Uses of Interface
org.biojava.bio.gui.sequence.SequenceRenderContext
Packages that use SequenceRenderContext
Package
Description
Graphical displays of biological sequences and associated annotations.
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Uses of SequenceRenderContext in org.biojava.bio.gui.sequence
Subinterfaces of SequenceRenderContext in org.biojava.bio.gui.sequenceModifier and TypeInterfaceDescriptioninterface
PairwiseRenderContext
encapsulates information required for the rendering of a pair of sequences.Classes in org.biojava.bio.gui.sequence that implement SequenceRenderContextModifier and TypeClassDescriptionclass
A stand-alone SequenceRenderContext to make it easy to render to an image.class
APairwiseSequencePanel
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
A panel that displays a Sequence.class
Deprecated.This doesn't handle loads of stuff.class
SubPairwiseRenderContext
is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.class
Allows a new renderer to "wrap" another one, replacing one or more values.class
TranslatedSequencePanel
is a panel that displays a Sequence.Methods in org.biojava.bio.gui.sequence that return SequenceRenderContextModifier and TypeMethodDescriptionAlignmentRenderer.contextForLabel
(SequenceRenderContext src, String 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 SequenceRenderContextModifier and TypeMethodDescriptionAlignmentRenderer.contextForLabel
(SequenceRenderContext src, String label) protected List
BumpedRenderer.doLayer
(SequenceRenderContext src, FeatureFilter filt) void
SixFrameRenderer.drawLine
(Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) draws required bar in correct translation frame.protected SequenceRenderContext
FilteringRenderer.getContext
(SequenceRenderContext src) double
AbiTraceRenderer.getDepth
(SequenceRenderContext src) double
AbstractBeadRenderer.getDepth
(SequenceRenderContext context) getDepth
calculates the depth required by this renderer to display its beads.double
AlignmentRenderer.getDepth
(SequenceRenderContext ctx) double
ArrowedFeatureRenderer.getDepth
(SequenceRenderContext src) double
BasicFeatureRenderer.getDepth
(SequenceRenderContext src) double
BasicImapRenderer.getDepth
(SequenceRenderContext context) double
BumpedRenderer.getDepth
(SequenceRenderContext src) double
EllipticalBeadRenderer.getDepth
(SequenceRenderContext context) getDepth
calculates the depth required by this renderer to display its beads.double
FeatureBlockSequenceRenderer.getDepth
(SequenceRenderContext src) double
FeatureLabelRenderer.getDepth
(SequenceRenderContext src) double
FeatureRenderer.getDepth
(SequenceRenderContext src) double
FilteringRenderer.getDepth
(SequenceRenderContext src) double
GappedRenderer.getDepth
(SequenceRenderContext src) double
GlyphFeatureRenderer.getDepth
(SequenceRenderContext src) Returns the depth property of this class.double
LabelledSequenceRenderer.getDepth
(SequenceRenderContext sRC) double
MultiLineRenderer.getDepth
(SequenceRenderContext src) double
OffsetRulerRenderer.getDepth
(SequenceRenderContext src) double
OverlayRendererWrapper.getDepth
(SequenceRenderContext src) double
PaddingRenderer.getDepth
(SequenceRenderContext src) double
RectangularBeadRenderer.getDepth
(SequenceRenderContext context) getDepth
calculates the depth required by this renderer to display its beads.double
RectangularImapRenderer.getDepth
(SequenceRenderContext context) double
RoundRectangularBeadRenderer.getDepth
(SequenceRenderContext context) getDepth
calculates the depth required by this renderer to display its beads.double
RulerRenderer.getDepth
(SequenceRenderContext src) double
SequenceRenderer.getDepth
(SequenceRenderContext src) Retrieve the depth of this renderer when rendering src.double
SequenceRendererWrapper.getDepth
(SequenceRenderContext src) double
SixFrameRenderer.getDepth
(SequenceRenderContext src) double
SixFrameZiggyRenderer.getDepth
(SequenceRenderContext src) double
StackedFeatureRenderer.getDepth
(SequenceRenderContext src) double
StopRenderer.getDepth
(SequenceRenderContext src) double
SymbolSequenceRenderer.getDepth
(SequenceRenderContext context) double
TickFeatureRenderer.getDepth
(SequenceRenderContext src) double
ZiggyFeatureRenderer.getDepth
(SequenceRenderContext src) double
ZiggyImapRenderer.getDepth
(SequenceRenderContext context) protected Shape
SimpleLabelRenderer.getLabelGlyph
(SequenceRenderContext src, FontRenderContext frc) double
AbiTraceRenderer.getMinimumLeader
(SequenceRenderContext src) double
AlignmentRenderer.getMinimumLeader
(SequenceRenderContext ctx) double
BumpedRenderer.getMinimumLeader
