Package org.biojava.bio.gui.sequence

Graphical displays of biological sequences and associated annotations.

Interface Summary

Interface	Description
BeadFeatureRenderer	BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.
CircularFeatureRenderer
CircularRenderer	Render information from a CircularRendererContext onto a graphics context.
CircularRendererContext	A context providing information for rendering sequences into circular coordinate systems.
FeatureLabelRenderer.LabelMaker
FeatureRenderer
FeatureSource	A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
ImageMap	ImageMap represents a collection of image map hotspots.
ImageMapRenderer	ImageMapRenderers create strings representing Features suitable for use in HTML image maps.
LabelRenderer	The interface for things that can render labels for a line of information about a sequence.
OverlayMarker	This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern.
PairwiseRenderContext	PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences.
PairwiseSequenceRenderer	PairwiseSequenceRenderers render information about the relationship between two sequences.
SequenceRenderContext	A context within which sequence information may be rendered.
SequenceRenderer	The interface for things that can render a line of information about a sequence.
SequenceViewerListener
SequenceViewerMotionListener

Class Summary

Class	Description
AbiTraceRenderer	Renders an ABI trace file as a chromatogram graph.
AbstractBeadRenderer	AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractPeptideDigestRenderer	A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AlignmentRenderer
ArrowedFeatureRenderer	A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
BasicFeatureRenderer
BasicImapRenderer	BasicImapRenderer is a decorator for BasicFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the BasicFeatureRenderer.
BumpedRenderer
CircularFeatureFilteringRenderer
CircularFeaturesRenderer
CircularMLR	Renders multiple renderers, each in their own concentric rings.
CircularPaddedRenderer
CircularRendererPanel	Renders a sequence as a circle using a CircularRenderer.
CrosshairRenderer	CrosshairRenderer draws a crosshair, optionally with coordinates.
EllipticalBeadRenderer	EllipticalBeadRenderer renders features as simple ellipses.
FeatureBlockSequenceRenderer	FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
FeatureLabelRenderer
FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.SourceLabelMaker
FeatureLabelRenderer.TypeLabelMaker
FilteringRenderer
GappedRenderer	A renderer that will display a gapped sequence as a discontinuous series of regions.
GlyphFeatureRenderer	A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
GUITools
HeadlessRenderContext	A stand-alone SequenceRenderContext to make it easy to render to an image.
ImageMap.ClientSide	ClientSide represents a client-side style image map.
ImageMap.HotSpot	HotSpots represent an image map hotspot.
ImageMap.ServerSide	ServerSide represents a server-side style image map.
LabelledSequenceRenderer	Renderer which draws a track of sequence with a textual label.
LabelRenderer.RenderNothing
LayeredRenderer	LayeredRenderer handles the lane offsets for MultiLineRenders.
LineInfo	Encapsulates the rendering info for a single line of the display.
MultiLineRenderer	MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.
OffsetRulerRenderer	OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
OverlayRendererWrapper	This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer.
PaddingRenderer	A renderer that adds padding before and after a delegate renderer.
PairwiseDiagonalRenderer	PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.
PairwiseFilteringRenderer	PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.
PairwiseOverlayRenderer	PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
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).
PairwiseSequenceRenderer.PairwiseRendererForwarder	PairwiseRendererForwarder forward events to other renderers.
PeptideDigestRenderer	A concrete AbstractPeptideDigestRenderer.
RectangularBeadRenderer	RectangularBeadRenderer renders features as simple rectangles.
RectangularImapRenderer	RectangularImapRenderer is a decorator for RectangularBeadRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the RectangularBeadRenderer.
RoundRectangularBeadRenderer	RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
RulerRenderer	RulerRenderer renders numerical scales in sequence coordinates.
SecondaryStructureFeatureRenderer	A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
SequencePanel	A panel that displays a Sequence.
SequencePanelWrapper	Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.
SequencePoster	Deprecated. This doesn't handle loads of stuff.
SequenceRenderContext.Border	The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.
SequenceRenderer.RendererForwarder
SequenceRendererWrapper	An implementation of SequenceRenderer that delegates rendering to another renderer.
SequenceViewerEvent	An event indicating that a mouse gesture was recognised within a widget that renders sequences.
SequenceViewerMotionSupport
SequenceViewerSupport
SimpleLabelRenderer
SixFrameRenderer	Class that handles drawing in six frames for other classes.
SixFrameZiggyRenderer	A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
StackedFeatureRenderer	Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout.
StopRenderer	Compute sites of stop codons.
SubCircularRendererContext	A renderer context that allows some or all properties of another context to be over-ridden.
SubPairwiseRenderContext	SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
SubSequenceRenderContext	Allows a new renderer to "wrap" another one, replacing one or more values.
SymbolSequenceRenderer	SymbolSequenceRenderer renders symbols of a SymbolList.
TickFeatureRenderer
TranslatedSequencePanel	TranslatedSequencePanel is a panel that displays a Sequence.
ZiggyFeatureRenderer	A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.
ZiggyImapRenderer	ZiggyImapRenderer is a decorator for ZiggyFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the ZiggyFeatureRenderer.