org.biojava.bio.gui.sequence

Class OffsetRulerRenderer

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.gui.sequence.OffsetRulerRenderer

All Implemented Interfaces:

SequenceRenderer, Changeable

public class OffsetRulerRenderer
extends AbstractChangeable
implements SequenceRenderer

OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence. For example if the Protein contained an N-Terminal His tag then coordinate 1 should correspond to the start of the protein, not the tag. This implementation borrows heavily from RulerRenderer

Since:

1.5

Author:

Mark Southern

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	OFFSET
static ChangeType	TICKS
static int	TICKS_DOWN
static int	TICKS_UP

Constructor Summary

Constructors

Constructor and Description
OffsetRulerRenderer()
OffsetRulerRenderer(int tickDirection, int sequenceOffset)

Method Summary

Methods

Modifier and Type	Method and Description
double	getDepth(SequenceRenderContext src) Retrieve the depth of this renderer when rendering src.
double	getMinimumLeader(SequenceRenderContext context) Retrieve the minimum leading distance for this renderer when rendering src.
double	getMinimumTrailer(SequenceRenderContext context) Retrieve the minimum trailing distance for this renderer when rendering src.
int	getSequenceOffset()
int	getTickDirection()
void	paint(Graphics2D g2, SequenceRenderContext context) Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
SequenceViewerEvent	processMouseEvent(SequenceRenderContext context, MouseEvent me, List path) Produce a SequenceViewerEvent in response to a mouse gesture.
void	setSequenceOffset(int offset)
void	setTickDirection(int dir)

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

OFFSET

public static final ChangeType OFFSET

TICKS

public static final ChangeType TICKS

TICKS_UP

public static final int TICKS_UP

See Also:

Constant Field Values

TICKS_DOWN

public static final int TICKS_DOWN

See Also:

Constant Field Values

Constructor Detail

OffsetRulerRenderer

public OffsetRulerRenderer()
                    throws IllegalArgumentException

Throws:

IllegalArgumentException

OffsetRulerRenderer

public OffsetRulerRenderer(int tickDirection,
                   int sequenceOffset)
                    throws IllegalArgumentException

Throws:

IllegalArgumentException

Method Detail

setSequenceOffset

public void setSequenceOffset(int offset)
                       throws ChangeVetoException

Throws:

ChangeVetoException

getSequenceOffset

public int getSequenceOffset()

setTickDirection

public void setTickDirection(int dir)
                      throws ChangeVetoException

Throws:

ChangeVetoException

getTickDirection

public int getTickDirection()

getMinimumLeader

public double getMinimumLeader(SequenceRenderContext context)

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

Parameters:

context - the SequenceRenderContext to return info for

Returns:

the leading distance of the renderer for that sequence panel

getMinimumTrailer

public double getMinimumTrailer(SequenceRenderContext context)

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

Parameters:

context - the SequenceRenderContext to return info for

Returns:

the trailing distance of the renderer for that sequence panel

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

Parameters:

src - the SequenceRenderContext to return info for

Returns:

the depth of the renderer for that sequence panel

paint

public void paint(Graphics2D g2,
         SequenceRenderContext context)

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

Parameters:

g2 - the Graphics2D to render to

context - the SequenceRenderContext that encapsulates the information to render

processMouseEvent

public SequenceViewerEvent processMouseEvent(SequenceRenderContext context,
                                    MouseEvent me,
                                    List path)

Description copied from interface: SequenceRenderer

Produce a SequenceViewerEvent in response to a mouse gesture.

A SequenceRenderer that performs any form of coordinate remapping should ensure that it appropriately transforms the mouse event. However, in the SequenceViewerEvent returned, the MouseEvent should be in untransformed coordinates.

The SequenceRenderer implementation should append itself to the path list before constructing the SequenceViewerEvent.

Specified by:

processMouseEvent in interface SequenceRenderer

Parameters:

context - the SequenceRenderContext currently in scope

me - a MouseEvent that caused this request

path - the List of SequenceRenderer instances passed through so far

Returns:

a SequenceViewerEvent encapsulating the mouse gesture