A B C D E F G H I L M O P R S T U V X Y Z _

A

AbiTraceRenderer - Class in org.biojava.bio.gui.sequence

Renders an ABI trace file as a chromatogram graph.

AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer

AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence

AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.

AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Creates a new AbstractBeadRenderer with no delegates.

AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Creates a new AbstractBeadRenderer object.

AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence

A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.

AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

addChangeListener adds a listener for all types of change.

addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

addChangeListener adds a listener for specific types of change.

addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel

addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

addChangeListener adds a listener for all types of change.

addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

addChangeListener adds a listener for specific types of change.

addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap

addHotSpot adds a hotspot to the map.

addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide

addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide

addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Add a piece of text to this renderer's label

addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter

addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter

addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter

addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter

addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR

addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

addRenderer adds a renderer as a new track.

addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

addRenderer adds a renderer.

addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport

addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

addSequenceViewerListener adds a listener for mouse click SequenceViewerEvents.

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport

addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

addSequenceViewerMotionListener adds a listener for mouse motion SequenceViewerEvents.

AlignmentRenderer - Class in org.biojava.bio.gui.sequence

AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer

AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence

A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer

ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

ArrowGlyph - Class in org.biojava.bio.gui.glyph

A Glyph that paints an arrow shape within the bounds.

ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph

Creates a new ArrowGlyph, which is filled with the color blue by default.

ArrowGlyph(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph

Creates a new ArrowGlyph, which is filled with the given color.

ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph

This constructs an arrow in the given bounds, which is colored blue.

ArrowGlyph(Rectangle2D.Float, Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph

Constructor which sets both the size of this arrow and its color.

B

BarLogoPainter - Class in org.biojava.bio.gui

A logo painter that paints in bars.

BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter

BasicFeatureRenderer - Class in org.biojava.bio.gui.sequence

BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer

BasicImapRenderer - Class in org.biojava.bio.gui.sequence

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.

BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.BasicImapRenderer

Creates a new BasicImapRenderer.

beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

BeadFeatureRenderer - Interface in org.biojava.bio.gui.sequence

BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.

beadFill - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

beadOutline - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

beadStroke - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

BlockPainter - Interface in org.biojava.bio.gui

Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

BumpedRenderer - Class in org.biojava.bio.gui.sequence

BumpedRenderer() - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer

BumpedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer

BumpedRenderer(SequenceRenderer, int, int) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer

C

calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel

calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap

CIRCLE indicates a circular image map hotspot.

CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence

CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer

CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence

CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence

CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

CircularMLR - Class in org.biojava.bio.gui.sequence

Renders multiple renderers, each in their own concentric rings.

CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR

CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence

CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer

CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer

CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer

CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer

CircularRenderer - Interface in org.biojava.bio.gui.sequence

Render information from a CircularRendererContext onto a graphics context.

CircularRendererContext - Interface in org.biojava.bio.gui.sequence

A context providing information for rendering sequences into circular coordinate systems.

CircularRendererPanel - Class in org.biojava.bio.gui.sequence

Renders a sequence as a circle using a CircularRenderer.

CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel

clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

clearRenderers removes all renderers from this renderer.

clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

clearRenderers removes all the renderers.

ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide

Creates a new ClientSide image map.

containsFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns true if the given FeatureFilter is already contained in this renderer.

contextForLabel(SequenceRenderContext, String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree

Labels Sequence objects with their name, Annotations with the tag Annotations, Features with the tag Features and other objects with the toString value.

coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer

coordinateDisplayOn toggles the display of sequence coordinates.

createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools

createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools

createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer

CrosshairRenderer - Class in org.biojava.bio.gui.sequence

CrosshairRenderer draws a crosshair, optionally with coordinates.

CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer

Creates a new CrosshairRenderer in light grey with coordinates displayed.

CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer

Creates a new CrosshairRenderer of the specified colour, with coordinates displayed.

D

delegates - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer

DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Constant DEPTH indicating a change to the depth of the renderer.

DEPTH - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer

DIGEST - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer

dimensionRatio - Variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Constant DISPLACEMENT indicating a change to the Y-axis displacement of the features.

DistributionLogo - Class in org.biojava.bio.gui

The GUI component for rendering a DistributionLogo.

DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo

Create a new DistributionLogo object.

DNAStyle - Class in org.biojava.bio.gui

A simple implementation of SymbolStyle optimized for DNA.

DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle

doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

doRefreshRenderers() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

draws required bar in correct translation frame.

E

EllipticalBeadRenderer - Class in org.biojava.bio.gui.sequence

EllipticalBeadRenderer renders features as simple ellipses.

EllipticalBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

Creates a new EllipticalBeadRenderer object with the default settings.

EllipticalBeadRenderer(double, double, Paint, Paint, Stroke, double) - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

Creates a new EllipticalBeadRenderer.

entropy(Distribution, Symbol) - Static method in class org.biojava.bio.gui.DistributionLogo

Calculate the information content of a symbol in bits.

equals(Object) - Method in class org.biojava.bio.gui.sequence.SequencePanel

F

FEATURE_COLLAPSING - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

FEATURE_RENDERER - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

FeatureBlockSequenceRenderer - Class in org.biojava.bio.gui.sequence

FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.

FeatureBlockSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

Creates a new FeatureBlockSequenceRenderer which uses a BasicFeatureRenderer as its renderer.

