org.biojava.bio.gui.sequence (BioJava-1.5-beta API)
Keywords: org.biojava.bio.gui.sequence package

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## 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.

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