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| Interface Summary | |
| Drawable | |
| DrawableArc | |
| DrawableVertex | |
| Positionable | |
| Class Summary | |
| CommandLineDriver | |
| DefaultDrawConstraintArc | |
| DefaultDrawConstraintVertex | |
| DefaultDrawLinkArc | |
| DefaultDrawLinkNodalArc | |
| DefaultDrawLinkNodalVertex | |
| DefaultDrawLinkVertex | |
| DefaultDrawNodalVertex | |
| DrawArc | |
| DrawVertex | |
| Editor | |
| EditorPanel | |
| Gui | |
| GUITool | A GUITool instance provides a window in which as user make interact with the repository. |
| MatchingTool | |
| PathwayOptimiserTool | A PathwayOptimiserTool instance provides a dialog box displaying the result of running pathway optimisation on the given pathway. |
| PatternWritingTool | |
| PinBoardLayout | |
| ReportException | A Window to display a Java Exception. |
| Syntax | |
| UserAction | |
| UserActionClass | |
| UserActionResult | |
| Exception Summary | |
| CommandLineException | |
| ConfigException | |
| EditorException | |
| SemanticException | |
| SyntaxException | |
| UnexpectedTokenException | |
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