FeatureBlockSequenceRenderer(FeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

Creates a new FeatureBlockSequenceRenderer which uses the specified FeatureRenderer.

FeatureLabelRenderer - Class in org.biojava.bio.gui.sequence

FeatureLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer

FeatureLabelRenderer(FeatureLabelRenderer.LabelMaker) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer

FeatureLabelRenderer.AnnotationLabelMaker - Class in org.biojava.bio.gui.sequence

FeatureLabelRenderer.LabelMaker - Interface in org.biojava.bio.gui.sequence

FeatureLabelRenderer.SourceLabelMaker - Class in org.biojava.bio.gui.sequence

FeatureLabelRenderer.TypeLabelMaker - Class in org.biojava.bio.gui.sequence

FeatureRenderer - Interface in org.biojava.bio.gui.sequence

FeatureSource - Interface in org.biojava.bio.gui.sequence

A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.

FeatureTree - Class in org.biojava.bio.gui

FeatureTree is GUI tree to display the features and annotations of the sequences in a SequenceDB Nested Features are displayed as expandable leaves.

FeatureTree() - Constructor for class org.biojava.bio.gui.FeatureTree

Create a new FeatureTree

FILL - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Constant FILL indicating a change to the fill of the features.

FILL - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

FILL - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer

fillPaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle

fillPaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle

fillPaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle

fillPaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle

Return the fill paint for a symbol.

FILTER - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer

filter - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer

FILTER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

Constant FILTER indicating a change to the renderer's filter.

filter - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

filter is the filter applied to both FeatureHolders.

FilteringRenderer - Class in org.biojava.bio.gui.sequence

FilteringRenderer() - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer

FilteringRenderer(SequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer

fireMouseClicked(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport

fireMouseDragged(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport

fireMouseMoved(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport

fireMousePressed(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport

fireMouseReleased(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport

firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.StackedLogoPainter

firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.StackedLogoPainter

firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.StackedLogoPainter

firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.StackedLogoPainter

firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter

firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter

firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter

firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.TextLogoPainter

fList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

G

GappedRenderer - Class in org.biojava.bio.gui.sequence

A renderer that will display a gapped sequence as a discontinuous series of regions.

GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer

GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer

generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder

generateEvent generates events in response to layout change and repaint requests.

generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

Gets the Alignment - one of LEADING, TRAILING or CENTER.

getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle

getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Return the angle for an index into a sequence.

getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadDepth returns the depth of a single bead produced by this renderer.

getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

getBeadDepth returns the depth of a single bead produced by the renderer.

getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadDisplacement returns the displacement of beads from the centre line of the renderer.

getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

getBeadDisplacement returns the displacement of beads from the centre line of the renderer.

getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadFill returns the bead fill paint.

getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadOutline returns the bead outline paint.

getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getBeadStroke returns the bead outline stroke.

getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo

getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext

getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph

getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph

getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

getBounds() - Method in interface org.biojava.bio.gui.LogoContext

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getChangeSupport lazily instantiates a helper for change listeners.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getChangeSupport lazily instantiates a helper for change listeners.

getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

Returns true if this class collapses to zero depth when there are no visible features.

getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

getCoordinates returns the hotspot coordinates.

getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer

getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR

getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer

getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer

Get the depth needed for this renderer.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the depth property of this class.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

getDepth returns the total depth of a list of SequenceRenderers.

getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

getDepth calculates the depth required by this renderer to display its beads.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Retrieve the depth of this renderer when rendering src.

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

getDimensionRatio returns the maximum ratio of long dimension to short dimension of the bead.

getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getDirection returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the current rendering direction.

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the current rendering direction.

getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getDirection returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo

Retrieve the currently rendered dist.

getDistribution() - Method in interface org.biojava.bio.gui.LogoContext

getFeatureFilter(int) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the ith FeatureFilter in this renderer.

getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource

getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getFeatureRenderer returns the currently active renderer.

getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

The features to render.

getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getFeatures returns all of the Features belonging to the currently rendered Sequence.

getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel

getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

The features to render.

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getFeatures returns all of the Features belonging to the currently rendered Sequence.

getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Get the background color of the label area.

getFillPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

Returns the paint properties of this glyph.

getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getFilter returns the current filter.

getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the Font attribute of the SequenceRenderContext object

getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getGlyphForFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Returns the Glyph object which is assigned to the given feature filter.

getGraphics() - Method in interface org.biojava.bio.gui.LogoContext

getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

getHeightScaling returns the state of the height scaling policy.

getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getHeightScaling returns the state of the height scaling policy.

getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

getImageMap returns the current image map.

getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

getImageMap returns the current image map.

getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

getImageMap returns the current image map.

getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Calculate the position in the sequence relating to the angle.

getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getLeadingBorder returns the leading border of the primary sequence.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.

getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the LeadingBorder attribute of the SequenceRenderContext object.

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getLeadingBorder returns the leading border.

getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the number of lines that the sequence will be rendered over.

getLogoFont() - Method in class org.biojava.bio.gui.TextBlock

Retrieve the current font.

getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter

Retrieve the current font.

getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo

Retrieve the current logo painter.

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

getMinimumLeader returns the maximum value of getMinimumLeader() for a list of SequenceRenderers.

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Retrieve the minimum leading distance for this renderer when rendering src.

