## Package org.biojava.bio.gui.sequence

Graphical displays of biological sequences and associated annotations.

See:
Description

Interface Summary
BeadFeatureRenderer: `BeadFeatureRenderer`s 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: `ImageMapRenderer`s create strings representing `Feature`s 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: `PairwiseSequenceRenderer`s 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 `FeatureRenderer`s 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: `HotSpot`s 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 `MultiLineRender`s.
LineInfo: Encapsulates the rendering info for a single line of the display.
MultiLineRenderer: `MultiLineRenderer` is a `SequenceRenderer` which collects a number of other `SequenceRenderer`s 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 `PairwiseRenderContext`s passed to it.
PairwiseOverlayRenderer: `PairwiseOverlayRenderer` allows a list of other `PairwiseSequenceRenderer`s 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.