org.biojava.bio.gui.sequence

Class SubPairwiseRenderContext

java.lang.Object

org.biojava.bio.gui.sequence.SubPairwiseRenderContext

All Implemented Interfaces:

SwingConstants, PairwiseRenderContext, SequenceRenderContext

public class SubPairwiseRenderContext
extends Object
implements PairwiseRenderContext

SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own. If any of the SymbolList, FeatureHolder or RangeLocation arguments are not null, their values are returned. Otherwise the delegate's method is called and its return value is returned instead.

Since:

1.2

Author:

Keith James, 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 and Description
SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange) Creates a new SubPairwiseRenderContext.

Method Summary

Methods

Modifier and Type	Method and 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
int	getSecondaryDirection() getSecondaryDirection returns the direction in which the secondary sequence is rendered.
FeatureHolder	getSecondaryFeatures() getSecondaryFeatures returns the features on the secondary sequence.
RangeLocation	getSecondaryRange() getSecondaryRange returns the range of the secondary sequence currently rendered.
SymbolList	getSecondarySymbols() getSecondarySymbols returns the symbols of the secondary sequence.
SymbolList	getSymbols() The SymbolList that is currently rendered by this SequenceRenderContext.
SequenceRenderContext.Border	getTrailingBorder() Gets the TrailingBorder attribute of the SequenceRenderContext object.
int	graphicsToSecondarySequence(double graphicsPos) graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.
int	graphicsToSecondarySequence(Point point) graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
int	graphicsToSequence(double graphicsPos) Converts a graphical position into a sequence coordinate.
int	graphicsToSequence(Point2D point) Converts a graphical position into a sequence coordinate.
double	secondarySequenceToGraphics(int sequencePos) secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.
double	sequenceToGraphics(int sequencePos) 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

SubPairwiseRenderContext

public SubPairwiseRenderContext(PairwiseRenderContext context,
                        SymbolList symbols,
                        SymbolList secondarySymbols,
                        FeatureHolder features,
                        FeatureHolder secondaryFeatures,
                        RangeLocation range,
                        RangeLocation secondaryRange)

Creates a new SubPairwiseRenderContext.

Parameters:

context - a PairwiseRenderContext to wrap. This should not be null.

symbols - a SymbolList to use instead of the delegate's. May be null.

secondarySymbols - a SymbolList to use instead of the delegate's. May be null.

features - a FeatureHolder to use instead of the delegate's. May be null.

secondaryFeatures - a FeatureHolder to use instead of the delegate's. May be null.

range - a RangeLocation to use instead of the delegate's. May be null.

secondaryRange - a RangeLocation to use instead of the delegate's. May be null.

Method Detail

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

getSecondarySymbols

public SymbolList getSecondarySymbols()

Description copied from interface: PairwiseRenderContext

getSecondarySymbols returns the symbols of the secondary sequence.

Specified by:

getSecondarySymbols in interface PairwiseRenderContext

Returns:

a SymbolList.

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

getSecondaryFeatures

public FeatureHolder getSecondaryFeatures()

Description copied from interface: PairwiseRenderContext

getSecondaryFeatures returns the features on the secondary sequence.

Specified by:

getSecondaryFeatures in interface PairwiseRenderContext

Returns:

a FeatureHolder.

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

getSecondaryRange

public RangeLocation getSecondaryRange()

Description copied from interface: PairwiseRenderContext

getSecondaryRange returns the range of the secondary sequence currently rendered.

Specified by:

getSecondaryRange in interface PairwiseRenderContext

Returns:

a RangeLocation.

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

getSecondaryDirection

public int getSecondaryDirection()

Description copied from interface: PairwiseRenderContext

getSecondaryDirection returns the direction in which the secondary sequence is rendered. This may be either HORIZONTAL or VERTICAL.

Specified by:

getSecondaryDirection in interface PairwiseRenderContext

Returns:

an int.

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

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

sequenceToGraphics

public double sequenceToGraphics(int sequencePos)

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:

sequencePos - Index within the sequence

Returns:

Equivalent graphical position in pixels

secondarySequenceToGraphics

public double secondarySequenceToGraphics(int sequencePos)

Description copied from interface: PairwiseRenderContext

secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.

Specified by:

secondarySequenceToGraphics in interface PairwiseRenderContext

Parameters:

sequencePos - an int.

Returns:

a double.

graphicsToSequence

public int graphicsToSequence(double graphicsPos)

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:

graphicsPos - 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

graphicsToSecondarySequence

public int graphicsToSecondarySequence(double graphicsPos)

Description copied from interface: PairwiseRenderContext

graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.

Specified by:

graphicsToSecondarySequence in interface PairwiseRenderContext

Parameters:

graphicsPos - a double.

Returns:

an int.

graphicsToSecondarySequence

public int graphicsToSecondarySequence(Point point)

Description copied from interface: PairwiseRenderContext

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

Specified by:

graphicsToSecondarySequence in interface PairwiseRenderContext

Parameters:

point - a Point.

Returns:

an int.

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