(SequenceRenderContext src) double
FeatureBlockSequenceRenderer.getMinimumLeader
(SequenceRenderContext src) double
FeatureLabelRenderer.getMinimumLeader
(SequenceRenderContext src) double
FilteringRenderer.getMinimumLeader
(SequenceRenderContext src) double
GappedRenderer.getMinimumLeader
(SequenceRenderContext src) double
LabelledSequenceRenderer.getMinimumLeader
(SequenceRenderContext sRC) double
MultiLineRenderer.getMinimumLeader
(SequenceRenderContext src) double
OffsetRulerRenderer.getMinimumLeader
(SequenceRenderContext context) double
OverlayRendererWrapper.getMinimumLeader
(SequenceRenderContext src) double
PaddingRenderer.getMinimumLeader
(SequenceRenderContext src) double
RulerRenderer.getMinimumLeader
(SequenceRenderContext context) double
SequenceRenderer.getMinimumLeader
(SequenceRenderContext src) Retrieve the minimum leading distance for this renderer when rendering src.double
SequenceRendererWrapper.getMinimumLeader
(SequenceRenderContext src) double
SixFrameRenderer.getMinimumLeader
(SequenceRenderContext src) double
StopRenderer.getMinimumLeader
(SequenceRenderContext src) double
SymbolSequenceRenderer.getMinimumLeader
(SequenceRenderContext context) double
AbiTraceRenderer.getMinimumTrailer
(SequenceRenderContext src) double
AlignmentRenderer.getMinimumTrailer
(SequenceRenderContext ctx) double
BumpedRenderer.getMinimumTrailer
(SequenceRenderContext src) double
FeatureBlockSequenceRenderer.getMinimumTrailer
(SequenceRenderContext src) double
FeatureLabelRenderer.getMinimumTrailer
(SequenceRenderContext src) double
FilteringRenderer.getMinimumTrailer
(SequenceRenderContext src) double
GappedRenderer.getMinimumTrailer
(SequenceRenderContext src) double
LabelledSequenceRenderer.getMinimumTrailer
(SequenceRenderContext sRC) double
MultiLineRenderer.getMinimumTrailer
(SequenceRenderContext src) double
OffsetRulerRenderer.getMinimumTrailer
(SequenceRenderContext context) double
OverlayRendererWrapper.getMinimumTrailer
(SequenceRenderContext src) double
PaddingRenderer.getMinimumTrailer
(SequenceRenderContext src) double
RulerRenderer.getMinimumTrailer
(SequenceRenderContext context) double
SequenceRenderer.getMinimumTrailer
(SequenceRenderContext src) Retrieve the minimum trailing distance for this renderer when rendering src.double
SequenceRendererWrapper.getMinimumTrailer
(SequenceRenderContext src) double
SixFrameRenderer.getMinimumTrailer
(SequenceRenderContext src) double
StopRenderer.getMinimumTrailer
(SequenceRenderContext src) double
SymbolSequenceRenderer.getMinimumTrailer
(SequenceRenderContext context) double
LabelRenderer.getMinimumWidth
(SequenceRenderContext sp) Retrieve the minimum space required to render the label.double
LabelRenderer.RenderNothing.getMinimumWidth
(SequenceRenderContext src) double
SimpleLabelRenderer.getMinimumWidth
(SequenceRenderContext sp) static Location
GUITools.getVisibleRange
(SequenceRenderContext src, Graphics2D g2) protected List
BumpedRenderer.layer
(SequenceRenderContext src) protected SequenceRenderContext
GappedRenderer.makeContext
(SequenceRenderContext src, RangeLocation loc) void
AbiTraceRenderer.paint
(Graphics2D g, SequenceRenderContext ctxt) void
AlignmentRenderer.paint
(Graphics2D g, SequenceRenderContext ctx) void
BumpedRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
FeatureBlockSequenceRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
FilteringRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
GappedRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
LabelledSequenceRenderer.paint
(Graphics2D g, SequenceRenderContext sRC) void
LabelRenderer.paint
(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
(Graphics2D g, SequenceRenderContext sp, int min, int max, SequenceRenderContext.Border border) void
MultiLineRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
OffsetRulerRenderer.paint
(Graphics2D g2, SequenceRenderContext context) void
OverlayRendererWrapper.paint
(Graphics2D g, SequenceRenderContext src) void
PaddingRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
RulerRenderer.paint
(Graphics2D g2, SequenceRenderContext context) void
SequenceRenderer.paint
(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
SequenceRendererWrapper.paint
(Graphics2D g, SequenceRenderContext src) void
SimpleLabelRenderer.paint
(Graphics2D g, SequenceRenderContext sp, int min, int max, SequenceRenderContext.Border side) void
SixFrameRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
StopRenderer.paint
(Graphics2D g, SequenceRenderContext src) void
SymbolSequenceRenderer.paint
