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## Uses of Class
biouml.model.DiagramElement

Packages that use DiagramElement
biouml.model |
biouml.model.dynamics |
biouml.model.util |
biouml.plugins.matlab |
biouml.plugins.sbml |
biouml.plugins.simulation |
biouml.plugins.simulation.java |
biouml.standard.diagram |
biouml.standard.filter |
biouml.workbench.diagram |

Uses of DiagramElement in biouml.model

Subclasses of DiagramElement in biouml.model
`class` | `Compartment` General definition of the compartment as a container for nodes and edges between them.
`class` | `Diagram`
`class` | `Edge` Edge is directed relation between two diagram nodes, called "input" and "output".
`class` | `EquivalentNodeGroup` Group of equivalent nodes.
`class` | `Node` Diagram node element

Methods in biouml.model that return DiagramElement
`DiagramElement` | `SemanticController.createInstance(Compartment compartment, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)`
`DiagramElement` | `Role.getDiagramElement()`
`DiagramElement` | `Node.clone(Compartment newParent, java.lang.String newName)`
`DiagramElement` | `Edge.clone(Compartment newParent, java.lang.String newName)`
`DiagramElement` | `DiagramElement.clone(Compartment newParent, java.lang.String newName)`
`DiagramElement` | `Diagram.clone(DataCollection origin, java.lang.String newName)`
`DiagramElement` | `DefaultSemanticController.createInstance(Compartment compartment, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)`
`DiagramElement` | `Compartment.clone(Compartment newParent, java.lang.String newName)`

Methods in biouml.model with parameters of type DiagramElement
`boolean` | `SemanticController.canAccept(Compartment compartment, DiagramElement de)`
`boolean` | `SemanticController.remove(DiagramElement de)` Removes the diagram element and all related edges.
`boolean` | `SemanticController.isResizable(DiagramElement diagramElement)`
`Role` | `Role.clone(DiagramElement de)` Creates copy of the object and asstiate it with specified diagram element.
`void` | `DiagramViewBuilder.hideElement(DiagramElement element)`
`void` | `DiagramViewBuilder.removeElement(DiagramElement element)`
`boolean` | `DiagramTypeConverter.ConditionalConverter.isSuitable(DiagramElement de, DiagramType type)`
`protected void` | `DiagramTypeConverter.ConditionalConverter.message(java.lang.StringBuffer buf, DiagramElement de, Diagram diagram)`
`boolean` | `DefaultSemanticController.canAccept(Compartment compartment, DiagramElement de)`
`boolean` | `DefaultSemanticController.isResizable(DiagramElement diagramElement)`
`boolean` | `DefaultSemanticController.remove(DiagramElement de)` Removes the diagram element and all related edges.
`void` | `DefaultDiagramViewBuilder.hideElement(DiagramElement element)`
`void` | `DefaultDiagramViewBuilder.removeElement(DiagramElement element)`
`protected void` | `AbstractFilter.restoreView(DiagramElement de)`

Uses of DiagramElement in biouml.model.dynamics

Fields in biouml.model.dynamics declared as DiagramElement
`protected DiagramElement` | `VariableRole.diagramElement`

Methods in biouml.model.dynamics that return DiagramElement
`DiagramElement` | `VariableRole.getDiagramElement()`
`DiagramElement` | `EModelRoleSupport.getDiagramElement()`

Methods in biouml.model.dynamics with parameters of type DiagramElement
`static java.lang.String` | `VariableRole.createName(DiagramElement de)` Returns name of DataElement including all compartment names.
`Role` | `VariableRole.clone(DiagramElement de)` Creates variable copy and assotiate it with specified diagram element.
`Role` | `Equation.clone(DiagramElement de)` Creates equation copy and assitiate it with specified diagram element.
`Role` | `EModelRoleSupport.clone(DiagramElement de)` Throws UnsupportedOperationException.
`Role` | `EModel.clone(DiagramElement de)` Unsupported yet.
`java.lang.String` | `EModel.getQualifiedName(java.lang.String name, DiagramElement de)` Resolves brief variable name to fully qualified variable name, using information from corresponding DiagramElement.
`protected static void` | `DAEModelUtilities.fillVarASTMap(DiagramElement de, java.util.Map map, EModel emodel)`

Constructors in biouml.model.dynamics with parameters of type DiagramElement
`VariableRole(DataCollection origin, DiagramElement diagramElement, double initialValue)`
`VariableRole(DiagramElement diagramElement, double initialValue)`
`Transition(DiagramElement de)`
`State(DiagramElement de)`
`Function(DiagramElement diagramElement)`
`Event(DiagramElement de, java.lang.String name)`
`Event(DiagramElement de, java.lang.String trigger, java.lang.String delay, Assignment[] actions)`
`Equation(DiagramElement de, java.lang.String type, java.lang.String variable)`
`Equation(DiagramElement de, java.lang.String type, java.lang.String variable, java.lang.String formula)`
`EModelRoleSupport(DiagramElement diagramElement)`
`EModel(DiagramElement de)`

