Package org.biojava.bio.gui.sequence

Graphical displays of biological sequences and associated annotations.

See:
          Description

Interface Summary
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
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.
 

Package org.biojava.bio.gui.sequence Description

Graphical displays of biological sequences and associated annotations.