Package org.biojava.bio.gui.sequence

Class PairwiseDiagonalRenderer

  • All Implemented Interfaces:
    java.io.Serializable, PairwiseSequenceRenderer, Changeable
    public class PairwiseDiagonalRenderer
extends AbstractChangeable
implements PairwiseSequenceRenderer, java.io.Serializable

    PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line. The effect produced is similar to a dotplot. This implementation requires that these regions be represented by SimilarityPairFeatures.

    Drawing outside the visible area using a range of valid doubles may cause Java to hang (Sun JDK 1.3.1 on Linux, Compaq JDK 1.3.1 on Tru64, but not Sun JDK 1.4.0-beta2-b77 on Linux). I got round this by manual clipping of the lines to the clip area. The code uses an implementation of the Cohen-Sutherland line-clipping algorithm which clips lines to within a rectangle.

    The clipping code is taken from Computer Graphics for Java Programmers by Leen Ammeraal (1998, ISBN 0-471-98142-7) and cosmetically altered to support Java2D objects. Any bugs introduced are my responsibility.

    Since:
    1.2
    Author:
    Keith James, Leen Ammeraal
    See Also:
    Serialized Form

    • Field Detail

      • OUTLINE

        public static final ChangeType OUTLINE
        Constant OUTLINE indicating a change to the fill of the features.

      • line

        protected java.awt.geom.Line2D.Float line
        line is the line to be drawn for each feature.

      • outline

        protected java.awt.Paint outline
        outline is the line colour.

    • Constructor Detail

      • PairwiseDiagonalRenderer

        public PairwiseDiagonalRenderer()
        Creates a new PairwiseDiagonalRenderer which will draw black lines.

      • PairwiseDiagonalRenderer

        public PairwiseDiagonalRenderer​(java.awt.Paint outline)
        Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint.
        Parameters:
        outline - a Paint.

    • Method Detail

      • paint

        public void paint​(java.awt.Graphics2D g2,
                  PairwiseRenderContext context)
        paint renders the feature as a simple line.
        Specified by:
        paint in interface PairwiseSequenceRenderer
        Parameters:
        g2 - a Graphics2D.
        context - a PairwiseRenderContext.

      • getOutline

        public java.awt.Paint getOutline()
        getOutline returns the colour used to draw the lines.
        Returns:
        a Paint.

      • setOutline

        public void setOutline​(java.awt.Paint outline)
                throws ChangeVetoException
        setOutline sets the the colour used to draw the lines.
        Parameters:
        outline - a Paint.
        Throws:
        ChangeVetoException - if an error occurs.

      • processMouseEvent

        public SequenceViewerEvent processMouseEvent​(PairwiseRenderContext context,
                                             java.awt.event.MouseEvent me,
                                             java.util.List path)
        processMouseEvent acts on a mouse gesture. The target object is a FeatureHolder containing the features on the primary sequence which contain the mouse pointer.
        Specified by:
        processMouseEvent in interface PairwiseSequenceRenderer
        Parameters:
        context - a PairwiseRenderContext.
        me - a MouseEvent.
        path - a List.
        Returns:
        a SequenceViewerEvent.