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer

getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

getMinimumTrailer returns the maximum value of getMinimumTrailer() for a list of SequenceRenderers.

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Retrieve the minimum trailing distance for this renderer when rendering src.

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer

getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer

Retrieve the minimum space required to render the label.

getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing

getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

getMouseEvent() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent

Get the mouse event that caused this.

getOffset() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Get the angle through which the origin of the sequence is rotated through.

getOffset() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

getOffset() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getOuterPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

Returns the paint properties of the outer line of this glyph.

getOutline() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

getOutline() - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer

getOutline returns the colour used to draw the lines.

getOutline() - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

getOutline returns the colour used to draw the lines.

getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

getOutline() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

getOutline() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

getPadding() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

Retrieve the current padding.

getPaint() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

getPaint() - Method in class org.biojava.bio.gui.glyph.TurnGlyph

getPath() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent

Get the list of SequenceRenderer instances that were passed through to produce this event

getPos() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent

Get the offset within the sequence - the symbol index.

getRadius() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

Get the current radius at which data should be rendered.

getRadius() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

getRadius() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getRange() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getRange returns a RangeLocation representing the region of the sequence currently being rendered.

getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanel

getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getRange() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

The range of the SymbolList to render.

getRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getRange() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getRange() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getRange returns a RangeLocation representing the region of the sequence currently being rendered.

getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

getRanges() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getRecurse returns the recursion flag of the filter.

getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

getRenderer() - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getRenderer return the current renderer.

getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getRenderer returns the current PairwiseSequenceRenderer.

getRenderer() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getRenderer() - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

getRenderer() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getRenderer returns the current SequenceRenderer.

getRenderingHints() - Method in class org.biojava.bio.gui.DistributionLogo

getRenderingHints() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers.

getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanel

getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getRenderingHints returns the RenderingHints currently being used by the Graphics2D instances of delegate renderers.

getScale() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getScale() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getScale returns the scale in pixels per Symbol.

getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the current scale.

getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getScale() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the current scale.

getScale() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the scale as pixels per Symbol

getScale() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getScale() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getScale() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getScale returns the scale in pixels per Symbol.

getSecondaryDirection() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

getSecondaryDirection returns the direction in which the secondary sequence is rendered.

getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondaryDirection returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL.

getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getSecondaryFeatures() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

getSecondaryFeatures returns the features on the secondary sequence.

getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.

getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

getSecondaryRange returns the range of the secondary sequence currently rendered.

getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondaryRange returns a RangeLocation representing the region of the secondary sequence currently being rendered.

getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondarySequence returns the entire secondary Sequence currently being rendered.

getSecondarySymbols() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

getSecondarySymbols returns the symbols of the secondary sequence.

getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.

getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSecondarySymbolTranslation returns the current translation in Symbols which will be applied when rendering.

getSequence() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

getSequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSequence returns the entire Sequence currently being rendered.

getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanel

getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getSequence() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getSequence returns the entire Sequence currently being rendered.

getSequenceOffset() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getShape(List, List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils

getShape(List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils

getShape(int[], int[]) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils

getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

Gets the current size of the border in pixels.

getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the current spacer value

getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle

getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle

getStyle() - Method in class org.biojava.bio.gui.DistributionLogo

Retrieve the current style.

getStyle() - Method in interface org.biojava.bio.gui.LogoContext

getSubContext(PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

getSubContext creates a new context which has FeatureHolders filtered using the current filter.

getSymbols() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext

The SymbolList that is currently rendered by this context.

getSymbols() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getSymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSymbols returns all of the Symbols belonging to the currently rendered Sequence.

getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the currently rendered SymbolList

getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the currently rendered SymbolList

getSymbols() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

The SymbolList that is currently rendered by this SequenceRenderContext.

getSymbols() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext

getSymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getSymbols() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getSymbols() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getSymbols returns all of the Symbols belonging to the currently rendered Sequence.

getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.

getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getSymbolTranslation returns the current translation in Symbols which will be applied when rendering.

getTarget() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent

Get the Object that was the target of the mouse gesture or null if the mouse is not gesturing over any recognizable rendered object.

getTextColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Get the color of the label text

getTickDirection() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo

getTrace() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

getTrackLayout() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getTrailingBorder returns the trailing border of the primary sequence.

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel

Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.

getTrailingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Gets the TrailingBorder attribute of the SequenceRenderContext object.

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getTrailingBorder returns the trailing border.

getTrailingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

getType() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

getType returns the type of hotspot.

getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

getURL returns the hotspot URL.

getUserObject() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

getUserObject returns the current user object (or null).

getVisibleRange(SequenceRenderContext, Graphics2D) - Static method in class org.biojava.bio.gui.sequence.GUITools

getVisibleRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getVisibleSecondarySymbolCount returns the maximum number of secondary Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.

getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the PairwiseSequencePanel at the current scale.

getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

getVisibleSymbolCount returns the maximum number of Symbols which can be rendered in the visible area (excluding all borders) of the TranslatedSequencePanel at the current scale.

getWrap() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

getWrap() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

getWrapIncrement() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

gList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Glyph - Interface in org.biojava.bio.gui.glyph

The Glyph interface for painting a shape within bounds

GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence

A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter

GlyphFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

GlyphUtils - Class in org.biojava.bio.gui.glyph

Utils class used by Glyph implementors.

graphicsToSecondarySequence(double) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.

graphicsToSecondarySequence(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

graphicsToSequence converts a graphical position to a sequence index.

