Package org.biojava.bio.gui.sequence
package org.biojava.bio.gui.sequence
Graphical displays of biological sequences and associated annotations.
-
ClassDescriptionRenders an ABI trace file as a chromatogram graph.
AbstractBeadRendereris a an abstract base class for the creation ofFeatureRenderers which use a 'string of beads' metaphor for displaying features.A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRendererBasicImapRendereris a decorator forBasicFeatureRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by theBasicFeatureRenderer.BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.Renders multiple renderers, each in their own concentric rings.Render information from a CircularRendererContext onto a graphics context.A context providing information for rendering sequences into circular coordinate systems.Renders a sequence as a circle using a CircularRenderer.CrosshairRendererdraws a crosshair, optionally with coordinates.EllipticalBeadRendererrenders features as simple ellipses.FeatureBlockSequenceRendererforms a bridge betweenSequencerendering andFeaturerendering.A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.A renderer that will display a gapped sequence as a discontinuous series of regions.A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilterA stand-alone SequenceRenderContext to make it easy to render to an image.ImageMaprepresents a collection of image map hotspots.ClientSiderepresents a client-side style image map.HotSpots represent an image map hotspot.ServerSiderepresents a server-side style image map.ImageMapRenderers create strings representingFeatures suitable for use in HTML image maps.Renderer which draws a track of sequence with a textual label.The interface for things that can render labels for a line of information about a sequence.LayeredRendererhandles the lane offsets forMultiLineRenders.Encapsulates the rendering info for a single line of the display.MultiLineRendereris aSequenceRendererwhich collects a number of otherSequenceRenderers each of which render their own view of aSequence.OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern.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.A renderer that adds padding before and after a delegate renderer.PairwiseDiagonalRendererrenders a region of similarity between two sequences as a straight line.PairwiseFilteringRendererwraps aPairwiseSequenceRendererand filters thePairwiseRenderContexts passed to it.PairwiseOverlayRendererallows a list of otherPairwiseSequenceRenderers to superimpose their output.PairwiseRenderContextencapsulates information required for the rendering of a pair of sequences.APairwiseSequencePanelis 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).PairwiseSequenceRenderers render information about the relationship between two sequences.PairwiseRendererForwarderforward events to other renderers.A concrete AbstractPeptideDigestRenderer.RectangularBeadRendererrenders features as simple rectangles.RectangularImapRendereris a decorator forRectangularBeadRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by theRectangularBeadRenderer.RoundRectangularBeadRendererrenders features as rectangles with rounded corners.RulerRendererrenders numerical scales in sequence coordinates.A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).A panel that displays a Sequence.Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.Deprecated.This doesn't handle loads of stuff.A context within which sequence information may be rendered.The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.The interface for things that can render a line of information about a sequence.An implementation of SequenceRenderer that delegates rendering to another renderer.An event indicating that a mouse gesture was recognised within a widget that renders sequences.Class that handles drawing in six frames for other classes.A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.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.Compute sites of stop codons.A renderer context that allows some or all properties of another context to be over-ridden.SubPairwiseRenderContextis a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.Allows a new renderer to "wrap" another one, replacing one or more values.SymbolSequenceRendererrenders symbols of aSymbolList.TranslatedSequencePanelis a panel that displays a Sequence.A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.ZiggyImapRendereris a decorator forZiggyFeatureRendererwhich adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by theZiggyFeatureRenderer.