Graphical displays of biological sequences and associated annotations.
Interface Summary Interface Description BeadFeatureRenderer
BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.
CircularFeatureRenderer CircularRendererRender information from a CircularRendererContext onto a graphics context. CircularRendererContextA context providing information for rendering sequences into circular coordinate systems. FeatureLabelRenderer.LabelMaker FeatureRenderer FeatureSourceA closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence. ImageMap
ImageMaprepresents a collection of image map hotspots.
ImageMapRenderers create strings representing
Features suitable for use in HTML image maps.
LabelRendererThe interface for things that can render labels for a line of information about a sequence. OverlayMarkerThis is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern. PairwiseRenderContext
PairwiseRenderContextencapsulates information required for the rendering of a pair of sequences.
PairwiseSequenceRenderers render information about the relationship between two sequences.
SequenceRenderContextA context within which sequence information may be rendered. SequenceRendererThe interface for things that can render a line of information about a sequence. SequenceViewerListener SequenceViewerMotionListener
Class Summary Class Description AbiTraceRendererRenders an ABI trace file as a chromatogram graph. AbstractBeadRenderer
AbstractBeadRendereris a an abstract base class for the creation of
FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractPeptideDigestRendererA SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display. AlignmentRenderer ArrowedFeatureRendererA Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer BasicFeatureRenderer BasicImapRenderer
BasicImapRendereris a decorator for
BasicFeatureRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the
BumpedRenderer CircularFeatureFilteringRenderer CircularFeaturesRenderer CircularMLRRenders multiple renderers, each in their own concentric rings. CircularPaddedRenderer CircularRendererPanelRenders a sequence as a circle using a CircularRenderer. CrosshairRenderer
CrosshairRendererdraws a crosshair, optionally with coordinates.
EllipticalBeadRendererrenders features as simple ellipses.
FeatureBlockSequenceRendererforms a bridge between
FeatureLabelRenderer FeatureLabelRenderer.AnnotationLabelMaker FeatureLabelRenderer.SourceLabelMaker FeatureLabelRenderer.TypeLabelMaker FilteringRenderer GappedRendererA renderer that will display a gapped sequence as a discontinuous series of regions. GlyphFeatureRendererA FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter GUITools HeadlessRenderContextA stand-alone SequenceRenderContext to make it easy to render to an image. ImageMap.ClientSide
ClientSiderepresents a client-side style image map.
HotSpots represent an image map hotspot.
ServerSiderepresents a server-side style image map.
LabelledSequenceRendererRenderer which draws a track of sequence with a textual label. LabelRenderer.RenderNothing LayeredRenderer
LayeredRendererhandles the lane offsets for
LineInfoEncapsulates the rendering info for a single line of the display. MultiLineRenderer
SequenceRendererwhich collects a number of other
SequenceRenderers each of which render their own view of a
OffsetRulerRendererOffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence. OverlayRendererWrapperThis 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. PaddingRendererA renderer that adds padding before and after a delegate renderer. PairwiseDiagonalRenderer
PairwiseDiagonalRendererrenders a region of similarity between two sequences as a straight line.
PairwiseSequenceRendererand filters the
PairwiseRenderContexts passed to it.
PairwiseOverlayRendererallows a list of other
PairwiseSequenceRenderers to superimpose their output.
PairwiseSequencePanelis 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).
PairwiseRendererForwarderforward events to other renderers.
PeptideDigestRendererA concrete AbstractPeptideDigestRenderer. RectangularBeadRenderer
RectangularBeadRendererrenders features as simple rectangles.
RectangularImapRendereris a decorator for
RectangularBeadRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the
RoundRectangularBeadRendererrenders features as rectangles with rounded corners.
RulerRendererrenders numerical scales in sequence coordinates.
SecondaryStructureFeatureRendererA GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands). SequencePanelA panel that displays a Sequence. SequencePanelWrapperHandles 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.BorderThe 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 SequenceRendererWrapperAn implementation of SequenceRenderer that delegates rendering to another renderer. SequenceViewerEventAn event indicating that a mouse gesture was recognised within a widget that renders sequences. SequenceViewerMotionSupport SequenceViewerSupport SimpleLabelRenderer SixFrameRendererClass that handles drawing in six frames for other classes. SixFrameZiggyRendererA feature renderer that computes the data necessary to render multi-exon transcripts without CDS data. StackedFeatureRendererAllows 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. StopRendererCompute sites of stop codons. SubCircularRendererContextA renderer context that allows some or all properties of another context to be over-ridden. SubPairwiseRenderContext
SubPairwiseRenderContextis a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
SubSequenceRenderContextAllows a new renderer to "wrap" another one, replacing one or more values. SymbolSequenceRenderer
SymbolSequenceRendererrenders symbols of a
TranslatedSequencePanelis a panel that displays a Sequence.
ZiggyFeatureRendererA feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags. ZiggyImapRenderer
ZiggyImapRendereris a decorator for
ZiggyFeatureRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the