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

graphicsToSequence converts a graphical position to a sequence index.

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePanel

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Converts a graphical position into a sequence coordinate.

graphicsToSequence(Point2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Converts a graphical position into a sequence coordinate.

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

graphicsToSequence converts a graphical position to a sequence index.

graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

graphicsToSequence converts a graphical position to a sequence index.

GUITools - Class in org.biojava.bio.gui.sequence

H

hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel

hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

hashCode() - Method in class org.biojava.bio.gui.sequence.SequencePanel

hasListeners() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

hasListeners() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

hasListeners() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

hasListeners() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

hasListeners returns true if there are active listeners for BioJava events.

hasListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel

hasListeners() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

hasListeners returns true if there are active listeners for BioJava events.

hasListeners(String) - Method in class org.biojava.bio.gui.StackedLogoPainter

hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter

HeadlessRenderContext - Class in org.biojava.bio.gui.sequence

A stand-alone SequenceRenderContext to make it easy to render to an image.

HeadlessRenderContext(Sequence, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.HeadlessRenderContext

HEIGHTSCALING - Static variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

Constant HEIGHTSCALING indicating a change to the feature height scaling policy.

HelixGlyph - Class in org.biojava.bio.gui.glyph

A Glyph that paints a Helix within the bounds

HelixGlyph() - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph

HelixGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph

HotSpot(String, URL, Integer[]) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot

Creates a new HotSpot with a null user object.

HotSpot(String, URL, Integer[], Object) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot

Creates a new HotSpot.

hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide

hotSpots() - Method in interface org.biojava.bio.gui.sequence.ImageMap

hotSpots iterates over the hotspots in the map

hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide

I

ImageMap - Interface in org.biojava.bio.gui.sequence

ImageMap represents a collection of image map hotspots.

ImageMap.ClientSide - Class in org.biojava.bio.gui.sequence

ClientSide represents a client-side style image map.

ImageMap.HotSpot - Class in org.biojava.bio.gui.sequence

HotSpots represent an image map hotspot.

ImageMap.ServerSide - Class in org.biojava.bio.gui.sequence

ServerSide represents a server-side style image map.

ImageMapRenderer - Interface in org.biojava.bio.gui.sequence

ImageMapRenderers create strings representing Features suitable for use in HTML image maps.

initComponents() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

INSTANCE - Static variable in class org.biojava.bio.gui.sequence.LayeredRenderer

Static LayeredRenderer INSTANCE used by MultiLineRenderers.

isActive() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

isActive returns true if both the Sequences to be rendered and the PairwiseHomologyRenderer are not null.

isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanel

isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

isActive() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

isActive() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

isActive returns true if both the Sequence to be rendered and the SequenceRenderer are not null.

isScaleByInformation() - Method in class org.biojava.bio.gui.DistributionLogo

isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel

isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

L

LABEL - Static variable in class org.biojava.bio.gui.sequence.AlignmentRenderer

LABEL - Static variable in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

LABEL_MAKER - Static variable in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

LabelledSequenceRenderer - Class in org.biojava.bio.gui.sequence

Renderer which draws a track of sequence with a textual label.

LabelledSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Creates new LabelledSequenceRenderer with default width and depth;

LabelledSequenceRenderer(String, SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

LabelledSequenceRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Creates new LabelledSequenceRenderer with the specified width and depth.

LabelRenderer - Interface in org.biojava.bio.gui.sequence

The interface for things that can render labels for a line of information about a sequence.

LabelRenderer.RenderNothing - Class in org.biojava.bio.gui.sequence

LANE - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

layer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

LayeredRenderer - Class in org.biojava.bio.gui.sequence

LayeredRenderer handles the lane offsets for MultiLineRenders.

LayeredRenderer() - Constructor for class org.biojava.bio.gui.sequence.LayeredRenderer

LAYOUT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext

line - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

line is the line to be drawn for each feature.

LineInfo - Class in org.biojava.bio.gui.sequence

Encapsulates the rendering info for a single line of the display.

LineInfo() - Constructor for class org.biojava.bio.gui.sequence.LineInfo

LogoContext - Interface in org.biojava.bio.gui

LogoPainter - Interface in org.biojava.bio.gui

The interface for something that will draw the sequence logo for a state.

M

makeContext(SequenceRenderContext, RangeLocation) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

makeLabel(Feature) - Method in interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker

makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker

makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker

mouseClicked(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener

mouseDragged(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener

mouseMoved(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener

mousePressed(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener

mouseReleased(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener

MultiLineRenderer - Class in org.biojava.bio.gui.sequence

MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.

MultiLineRenderer() - Constructor for class org.biojava.bio.gui.sequence.MultiLineRenderer

O

OFFSET - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

OffsetRulerRenderer - Class in org.biojava.bio.gui.sequence

OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.

OffsetRulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer

OffsetRulerRenderer(int, int) - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer

org.biojava.bio.gui - package org.biojava.bio.gui

Graphical interfaces for biojava objects.

org.biojava.bio.gui.glyph - package org.biojava.bio.gui.glyph

Glyphs implementations that draw shapes into SequenceRenderers

org.biojava.bio.gui.sequence - package org.biojava.bio.gui.sequence

Graphical displays of biological sequences and associated annotations.

org.biojava.bio.gui.sequence.tracklayout - package org.biojava.bio.gui.sequence.tracklayout

Classes for the handling of the layout of a WrappedSequencePanel.

