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AlignmentRenderer (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.utils.AbstractChangeable
      • org.biojava.bio.gui.sequence.SequenceRendererWrapper
        • org.biojava.bio.gui.sequence.AlignmentRenderer
  • All Implemented Interfaces:
    Serializable, SequenceRenderer, Changeable
    public class AlignmentRenderer
extends SequenceRendererWrapper
    Author:
    Matthew Pocock, Thomas Down
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer

        SequenceRenderer.RendererForwarder

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static ChangeType LABEL  

      • Fields inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

        RENDERER

    • Constructor Summary

      Constructors 
      Constructor Description
      AlignmentRenderer()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      SequenceRenderContext contextForLabel​(SequenceRenderContext src, String label)  
      double getDepth​(SequenceRenderContext ctx)

      Retrieve the depth of this renderer when rendering src.
      String getLabel()  
      double getMinimumLeader​(SequenceRenderContext ctx)

      Retrieve the minimum leading distance for this renderer when rendering src.
      double getMinimumTrailer​(SequenceRenderContext ctx)

      Retrieve the minimum trailing distance for this renderer when rendering src.
      void paint​(Graphics2D g, SequenceRenderContext ctx)

      Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
      void setLabel​(String label)  

      • Methods inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper

        getChangeSupport, getRenderer, processMouseEvent, setRenderer

      • Methods inherited from class org.biojava.utils.AbstractChangeable

        addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • LABEL

        public static ChangeType LABEL

    • Constructor Detail

      • AlignmentRenderer

        public AlignmentRenderer()

    • Method Detail

      • setLabel

        public void setLabel​(String label)
              throws ChangeVetoException
        Throws:
        ChangeVetoException

      • getLabel

        public String getLabel()

      • getDepth

        public double getDepth​(SequenceRenderContext ctx)

        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
        Overrides:
        getDepth in class SequenceRendererWrapper
        Parameters:
        ctx - the SequenceRenderContext to return info for
        Returns:
        the depth of the renderer for that sequence panel

      • getMinimumLeader

        public double getMinimumLeader​(SequenceRenderContext ctx)

        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
        Overrides:
        getMinimumLeader in class SequenceRendererWrapper
        Parameters:
        ctx - the SequenceRenderContext to return info for
        Returns:
        the leading distance of the renderer for that sequence panel

      • getMinimumTrailer

        public double getMinimumTrailer​(SequenceRenderContext ctx)

        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
        Overrides:
        getMinimumTrailer in class SequenceRendererWrapper
        Parameters:
        ctx - the SequenceRenderContext to return info for
        Returns:
        the trailing distance of the renderer for that sequence panel

      • paint

        public void paint​(Graphics2D g,
                  SequenceRenderContext ctx)

        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
        Overrides:
        paint in class SequenceRendererWrapper
        Parameters:
        g - the Graphics2D to render to
        ctx - the SequenceRenderContext that encapsulates the information to render

      • contextForLabel

        public SequenceRenderContext contextForLabel​(SequenceRenderContext src,
                                             String label)