(Graphics2D g2, SequenceRenderContext context) AbiTraceRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) AbstractBeadRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) processMouseEvent
defines the behaviour on revieving a mouse event.ArrowedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) BumpedRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) FeatureBlockSequenceRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) FeatureLabelRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) FeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) FilteringRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) GlyphFeatureRenderer.processMouseEvent
(FeatureHolder fh, SequenceRenderContext src, MouseEvent me) LabelledSequenceRenderer.processMouseEvent
(SequenceRenderContext sRC, MouseEvent mE, List path) MultiLineRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) OffsetRulerRenderer.processMouseEvent
(SequenceRenderContext context, MouseEvent me, List path) OverlayRendererWrapper.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) PaddingRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) RectangularImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) RulerRenderer.processMouseEvent
(SequenceRenderContext context, MouseEvent me, List path) SequenceRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) Produce a SequenceViewerEvent in response to a mouse gesture.SequenceRendererWrapper.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) SixFrameRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) SixFrameZiggyRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) StackedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) StopRenderer.processMouseEvent
(SequenceRenderContext src, MouseEvent me, List path) SymbolSequenceRenderer.processMouseEvent
(SequenceRenderContext context, MouseEvent me, List path) TickFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) abstract void
AbstractBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
should be overridden by the concreteBeadRenderer
.void
BeadFeatureRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
should implement rendering for this bead type only.void
EllipticalBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as simple ellipse.void
RectangularBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as simple rectangle.void
RectangularImapRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) void
RoundRectangularBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as a rectangle with rounded corners.void
AbstractBeadRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) renderFeature
draws a feature using the supplied graphics context.void
ArrowedFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
BasicFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
BasicImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) void
FeatureLabelRenderer.renderFeature
(Graphics2D g, Feature feat, SequenceRenderContext src) void
FeatureRenderer.renderFeature
(Graphics2D g2, Feature feat, SequenceRenderContext context) void
GlyphFeatureRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext src) void
RectangularImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) void
SixFrameZiggyRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext context) void
StackedFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
TickFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
ZiggyFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext context) void
ZiggyImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) void
BasicImapRenderer.renderImageMap
(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap
writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.void
ImageMapRenderer.renderImageMap
(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap
renders theFeature
as set of image map hotspots.void
RectangularImapRenderer.renderImageMap
(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap
writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.void
ZiggyImapRenderer.renderImageMap
(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap
writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.void
SixFrameRenderer.renderLocation
(Graphics2D g, SequenceRenderContext src, Location loc) Render another "exon" in the correct translation frame.SixFrameRenderer.sequenceExtentOfPixels
(SequenceRenderContext src) Constructors in org.biojava.bio.gui.sequence with parameters of type SequenceRenderContextModifierConstructorDescriptionSubSequenceRenderContext
(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range) SubSequenceRenderContext
(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)