OUTLINE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Constant OUTLINE indicating a change to the outline paint of the features.

OUTLINE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

OUTLINE - Static variable in class org.biojava.bio.gui.sequence.CrosshairRenderer

Constant OUTLINE indicating a change to the crosshair paint.

OUTLINE - Static variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

Constant OUTLINE indicating a change to the fill of the features.

outline - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

outline is the line colour.

OUTLINE - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer

outlinePaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle

outlinePaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle

outlinePaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle

outlinePaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle

Return the outline paint for a symbol.

OverlayMarker - Interface in org.biojava.bio.gui.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.

OverlayRendererWrapper - Class in org.biojava.bio.gui.sequence

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.

OverlayRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper

OverlayRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper

P

PADDING - Static variable in class org.biojava.bio.gui.sequence.PaddingRenderer

Event type for when the size of the padding changes.

PaddingRenderer - Class in org.biojava.bio.gui.sequence

A renderer that adds padding before and after a delegate renderer.

PaddingRenderer() - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer

Build a new PaddingRenderer with zero padding.

PaddingRenderer(SequenceRenderer, double) - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer

Build a new PaddingRenderer that wraps renderer and has padding depth padding.

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer

paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR

paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer

paint(Graphics2D, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer

Paint this renderer.

paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer

Render a label for the information for sp to g.

paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing

paint(Graphics2D, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

paint renders the feature as a simple line.

paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

paint applies all renderers in the order in which they were added.

paint(Graphics2D, PairwiseRenderContext) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer

paints some or all of the information about the sequence pair.

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

paint(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

paint(Graphics2D, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer

paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in interface org.biojava.bio.gui.BlockPainter

paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.PlainBlock

paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.TextBlock

paintComponent(Graphics) - Method in class org.biojava.bio.gui.DistributionLogo

Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanel

Paint this component.

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Paint this component.

paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

paintComponent paints this component.

paintLogo(LogoContext) - Method in class org.biojava.bio.gui.BarLogoPainter

paintLogo(LogoContext) - Method in interface org.biojava.bio.gui.LogoPainter

Render the state from sl onto the graphics object g.

paintLogo(LogoContext) - Method in class org.biojava.bio.gui.StackedLogoPainter

paintLogo(LogoContext) - Method in class org.biojava.bio.gui.TextLogoPainter

PairwiseDiagonalRenderer - Class in org.biojava.bio.gui.sequence

PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.

PairwiseDiagonalRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

Creates a new PairwiseDiagonalRenderer which will draw black lines.

PairwiseDiagonalRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

Creates a new PairwiseDiagonalRenderer which will draw lines using the specified Paint.

PairwiseFilteringRenderer - Class in org.biojava.bio.gui.sequence

PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.

PairwiseFilteringRenderer(PairwiseSequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

Creates a new PairwiseFilteringRenderer which uses a filter which accepts all features.

PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

Creates a new PairwiseFilteringRenderer.

PairwiseOverlayRenderer - Class in org.biojava.bio.gui.sequence

PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.

PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

Creates a new, empty PairwiseOverlayRenderer.

PairwiseRenderContext - Interface in org.biojava.bio.gui.sequence

PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences.

PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder

Creates a new PairwiseRendererForwarder.

PairwiseSequencePanel - Class in org.biojava.bio.gui.sequence

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).

PairwiseSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequencePanel

Creates a new PairwiseSequencePanel with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).

PairwiseSequenceRenderer - Interface in org.biojava.bio.gui.sequence

PairwiseSequenceRenderers render information about the relationship between two sequences.

PairwiseSequenceRenderer.PairwiseRendererForwarder - Class in org.biojava.bio.gui.sequence

PairwiseRendererForwarder forward events to other renderers.

pcs - Variable in class org.biojava.bio.gui.sequence.SequencePanel.Border

pcs - Variable in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

PeptideDigestRenderer - Class in org.biojava.bio.gui.sequence

A concrete AbstractPeptideDigestRenderer.

PeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer

PeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer

PeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer

PlainBlock - Class in org.biojava.bio.gui

A painter that just draws a block (or bar).

PlainBlock() - Constructor for class org.biojava.bio.gui.PlainBlock

PlainStyle - Class in org.biojava.bio.gui

A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling.

PlainStyle() - Constructor for class org.biojava.bio.gui.PlainStyle

PlainStyle(Paint, Paint) - Constructor for class org.biojava.bio.gui.PlainStyle

point - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer

point is the current location (in sequence coordinates) of the crosshair in the X and Y sequences.

POLY - Static variable in interface org.biojava.bio.gui.sequence.ImageMap

POLY indicates a polygonal image map hotspot.

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

processMouseEvent defines the behaviour on revieving a mouse event.

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer

processMouseEvent processes any MouseEvents directed to the renderer.

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

processMouseEvent(List, MouseEvent, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

processMouseEvent acts on a mouse gesture.

processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.

processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer

processMouseEvent produces a SequenceViewerEvent in response to a mouse gesture.

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.RulerRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer

Produce a SequenceViewerEvent in response to a mouse gesture.

