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
    • 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.