Package edu.mssm.crover.domain2d

Provides implementations of the algorithms we developed for the drawing of Residue-based diagrams.

See:
          Description

Interface Summary
AbstractModel  
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.
BrushingModelInterface  
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.
DraggingModelInterface This class is the model to determine if a residue can be dragged with the mouse to another location (by user interaction), or if the position is fixed (determined only by the layout algorithm for instance).
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.
SelectableObject  
SelectedModelInterface  
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  
check_bernstein  
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.
LineDrawing The Drawing of a line.
LineDrawingTranslator Translates Line_Annotation to a Drawing to be rendered on a Diagram.
LoopTemplateSelectorImpl An experimental implementation of the LoopTemplateSelector.
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
 

Package edu.mssm.crover.domain2d Description

Provides implementations of the algorithms we developed for the drawing of Residue-based diagrams.

Package Specification

Related Documentation

The following reference describes the algorithms that the package implements.
\@Article{RbDe99,
  author =       {Campagne, F. and Weintein, H.},
  title =        {Schematic representation of residue-based protein-context
                  dependant data: an application to transmembrane proteins},
  journal =      {J. Of Molec. Graph. \& Mod. },
  year =         {1999},
  OPTkey =       {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTpages =     {},
  OPTmonth =     {},
  note =         {in press},
  OPTannote =    {}
}
For an example of use, see the Residue-based Diagram editor web service http://transport.physbio.mssm.edu:8080/rbde/RbDe.html



Copyright © 2004 Weill Cornell Medical College. All Rights Reserved.