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.StopRenderer

processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

R

RATIO - Static variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

Constant RATIO indicating a change to the minimum allowed ratio of long axis to short axis of the features.

RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap

RECT indicates a rectangular image map hotspot.

rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

RectangleGlyph - Class in org.biojava.bio.gui.glyph

A Glyph that paints a rectangle shape within the bounds.

RectangleGlyph() - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph

RectangleGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph

RectangleGlyph(Paint) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph

RectangularBeadRenderer - Class in org.biojava.bio.gui.sequence

RectangularBeadRenderer renders features as simple rectangles.

RectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer

Creates a new RectangularBeadRenderer with the default settings.

RectangularBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer

Creates a new RectangularBeadRenderer.

RectangularImapRenderer - Class in org.biojava.bio.gui.sequence

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.

RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.RectangularImapRenderer

Creates a new RectangularImapRenderer.

RECURSE - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer

recurse - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer

RECURSE - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

Constant RECURSE indicating a change to the renderer's filter recursion flag.

recurse - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

recurse indicates whether the filter should recurse through any subfeatures.

refreshSequencePanels() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

removeChangeListener removes a listener.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

removeChangeListener removes a listener.

removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel

removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

removeChangeListener removes a listener.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

removeChangeListener removes a listener.

removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

removeDelegateRenderer removes any association of the given OptimizableFilter with a BeadFeatureRenderer.

removeFilterWithGlyph(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

removeLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Remove a piece of text from the label

removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter

removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter

removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter

removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter

removeRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR

removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

removeRenderer removes a renderer.

removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

removeRenderer removes a renderer.

removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport

removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

removeSequenceViewerListener removes a listener for mouse click SequenceViewerEvents.

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport

removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

addSequenceViewerMotionListener removes a listener for mouse motion SequenceViewerEvents.

render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

render(Graphics2D) - Method in interface org.biojava.bio.gui.glyph.Glyph

render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.HelixGlyph

render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TurnGlyph

render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

renderBead should be overridden by the concrete BeadRenderer.

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

renderBead should implement rendering for this bead type only.

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

renderBead renders features as simple ellipse.

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

renderBead renders features as simple rectangle.

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

renderBead renders features as a rectangle with rounded corners.

RENDERER - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

RENDERER - Static variable in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

Constant RENDERER indicating a change to the renderer.

RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.

RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePanel

RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

RENDERER - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

Constant RENDERER is a ChangeType which indicates a change to the renderer, requiring a layout update.

RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder

RENDERERS - Static variable in class org.biojava.bio.gui.sequence.MultiLineRenderer

renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer

RENDERERS - Static variable in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

Constant RENDERERS indicating a change to the renderers handled by the overlay.

RENDERERS - Static variable in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

renderFeature draws a feature using the supplied graphics context.

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

renderFeature(Graphics2D, Feature, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.

renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.ImageMapRenderer

renderImageMap renders the Feature as set of image map hotspots.

renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

renderImageMap writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.

renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.

renderLocation(Graphics2D, SequenceRenderContext, Location) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

Render another "exon" in the correct translation frame.

RenderNothing() - Constructor for class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing

REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext

resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count.

resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanel

resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

resizeAndValidate sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count.

RoundRectangularBeadRenderer - Class in org.biojava.bio.gui.sequence

RoundRectangularBeadRenderer renders features as rectangles with rounded corners.

RoundRectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

Creates a new RoundRectangularBeadRenderer object with the default settings.

RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double) - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer

Creates a new RoundRectangularBeadRenderer.

RulerRenderer - Class in org.biojava.bio.gui.sequence

RulerRenderer renders numerical scales in sequence coordinates.

RulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer

Creates a new RulerRenderer with the default setting of ticks pointing downwards.

RulerRenderer(int) - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer

Creates a new RulerRenderer with the specified tick direction.

S

scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

secondarySequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext

secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.

secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

secondarySequenceToGraphics converts a sequence index to a graphical position.

secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

SecondaryStructureFeatureRenderer - Class in org.biojava.bio.gui.sequence

A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).

SecondaryStructureFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer

seqPanels - Variable in class org.biojava.bio.gui.sequence.SequencePanelWrapper

sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

SequencePanel - Class in org.biojava.bio.gui.sequence

A panel that displays a Sequence.

SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel

Create a new SequencePanel.

SequencePanel.Border - Class in org.biojava.bio.gui.sequence

SequencePanelWrapper - Class in org.biojava.bio.gui.sequence

Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.

SequencePanelWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequencePanelWrapper

Creates a new instance of WrappedSequencePanel

SequencePoster - Class in org.biojava.bio.gui.sequence

Deprecated.

This doesn't handle loads of stuff. Use SequencePoster.

SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Create a new SeqeuncePanel.

SequencePoster.Border - Class in org.biojava.bio.gui.sequence

Deprecated.

SequenceRenderContext - Interface in org.biojava.bio.gui.sequence

A context within which sequence information may be rendered.

SequenceRenderContext.Border - Class in org.biojava.bio.gui.sequence

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 - Interface in org.biojava.bio.gui.sequence

The interface for things that can render a line of information about a sequence.

SequenceRenderer.RendererForwarder - Class in org.biojava.bio.gui.sequence

SequenceRendererWrapper - Class in org.biojava.bio.gui.sequence

An implementation of SequenceRenderer that delegates rendering to another renderer.

SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper

Create a new renderer with no wrapped renderer.

SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper

Create a new wrapper with a wrapped renderer

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

sequenceToGraphics converts a sequence index to a graphical position.

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

sequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext

Converts a sequence index into a graphical coordinate.

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext

sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

sequenceToGraphics converts a sequence index to a graphical position.

SequenceViewerEvent - Class in org.biojava.bio.gui.sequence

An event indicating that a mouse gesture was recognised within a widget that renders sequences.

SequenceViewerEvent(Object, Object, int, MouseEvent, List) - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerEvent

Construct a SequenceViewerEvent with the given source, target, mouseEvent and path.

SequenceViewerListener - Interface in org.biojava.bio.gui.sequence

SequenceViewerMotionListener - Interface in org.biojava.bio.gui.sequence

SequenceViewerMotionSupport - Class in org.biojava.bio.gui.sequence

SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport

SequenceViewerSupport - Class in org.biojava.bio.gui.sequence

SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport

ServerSide() - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ServerSide

Creates a new ServerSide image map.

setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border

setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border

Deprecated.

setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

Sets the Alignment attribute of the Border object.

setArrowHeadSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

setBeadDepth(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setBeadDepth sets the depth of a single bead produced by this renderer.

setBeadDisplacement(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setBeadDisplacement sets the displacement of beads from the centre line of the renderer.

setBeadFill(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setBeadFill sets the bead fill paint.

setBeadOutline(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setBeadOutline sets the bead outline paint.

setBeadStroke(Stroke) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setBeadStroke sets the bead outline stroke.

setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

setBlockPainter(BlockPainter) - Method in class org.biojava.bio.gui.DistributionLogo

setBlockWidth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

setBounds(Rectangle2D.Float) - Method in interface org.biojava.bio.gui.glyph.Glyph

setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.HelixGlyph

setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TurnGlyph

setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

setCollapsing(boolean) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

Specifies if the renderer should collapse to zero depth when no features are visible (default true).

setDefaultPaint(Paint) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer

setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer.

setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer

setDelegateRenderer associates an OptimizableFilter with a BeadFeatureRenderer.

setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

setDelegateRenderer for the specified filter.

setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

setDepth(double) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo

setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

setDimensionRatio(double) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer

setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead.

setDirection(int) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

This method allows you to decide in which direction the arrow has to point.

setDirection(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setDirection sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL.

setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel

Set the direction that this SequencePanel renders in.

setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Set the direction that this SequencePoster renders in.

setDirection(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setDirection sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL.

setDistanceBetweenFeatures(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo

Set the dist to render.

setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer

setFeatureRenderer sets the renderer to be used.

setFeatureSource(FeatureSource) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

setFillColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Set the background color of the label area.

setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle

setFillPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

Allows you to set the paint properties of this glyph.

setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle

setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

setFilter sets the filter.

setFont(Font) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setGlyphForFilter(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer

Allows setting another Glyph object to be painted for the given FeatureFilter.

setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer

setHeightScaling sets the height scaling policy.

setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

setHeightScaling sets the height scaling policy.

setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer

setImageMap sets the current image map.

setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer

setImageMap sets the current image map.

setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer

setImageMap sets the current image map.

setKey(Object) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker

setLabel(String) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer

setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer

setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer

setLeadingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Set the absolute number of lines that the sequence will be rendered on.

setLogoFont(Font) - Method in class org.biojava.bio.gui.TextBlock

Set the current logo font.

setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter

Set the current logo font.

setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo

Set the logo painter.

setOffset(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

setOuterPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph

Allows setting the paint properties of the outer line of this glyph to the given value.

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer

setOutline sets the the colour used to draw the lines.

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer

setOutline sets the the colour used to draw the lines.

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer

setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle

setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle

setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

Set the padding.

setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph

Allows you to set the paint properties of this glyph, i.e., its color.

setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.TurnGlyph

Allows you to set the paint properties of this glyph, i.e., its color.

setRadius(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel

setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

setRange(RangeLocation) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

setRecurse sets the recursion flag on the filter.

setRenderer(CircularFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer

setRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Set the child renderer responsible for drawing the contents of this track

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper

setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer

setRenderer sets the renderer.

setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setRenderer sets the current PairwiseSequenceRenderer.

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper

setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setRenderer sets the current SequenceRenderer.

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.DistributionLogo

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanel

Use this to switch on effects like Anti-aliasing etc

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Use this to switch on effects like Anti-aliasing etc

setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setRenderingHints sets the RenderingHints which will be used by the Graphics2D instances of delegate renderers.

setScale(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setScale sets the scale in pixels per Symbol.

setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel

Set the scale.

setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Set the scale.

setScale(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setScale sets the scale in pixels per Symbol.

setScaleByInformation(boolean) - Method in class org.biojava.bio.gui.DistributionLogo

setSecondarySequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setSecondarySequence sets the secondary Sequence to be rendered.

setSecondarySymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setSecondarySymbolTranslation sets the translation in Symbols which will be applied when rendering.

setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel

setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setSequence sets the Sequence to be rendered.

setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.SequencePanel

Set the SymboList to be rendered.

setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Set the SymboList to be rendered.

setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

setSequence(Sequence) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setSequence sets the Sequence to be rendered.

setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree

Use this method to provide the sequences for the tree to work with.

setSequenceOffset(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border

Sets the size of the border in number of pixels.

setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

Set the number of pixels to leave blank between each block of sequence information.

setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo

Set the symbol style.

setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

setSymbolTranslation sets the translation in Symbols which will be applied when rendering.

setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

setSymbolTranslation sets the translation in Symbols which will be applied when rendering.

setTextColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

Set the color of the label text

setTickDirection(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer

setTrackLayout(TrackLayout) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer

setUserObject(Object) - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

setUserObject sets the user object.

setWrap(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper

setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

setWrap(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

setWrapIncrement(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout

setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

SimpleLabelRenderer - Class in org.biojava.bio.gui.sequence

SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer

SimpleSymbolStyle - Class in org.biojava.bio.gui

A no-frills implementation of SymbolStyle.

SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle

SimpleTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout

A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues

SimpleTrackLayout() - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

SimpleTrackLayout(Sequence, int) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout

SixFrameRenderer - Class in org.biojava.bio.gui.sequence

Class that handles drawing in six frames for other classes.

SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer

SixFrameZiggyRenderer - Class in org.biojava.bio.gui.sequence

A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.

SixFrameZiggyRenderer(SixFrameRenderer) - Constructor for class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer

SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer

sortPeptidesIntoLanes() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer

SourceLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker

StackedFeatureRenderer - Class in org.biojava.bio.gui.sequence

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.

StackedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.StackedFeatureRenderer

StackedLogoPainter - Class in org.biojava.bio.gui

A logo painter that paints in stacked areas.

StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter

startZiggy(StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.

startZiggy(StrandedFeature.Strand, int) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer

This method is called to initialise the renderer for a spliced transcript.

StopRenderer - Class in org.biojava.bio.gui.sequence

Compute sites of stop codons.

StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer

STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer

Constant STROKE indicating a change to the outline stroke of the features.

SubCircularRendererContext - Class in org.biojava.bio.gui.sequence

A renderer context that allows some or all properties of another context to be over-ridden.

SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double) - Constructor for class org.biojava.bio.gui.sequence.SubCircularRendererContext

Create a new sub context.

SubPairwiseRenderContext - Class in org.biojava.bio.gui.sequence

SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.

SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubPairwiseRenderContext

Creates a new SubPairwiseRenderContext.

SubSequenceRenderContext - Class in org.biojava.bio.gui.sequence

Allows a new renderer to "wrap" another one, replacing one or more values.

SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext

SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext

SymbolSequenceRenderer - Class in org.biojava.bio.gui.sequence

SymbolSequenceRenderer renders symbols of a SymbolList.

SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer

SymbolStyle - Interface in org.biojava.bio.gui

The interface for things that say how to paint a symbol.

T

TextBlock - Class in org.biojava.bio.gui

A BlockPainter that renders letters in proportion to the size of the signal.

TextBlock() - Constructor for class org.biojava.bio.gui.TextBlock

TextLogoPainter - Class in org.biojava.bio.gui

A logo painter that paints in stacked letters.

TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter

TickFeatureRenderer - Class in org.biojava.bio.gui.sequence

TickFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.TickFeatureRenderer

TICKS - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer

TICKS_DOWN indicates that the ticks will point downwards from a baseline.

TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer

TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer

TICKS_UP indicates that the ticks will point upwards from a baseline.

toggleSelectionStatus() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

toString() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer

toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide

toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot

toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide

toString() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer

toString() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent

totalBits(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo

Retrieve the maximal number of bits possible for this type of dist.

totalInformation(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo

Calculates the total information of the dist in bits.

TRACE - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer

TrackLayout - Interface in org.biojava.bio.gui.sequence.tracklayout

An interface for the handling of the layout of a WrappedSequencePanel.

TranslatedSequencePanel - Class in org.biojava.bio.gui.sequence

TranslatedSequencePanel is a panel that displays a Sequence.

TranslatedSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.TranslatedSequencePanel

Creates a new TranslatedSequencePanel with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).

TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel

Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.

TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel

Constant TRANSLATION is a ChangeType which indicates a change to the translation, requiring a paint update.

TurnGlyph - Class in org.biojava.bio.gui.glyph

A Glyph that paints a wide 'H' line within the bounds

TurnGlyph() - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph

TurnGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph

TurnGlyph(Paint, Stroke) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph

TwoHeadedArrowGlyph - Class in org.biojava.bio.gui.glyph

A Glyph that paints a two headed arrow within the bounds

TwoHeadedArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

TwoHeadedArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph

TypeLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker

U

UserDefinedTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout

An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges

UserDefinedTrackLayout(RangeLocation[]) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout

V

VALUES - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer

X

xHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer

xHair is the vertical line positioned along the X-axis.

Y

yHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer

yHair is the horizontal line positioned along the Y-axis.

Z

ZiggyFeatureRenderer - Class in org.biojava.bio.gui.sequence

A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.

ZiggyFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer

ZiggyImapRenderer - Class in org.biojava.bio.gui.sequence

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.

ZiggyImapRenderer(ZiggyFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.ZiggyImapRenderer

Creates a new ZiggyImapRenderer.

_

_addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

_addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

_removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer

_removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer

_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel

_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster

Deprecated.

A B C D E F G H I L M O P R S T U V X Y Z _