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
          Deprecated. This doesn't handle loads of stuff. Use SequencePoster.
 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
          Allows a new renderer to "wrap" another one, replacing one or more values.
 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)
           
protected  SequenceRenderContext GappedRenderer.makeContext(SequenceRenderContext src, RangeLocation loc)
           
 

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

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