Package apollo.gui.genomemap

Interface Summary

ApolloPanelHolderI	An interface that holds ApolloPanels.
ApolloPanelI	This was invented to eliminate all of the casting that was going on.
ContainerViewI
DragViewI	Defines the methods required for dragging.
DrawableTierManagerI
DropTargetViewI	Interface defining methods for handling a drop in a View
FeatureTierManagerI
KeyViewI	An interface representing a View object which accepts keyboard input.
ManagedViewI	An interface representing a View object which has defined extents eg a start and end base and has a tier manager to go with it.
PickViewI	An interface representing a View object which contains selectable Drawables.
PixelMaskI	A PixelMaskI can set pixels to be masked at a given level/yindex and be queried for a masking range at a given level
PopupViewI	An interface representing a View object which contains selectable Drawables.
RevCompListener
SelectViewI
StrandVisibilityListener	At the moment only for becoming visible, if need event for hiding as well then add another method (or variable) This is presently pase' and not used - was used by ViewMenu, but ViewMenu.ViewMenuListener now does the same thing in an easier fashion.
TierViewI
ViewI	An interface representing a View object which has defined extents eg a start and end base.

Class Summary

AnnotationView	A view to display annotations in
ApolloLayoutManager	An Abstract base ApolloLayoutManager class
ApolloPanel	This class is a container to hold and manage the various Views which are needed by Apollo.
ColumnApolloLayout	An ApolloLayoutManager which lays out its views in a single column.
ContainerView
DiscreteGraphView	This is a view for a discrete graph
DragView	A FeatureView which has extra methods to handle dragging.
DrawableTierManager
FastClippingGraphics
FeatureTier	A Tier to hold features.
FeatureTierManager	Extended from TierManager but still abstract (no layoutTiers methods) Implements FeatureTierManagerI which implements ControlledObjectI extends DrawableTierManager which extends TierManager which is where the ControlledObjectI methods are implemented.
FeatureView	FeatureView is a View for displaying DrawableSeqFeatures and DrawableFeatureSets (and maybe other Drawables), in linear tiers.
GraphView
GuideLine
LaidoutViewContainer
LinearView	A basic, non useful, implementation of the LinearViewI interface.
ManagedView	An extension of LinearView for drawing analysis results.
NavigationBar	This panel appears in the apollo frame and lets the user navigate to a new region, going left or right or zooming out from current coordinates, and selecting new chromosomes.
PixelMask	Class which records which pixels in a tier have been drawn already, used in drawing optimisation.
PlotUtil
ResultView	An extension of FeatureView for drawing analysis results.
Rubberband	Draws and controls the rubberband used for selections.
RubberbandRectangle	A rectangular rubberband.
ScaleView	Draw a scale line, BUT also draws sequence, and allows dragging of hairpins.
ScrollAdjustedView
Sites	Sites holds an array of integers which are the base positions for each site in a given frame and strand.
SiteTier
SiteTierManager
SiteView	A view to display sites (start and stop codons).
SplitterView
StrandedZoomableApolloPanel	The class which controls and renders the main feature display panel, containing an AnnotationView, ResultView and SiteView for each strand.
TierView	This class is the base class for FeatureView and SiteView.
TranslationView	Not used - work in progress or pase?