Uses of Interface
org.biojava.bio.gui.sequence.SequenceRenderContext

Packages that use SequenceRenderContext
org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations. 
 

Uses of SequenceRenderContext in org.biojava.bio.gui.sequence
 

Subinterfaces of SequenceRenderContext in org.biojava.bio.gui.sequence
 interface PairwiseRenderContext
          PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences.
 

Classes in org.biojava.bio.gui.sequence that implement SequenceRenderContext
 class HeadlessRenderContext
           A stand-alone SequenceRenderContext to make it easy to render to an image.
 class PairwiseSequencePanel
          A PairwiseSequencePanel is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).
 class SequencePanel
          A panel that displays a Sequence.
 class SequencePoster
          A panel that displays a Sequence.
 class SubPairwiseRenderContext
          SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
 class SubSequenceRenderContext
           
 class TranslatedSequencePanel
          TranslatedSequencePanel is a panel that displays a Sequence.
 

Methods in org.biojava.bio.gui.sequence that return SequenceRenderContext
 SequenceRenderContext AlignmentRenderer.contextForLabel(SequenceRenderContext src, java.lang.Object label)
           
protected  SequenceRenderContext FilteringRenderer.getContext(SequenceRenderContext src)
           
 

Methods in org.biojava.bio.gui.sequence with parameters of type SequenceRenderContext
 double BumpedRenderer.getDepth(SequenceRenderContext src)
           
 double BumpedRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double BumpedRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void BumpedRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent BumpedRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
protected  java.util.List BumpedRenderer.layer(SequenceRenderContext src)
           
protected  java.util.List BumpedRenderer.doLayer(SequenceRenderContext src, FeatureFilter filt)
           
 void RectangularBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as simple rectangle.
 double RectangularBeadRenderer.getDepth(SequenceRenderContext context)
          getDepth calculates the depth required by this renderer to display its beads.
 double ZiggyFeatureRenderer.getDepth(SequenceRenderContext src)
           
 void ZiggyFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 FeatureHolder ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 void EllipticalBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as simple ellipse.
 double EllipticalBeadRenderer.getDepth(SequenceRenderContext context)
          getDepth calculates the depth required by this renderer to display its beads.
 double SymbolSequenceRenderer.getDepth(SequenceRenderContext context)
           
 double SymbolSequenceRenderer.getMinimumLeader(SequenceRenderContext context)
           
 double SymbolSequenceRenderer.getMinimumTrailer(SequenceRenderContext context)
           
 void SymbolSequenceRenderer.paint(java.awt.Graphics2D g2, SequenceRenderContext context)
           
 SequenceViewerEvent SymbolSequenceRenderer.processMouseEvent(SequenceRenderContext context, java.awt.event.MouseEvent me, java.util.List path)
           
 double StackedFeatureRenderer.getDepth(SequenceRenderContext src)
           
 void StackedFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 FeatureHolder StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 double AlignmentRenderer.getDepth(SequenceRenderContext ctx)
           
 double AlignmentRenderer.getMinimumLeader(SequenceRenderContext ctx)
           
 double AlignmentRenderer.getMinimumTrailer(SequenceRenderContext ctx)
           
 void AlignmentRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext ctx)
           
 SequenceRenderContext AlignmentRenderer.contextForLabel(SequenceRenderContext src, java.lang.Object label)
           
 double LabelledSequenceRenderer.getMinimumLeader(SequenceRenderContext sRC)
           
 double LabelledSequenceRenderer.getMinimumTrailer(SequenceRenderContext sRC)
           
 double LabelledSequenceRenderer.getDepth(SequenceRenderContext sRC)
           
 SequenceViewerEvent LabelledSequenceRenderer.processMouseEvent(SequenceRenderContext sRC, java.awt.event.MouseEvent mE, java.util.List path)
           
 void LabelledSequenceRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext sRC)
           
 double StopRenderer.getDepth(SequenceRenderContext src)
           
 double StopRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double StopRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void StopRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent StopRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 void AbiTraceRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext ctxt)
           
 double AbiTraceRenderer.getDepth(SequenceRenderContext src)
           
 double AbiTraceRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double AbiTraceRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 SequenceViewerEvent AbiTraceRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 double FilteringRenderer.getDepth(SequenceRenderContext src)
           
 double FilteringRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double FilteringRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void FilteringRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent FilteringRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
protected  SequenceRenderContext FilteringRenderer.getContext(SequenceRenderContext src)
           
 void BeadFeatureRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead should implement rendering for this bead type only.
 double SequenceRendererWrapper.getDepth(SequenceRenderContext src)
           
 double SequenceRendererWrapper.getMinimumLeader(SequenceRenderContext src)
           
 double SequenceRendererWrapper.getMinimumTrailer(SequenceRenderContext src)
           
 void SequenceRendererWrapper.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent SequenceRendererWrapper.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 void ImageMapRenderer.renderImageMap(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderImageMap renders the Feature as set of image map hotspots.
 void RoundRectangularBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as a rectangle with rounded corners.
 double RoundRectangularBeadRenderer.getDepth(SequenceRenderContext context)
          getDepth calculates the depth required by this renderer to display its beads.
 void BasicFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 double BasicFeatureRenderer.getDepth(SequenceRenderContext src)
           
 FeatureHolder BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 void FeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 double FeatureRenderer.getDepth(SequenceRenderContext src)
           
