
GappedRenderer()
GappedRenderer(SequenceRenderer renderer)

Method Summary

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

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

Constructor Detail

GappedRenderer

public GappedRenderer()

GappedRenderer

public GappedRenderer(SequenceRenderer renderer)

Method Detail

getDepth

public double getDepth(SequenceRenderContext src)

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:

src - the SequenceRenderContext to return info for

Returns:

the depth of the renderer for that sequence panel

getMinimumLeader

public double getMinimumLeader(SequenceRenderContext src)

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:

src - the SequenceRenderContext to return info for

Returns:

the leading distance of the renderer for that sequence panel

getMinimumTrailer

public double getMinimumTrailer(SequenceRenderContext src)

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:

src - the SequenceRenderContext to return info for

Returns:

the trailing distance of the renderer for that sequence panel

paint

public void paint(Graphics2D g,
                  SequenceRenderContext src)

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

src - the SequenceRenderContext that encapsulates the information to render

makeContext

protected SequenceRenderContext makeContext(SequenceRenderContext src,
                                            RangeLocation loc)