Package org.biojava.bio.gui.sequence

Class SubSequenceRenderContext

java.lang.Object

org.biojava.bio.gui.sequence.SubSequenceRenderContext

All Implemented Interfaces:

SwingConstants, SequenceRenderContext

public class SubSequenceRenderContext
extends Object
implements SequenceRenderContext

Allows a new renderer to "wrap" another one, replacing one or more values.

Use this when implementing SequenceRenderer classes that modify the data that is passed on to delegate renderers e.g. filtering the features, transforming the sequence or moving the rendering co-ordinates.

Author:

Matthew Pocock

Nested Class Summary

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

SequenceRenderContext.Border

Field Summary

Fields inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

LAYOUT, REPAINT

Fields inherited from interface javax.swing.SwingConstants

BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST

Constructor Summary

Constructors

Constructor	Description
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)

Method Summary

Modifier and Type	Method	Description
int	getDirection()	Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
FeatureHolder	getFeatures()	The features to render.
Font	getFont()	Gets the Font attribute of the SequenceRenderContext object
SequenceRenderContext.Border	getLeadingBorder()	Gets the LeadingBorder attribute of the SequenceRenderContext object.
RangeLocation	getRange()	The range of the SymbolList to render.
double	getScale()	Gets the scale as pixels per Symbol
SymbolList	getSymbols()	The SymbolList that is currently rendered by this SequenceRenderContext.
SequenceRenderContext.Border	getTrailingBorder()	Gets the TrailingBorder attribute of the SequenceRenderContext object.
int	graphicsToSequence(double d)	Converts a graphical position into a sequence coordinate.
int	graphicsToSequence(Point2D point)	Converts a graphical position into a sequence coordinate.
double	sequenceToGraphics(int i)	Converts a sequence index into a graphical coordinate.

Methods inherited from class java.lang.Object

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

Constructor Detail

SubSequenceRenderContext

public SubSequenceRenderContext(SequenceRenderContext src,
                                SymbolList symbols,
                                FeatureHolder features,
                                RangeLocation range)

SubSequenceRenderContext

public SubSequenceRenderContext(SequenceRenderContext src,
                                SymbolList symbols,
                                FeatureHolder features,
                                RangeLocation range,
                                int symOffset)

Method Detail

getDirection

public int getDirection()

Description copied from interface: SequenceRenderContext

Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

Specified by:

getDirection in interface SequenceRenderContext

Returns:

The Direction value

getScale

public double getScale()

Description copied from interface: SequenceRenderContext

Gets the scale as pixels per Symbol

Specified by:

getScale in interface SequenceRenderContext

Returns:

The scale value

sequenceToGraphics

public double sequenceToGraphics(int i)

Description copied from interface: SequenceRenderContext

Converts a sequence index into a graphical coordinate. You will need to use this in conjunction with getDirection to correctly lay graphics out.

Specified by:

sequenceToGraphics in interface SequenceRenderContext

Parameters:

i - Index within the sequence

Returns:

Equivalent graphical position in pixels

graphicsToSequence

public int graphicsToSequence(double d)

Description copied from interface: SequenceRenderContext

Converts a graphical position into a sequence coordinate. You will need to have used getDirection to decide whether to use the x or y coordinate.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

d - A pixel position

Returns:

The corresponding sequence index

graphicsToSequence

public int graphicsToSequence(Point2D point)

Description copied from interface: SequenceRenderContext

Converts a graphical position into a sequence coordinate. This will use getDirection to decide whether to use the x or y coordinate.

Specified by:

graphicsToSequence in interface SequenceRenderContext

Parameters:

point - a point representing the position

Returns:

the corresponding sequence index

getSymbols

public SymbolList getSymbols()

Description copied from interface: SequenceRenderContext

The SymbolList that is currently rendered by this SequenceRenderContext.

Specified by:

getSymbols in interface SequenceRenderContext

Returns:

The Sequence value

getFeatures

public FeatureHolder getFeatures()

Description copied from interface: SequenceRenderContext

The features to render.

Specified by:

getFeatures in interface SequenceRenderContext

Returns:

a FeatureHolder with the Features to render

getRange

public RangeLocation getRange()

Description copied from interface: SequenceRenderContext

The range of the SymbolList to render.

Specified by:

getRange in interface SequenceRenderContext

Returns:

the RangeLocation specifying which indices (inclusive) to render

getLeadingBorder

public SequenceRenderContext.Border getLeadingBorder()

Description copied from interface: SequenceRenderContext

Gets the LeadingBorder attribute of the SequenceRenderContext object. This represents the space between the beginning of the rendering area and the beginning of the sequence.

Specified by:

getLeadingBorder in interface SequenceRenderContext

Returns:

The LeadingBorder value

getTrailingBorder

public SequenceRenderContext.Border getTrailingBorder()

Description copied from interface: SequenceRenderContext

Gets the TrailingBorder attribute of the SequenceRenderContext object. This represents the space between the end of the sequence and the end of the rendering area.

Specified by:

getTrailingBorder in interface SequenceRenderContext

Returns:

The TrailingBorder value

getFont

public Font getFont()

Description copied from interface: SequenceRenderContext

Gets the Font attribute of the SequenceRenderContext object

Specified by:

getFont in interface SequenceRenderContext

Returns:

The Font value