Class SixFrameRenderer

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.gui.sequence.SixFrameRenderer
All Implemented Interfaces:
SequenceRenderer, Changeable

public class SixFrameRenderer extends AbstractChangeable implements SequenceRenderer
Class that handles drawing in six frames for other classes. Suitable for use with CDS features particularly.

Partly based on Matthew Pocock's ZiggyFeatureRenderer.

Author:
David Huen
  • Constructor Details

  • Method Details

    • getDepth

      public double getDepth(SequenceRenderContext src)
      Description copied from interface: SequenceRenderer
      Retrieve the depth of this renderer when rendering src.

      The depth may vary between sequence panels - for example based upon sequence length. Each line of information in the SequenceRendererContext only renders a region of the sequence. The depth for one complete line may be different from that for another due to the sequence having more or less information in that region to show. For example, a feature renderer implementation may chose to collapse down to a depth of zero pixels if there are no features to render within a region.

      Specified by:
      getDepth in interface SequenceRenderer
      Parameters:
      src - the SequenceRenderContext to return info for
      Returns:
      the depth of the renderer for that sequence panel
    • getMinimumLeader

      Description copied from interface: SequenceRenderer
      Retrieve the minimum leading distance for this renderer when rendering src.

      The leading distance may vary between sequence panels - for example based upon sequence length.

      Specified by:
      getMinimumLeader in interface SequenceRenderer
      Parameters:
      src - the SequenceRenderContext to return info for
      Returns:
      the leading distance of the renderer for that sequence panel
    • getMinimumTrailer

      Description copied from interface: SequenceRenderer
      Retrieve the minimum trailing distance for this renderer when rendering src.

      The trailing distance may vary between sequence panels - for example based upon sequence length.

      Specified by:
      getMinimumTrailer in interface SequenceRenderer
      Parameters:
      src - the SequenceRenderContext to return info for
      Returns:
      the trailing distance of the renderer for that sequence panel
    • setFill

      public void setFill(Paint p) throws ChangeVetoException
      Throws:
      ChangeVetoException
    • getFill

      public Paint getFill()
    • setOutline

      public void setOutline(Paint p) throws ChangeVetoException
      Throws:
      ChangeVetoException
    • getOutline

      public Paint getOutline()
    • setBlockWidth

      public void setBlockWidth(double width) throws ChangeVetoException
      Throws:
      ChangeVetoException
    • getBlockWidth

      public double getBlockWidth()
    • startZiggy

      public void startZiggy(StrandedFeature.Strand strand)
      Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.
    • startZiggy

      public void startZiggy(StrandedFeature.Strand strand, int phase)
      This method is called to initialise the renderer for a spliced transcript.
      Parameters:
      strand - the strand that the transcipt is on.
      phase - the initial translation phase of transcript coding region.
    • renderLocation

      Render another "exon" in the correct translation frame.
    • sequenceExtentOfPixels

    • drawLine

      public void drawLine(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand)
      draws required bar in correct translation frame.
      Parameters:
      base - the sequence coordinate of the bar.
      strand - strand that the bar annotates.
    • paint

      public void paint(Graphics2D g, SequenceRenderContext src)
      Description copied from interface: SequenceRenderer
      Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
      Specified by:
      paint in interface SequenceRenderer
      Parameters:
      g - the Graphics2D to render to
      src - the SequenceRenderContext that encapsulates the information to render
    • processMouseEvent

      Description copied from interface: SequenceRenderer
      Produce a SequenceViewerEvent in response to a mouse gesture.

      A SequenceRenderer that performs any form of coordinate remapping should ensure that it appropriately transforms the mouse event. However, in the SequenceViewerEvent returned, the MouseEvent should be in untransformed coordinates.

      The SequenceRenderer implementation should append itself to the path list before constructing the SequenceViewerEvent.

      Specified by:
      processMouseEvent in interface SequenceRenderer
      Parameters:
      src - the SequenceRenderContext currently in scope
      me - a MouseEvent that caused this request
      path - the List of SequenceRenderer instances passed through so far
      Returns:
      a SequenceViewerEvent encapsulating the mouse gesture