Package org.biojava.bio.gui.sequence

Interface PairwiseRenderContext

All Superinterfaces:

SequenceRenderContext, SwingConstants

All Known Implementing Classes:

PairwiseSequencePanel, SubPairwiseRenderContext

public interface PairwiseRenderContext
extends SequenceRenderContext

PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences. No assumption is made as to whether the sequences are to be rendered in different directions (as in a dotplot) or in the same direction; this is left to the implementation. The leading and trailing borders refer to the primary sequence only.

Since:

1.2

Author:

Keith James

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

Method Summary

Modifier and Type	Method	Description
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.
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.
double	secondarySequenceToGraphics(int sequencePos)	secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.

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

getDirection, getFeatures, getFont, getLeadingBorder, getRange, getScale, getSymbols, getTrailingBorder, graphicsToSequence, graphicsToSequence, sequenceToGraphics

Method Detail

getSecondaryDirection

int getSecondaryDirection()

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

Returns:

an int.

getSecondarySymbols

SymbolList getSecondarySymbols()

getSecondarySymbols returns the symbols of the secondary sequence.

Returns:

a SymbolList.

getSecondaryFeatures

FeatureHolder getSecondaryFeatures()

getSecondaryFeatures returns the features on the secondary sequence.

Returns:

a FeatureHolder.

getSecondaryRange

RangeLocation getSecondaryRange()

getSecondaryRange returns the range of the secondary sequence currently rendered.

Returns:

a RangeLocation.

secondarySequenceToGraphics

double secondarySequenceToGraphics(int sequencePos)

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

Parameters:

sequencePos - an int.

Returns:

a double.

graphicsToSecondarySequence

int graphicsToSecondarySequence(double graphicsPos)

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

Parameters:

graphicsPos - a double.

Returns:

an int.

graphicsToSecondarySequence

int graphicsToSecondarySequence(Point point)

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

Parameters:

point - a Point.

Returns:

an int.