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

  • Method Details

    • 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.