 FeatureHolder FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 void SequenceRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
          Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
 double SequenceRenderer.getDepth(SequenceRenderContext src)
          Retrieve the depth of this renderer when rendering src.
 double SequenceRenderer.getMinimumLeader(SequenceRenderContext src)
          Retrieve the minimum leading distance for this renderer when rendering src.
 double SequenceRenderer.getMinimumTrailer(SequenceRenderContext src)
          Retrieve the minimum trailing distance for this renderer when rendering src.
 SequenceViewerEvent SequenceRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
          Produce a SequenceViewerEvent in response to a mouse gesture.
 void TickFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 double TickFeatureRenderer.getDepth(SequenceRenderContext src)
           
 FeatureHolder TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 void LabelRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext sp, int min, int max, SequenceRenderContext.Border border)
          Render a label for the information for sp to g.
 double LabelRenderer.getMinimumWidth(SequenceRenderContext sp)
          Retrieve the minimum space required to render the label.
 void LabelRenderer.RenderNothing.paint(java.awt.Graphics2D g, SequenceRenderContext sp, int min, int max, SequenceRenderContext.Border border)
           
 double LabelRenderer.RenderNothing.getMinimumWidth(SequenceRenderContext src)
           
 double FeatureLabelRenderer.getDepth(SequenceRenderContext src)
           
 double FeatureLabelRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double FeatureLabelRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void FeatureLabelRenderer.renderFeature(java.awt.Graphics2D g, Feature feat, SequenceRenderContext src)
           
 FeatureHolder FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 double RulerRenderer.getMinimumLeader(SequenceRenderContext context)
           
 double RulerRenderer.getMinimumTrailer(SequenceRenderContext context)
           
 double RulerRenderer.getDepth(SequenceRenderContext src)
           
 void RulerRenderer.paint(java.awt.Graphics2D g2, SequenceRenderContext context)
           
 SequenceViewerEvent RulerRenderer.processMouseEvent(SequenceRenderContext context, java.awt.event.MouseEvent me, java.util.List path)
           
 void RectangularImapRenderer.renderImageMap(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderImageMap writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.
 void RectangularImapRenderer.renderFeature(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 void RectangularImapRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 double RectangularImapRenderer.getDepth(SequenceRenderContext context)
           
 FeatureHolder RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 double PaddingRenderer.getDepth(SequenceRenderContext src)
           
 double PaddingRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double PaddingRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void PaddingRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent PaddingRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 double MultiLineRenderer.getDepth(SequenceRenderContext src)
           
 double MultiLineRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double MultiLineRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void MultiLineRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent MultiLineRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 double OverlayRendererWrapper.getDepth(SequenceRenderContext src)
           
 double OverlayRendererWrapper.getMinimumLeader(SequenceRenderContext src)
           
 double OverlayRendererWrapper.getMinimumTrailer(SequenceRenderContext src)
           
 void OverlayRendererWrapper.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent OverlayRendererWrapper.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 void ZiggyImapRenderer.renderImageMap(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
 void ZiggyImapRenderer.renderFeature(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 double ZiggyImapRenderer.getDepth(SequenceRenderContext context)
           
 FeatureHolder ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 FeatureHolder AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
          processMouseEvent defines the behaviour on revieving a mouse event.
 void AbstractBeadRenderer.renderFeature(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderFeature draws a feature using the supplied graphics context.
 double AbstractBeadRenderer.getDepth(SequenceRenderContext context)
          getDepth calculates the depth required by this renderer to display its beads.
abstract  void AbstractBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead should be overridden by the concrete BeadRenderer.
 double FeatureBlockSequenceRenderer.getDepth(SequenceRenderContext src)
           
 double FeatureBlockSequenceRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double FeatureBlockSequenceRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void FeatureBlockSequenceRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent FeatureBlockSequenceRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 double SixFrameZiggyRenderer.getDepth(SequenceRenderContext src)
           
 void SixFrameZiggyRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 FeatureHolder SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
protected  java.awt.Shape SimpleLabelRenderer.getLabelGlyph(SequenceRenderContext src, java.awt.font.FontRenderContext frc)
           
 double SimpleLabelRenderer.getMinimumWidth(SequenceRenderContext sp)
           
 void SimpleLabelRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext sp, int min, int max, SequenceRenderContext.Border side)
           
 double SixFrameRenderer.getDepth(SequenceRenderContext src)
           
 double SixFrameRenderer.getMinimumLeader(SequenceRenderContext src)
           
 double SixFrameRenderer.getMinimumTrailer(SequenceRenderContext src)
           
 void SixFrameRenderer.renderLocation(java.awt.Graphics2D g, SequenceRenderContext src, Location loc)
          Render another "exon" in the correct translation frame.
 java.util.List SixFrameRenderer.sequenceExtentOfPixels(SequenceRenderContext src)
           
 void SixFrameRenderer.drawLine(java.awt.Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand)
          draws required bar in correct translation frame.
 void SixFrameRenderer.paint(java.awt.Graphics2D g, SequenceRenderContext src)
           
 SequenceViewerEvent SixFrameRenderer.processMouseEvent(SequenceRenderContext src, java.awt.event.MouseEvent me, java.util.List path)
           
 

Constructors in org.biojava.bio.gui.sequence with parameters of type SequenceRenderContext
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)