org.biojava.bio.gui.sequence
Interface PairwiseRenderContext

All Superinterfaces:
SequenceRenderContext, javax.swing.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
 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(java.awt.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(java.awt.Point point)
graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

Parameters:
point - a Point.
Returns:
an int.