Package edu.mssm.crover.domain2d

Interface Summary

AnnotationParser	Parses an annotation and possibly produces a Drawing representation of it.
AnnotationsToDrawings	Translates annotations to graphical representations to be rendered on top of a given representation.
ConstrainedPoint
CoolPrint	This interface provides a way to print the children of a JPanel at full resolution.
CoolPrintRescale	Tags rendering classes that need to be rescaled.
Domain2D	This interface is implemented by all the sequence domains rendered on a DrawingSurface.
Drawing	Anything that is drawn on a DrawingSurface.
GlyphLink
HelixModel	Helix model.
LoopTemplate	Templates of control points for loops.
LoopTemplateSelector	Encapsulates the algorithms of LoopTemplate constructions or the collection of predifined templates.
ResidueColorScheme	ColorSchemes are like this...
ResidueGlyphFactory	Factory to create ResidueGlyphs.
ResidueGlyphRenderingAttributes	To set and get the ResidueGlyph rendering attributes.
ResidueModelFactory	Factory to create ResidueModels.
Solver

Class Summary

AbstractAnnotationsToDrawings	Translates annotation to graphical renderings for a Diagram.
AbstractLoopTemplate
AlgorithmicLoopTemplate
BasicResidueGlyphRenderingAttributes	Basic implementation of the ResidueGlyphRenderingAttributes interface.
BetaStrandDomain	Graphical representation of a beta strand subunit.
BetaStrandModel	Model for BetaStrandDomain.
BezierPath
BrushingModel
BrushingMouseListener
ColorAnnotationsColorScheme	Colors residues according to the sequence annotations.
CtermDomain	A C-terminal domain representation.
DBSModel	Dragging, Brushing, and Selection model.
DefaultHelixModel
Diagram	A Diagram is the representation of a Domain2D_Annotation model.
DiagramAnnotationsToDrawingsImpl	Translates annotation to graphical renderings for a Diagram.
DisulfidBridgeDrawing	The Drawing of a disulfid bridge.
DisulfidBridgeTranslator	Translates Disulfide_Annotation to a Drawing to be rendered on a Diagram.
Domain2D_ABuilder	Builds a Domain2D_Annotation from a Domain_Annotation.
Domain2D_Annotation	This annotation describes the information needed for the rendering of a two dimensional protein diagram.
DraggingModel	Dragging model.
DrawingSurface	Where the drawings are rendered.
DSLayoutManager	A Layout manager which is responsible for positioning Drawing objects on a DrawingSurface.
DummySolver
EllipsisGlyph	The EllipsisGlyph visually indicates that glyphs have been ellipsed from the representation.
ExtremityDomain	A domain to represent residues the beginning or end of a sequence.
ExtremityModel	Model for ExtremityDomain representations.
FreeLoop	A domain to represent residues of loops that connect two domains.
FreeLoopModel	Model for the FreeLoop representation.
GlyphLinkImpl	Associates a glyph to a geometrical area on the page.
GPCRDB_ColorScheme	The ColorScheme used by GPCRDB.
HelicalDomain	A helix secondary structure representation.
HelixLayout
InvalidDomain
JPanelImage
LayoutController	Offers a switch between the Cassowary first order constrain solver and the Reflex implementation.
LayoutParser	Parses the XML layout needed to generate diagrams.
LoopTemplateSelectorImpl	An experimental implementation of the LoopTemplateSelector.
MemLeakTestDiagram
MonotonousColorScheme	Colors all the residues the same.
MultiPointLoopTemplate	Provides a multiple control point bezier curve loop template.
NBezierPath	Path along a Bezier curve of n control points.
PrintablePanel	This class extends JPanel to provide support for printing hierarchies of components at high resolution.
ProteinSegmentDomain	Graphical representation of a protein segment.
ProteinSegmentLinkImpl	Associates a glyph to a geometrical area on the page.
ProteinSegmentModel	Model for BetaStrandDomain.
RAdd	Reflex addition.
RConstAdaptor	This reflex adaptor hides a variable from modifications.
RConstant	Reflex constant.
ReflexPoint	A Point implemented with two RExpressions.
REqual	Expression that force two values to be equal.
ResidueGlyph	A ResidueGlyph is the visual representation of a residue.
ResidueGlyphFactoryImpl	Factory to create ResidueGlyphs.
ResidueModel
ResidueNumberingDrawings
RExpression	Reflex expression.
RGE	Expression that is Greater or Equal than a given value.
Rotator	Rotates the Point2D containted in an array according to a plannar rotation.
RSub	Reflex substraction.
RVariable	Stores a value that can be changed.
SelectedModel
SelectionToVisualization
SharedResidueModelFactory	Factory to create residue models shared among different views.
TwoEndsDomain	Superclass for Secondary Structure Representation that present two ends (a start and an end point in the sequence).
TwoEndsDraggableDomain
TwoResidueLineDrawing	Drawing of a line that connects two residues.
UIStates
UniqueResidueModelFactory	The simplest implantation of ResidueModelFactory.

Exception Summary

InvalidRange	Thrown when the range cannot be displayed by a domain.
InvalidState
RInvalidChange
SolverInternalError

Error Summary