Uses of DiagramElement in biouml.model.util

Methods in biouml.model.util with parameters of type DiagramElement
`protected static void` | `DiagramXmlWriter.setTitle(org.w3c.dom.Element element, DiagramElement diagramElement)`
`protected static void` | `DiagramXmlWriter.setComment(org.w3c.dom.Element element, DiagramElement diagramElement)`
`protected void` | `DiagramXmlWriter.writeDiagramElement(org.w3c.dom.Element element, DiagramElement de)`
`protected static void` | `DiagramXmlReader.getTitle(org.w3c.dom.Element element, DiagramElement de)`
`protected void` | `DiagramXmlReader.writeDiagramElement(org.w3c.dom.Element element, DiagramElement de)`

Uses of DiagramElement in biouml.plugins.matlab

Fields in biouml.plugins.matlab declared as DiagramElement
`protected DiagramElement` | `MatlabErrorDialog.diagramElement`

Constructors in biouml.plugins.matlab with parameters of type DiagramElement
`MatlabErrorDialog(javax.swing.JDialog dialog, DiagramElement diagramElement, java.lang.String error)`
`MatlabErrorDialog(javax.swing.JFrame frame, DiagramElement diagramElement, java.lang.String error)`

Uses of DiagramElement in biouml.plugins.sbml

Methods in biouml.plugins.sbml that return DiagramElement
`DiagramElement` | `SbmlSemanticController.createInstance(Compartment parent, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)` Creates diagram element for the specified kernel type, parent compartment and location.

Methods in biouml.plugins.sbml with parameters of type DiagramElement
`protected java.lang.String` | `SbmlModelReader_21.readMath(org.w3c.dom.Element element, DiagramElement de)`
`protected java.lang.String` | `SbmlModelReader_11.readMath(java.lang.String formula, DiagramElement de)`
`boolean` | `SbmlModelReader.isSpecie(DiagramElement de)`
`boolean` | `SbmlModelReader.isReaction(DiagramElement de)`

Uses of DiagramElement in biouml.plugins.simulation

Methods in biouml.plugins.simulation with parameters of type DiagramElement
`java.lang.String` | `SimulationEngine.getQualifiedName(java.lang.String name, DiagramElement de)` Resolves brief varibale name to fully qualified variable name.
`protected void` | `SimulationEngine.initMath(DiagramElement de)` Initialize variable types and equations map.
`protected void` | `SimulationEngine.initAlgebraic(DiagramElement de)`
`protected void` | `SimulationEngine.parseEquation(DiagramElement de)`

Uses of DiagramElement in biouml.plugins.simulation.java

Methods in biouml.plugins.simulation.java that return DiagramElement
`DiagramElement` | `JavaSimulationEngine.processError(java.lang.String err, java.lang.String fileName, int row, int column)`

Uses of DiagramElement in biouml.standard.diagram

Fields in biouml.standard.diagram declared as DiagramElement
`protected DiagramElement` | `DiagramElementSelector.diagramElement`

Methods in biouml.standard.diagram that return DiagramElement
`DiagramElement` | `PathwaySimulationSemanticController.createInstance(Compartment parent, java.lang.Class type, java.awt.Point pt, ViewEditorPane viewEditor)`
`protected DiagramElement` | `PathwaySimulationSemanticController.createRule(Compartment parent, java.awt.Point pt, ViewEditorPane viewEditor)`
`DiagramElement` | `PathwaySemanticController.createInstance(Compartment parent, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)`
`DiagramElement` | `PathwaySemanticController.createDiagramElement(Base kernel, java.util.Set elements)`
`DiagramElement` | `DiagramElementSelector.getDiagramElement()`

Methods in biouml.standard.diagram with parameters of type DiagramElement
`protected void` | `PathwaySimulationDiagramViewBuilder.createReactionTitle(DiagramElement reactionNode, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`protected Diagram` | `PathwaySimulationDiagramViewBuilder.getDiagram(DiagramElement de)`
`boolean` | `PathwaySemanticController.remove(DiagramElement de)` Removes the diagram element and all related edges.
`protected void` | `PathwayDiagramViewBuilder.createReactionTitle(DiagramElement reaction, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`boolean` | `DiagramElementSelector.setDiagramElement(DiagramElement diagramElement)`
`boolean` | `DiagramElementSelector.isSuitable(DiagramElement de)`

Uses of DiagramElement in biouml.standard.filter

Methods in biouml.standard.filter with parameters of type DiagramElement
`Action` | `ValueActionFilter.getAction(DiagramElement de)`
`void` | `HighlightAction.apply(DiagramElement de)`
`void` | `HideAction.apply(DiagramElement de)`
`void` | `CompositeHighlightAction.apply(DiagramElement de)`
`protected void` | `BiopolimerDiagramFilter.restoreView(DiagramElement de)`
`Action` | `ActionFilter.getAction(DiagramElement de)` Returns action, that should be applied to the specified diagram element, if it satisfies to the filter condition or null otherwise.
`void` | `Action.apply(DiagramElement de)` Apllies the action to the specified diagram element.

Uses of DiagramElement in biouml.workbench.diagram

Fields in biouml.workbench.diagram declared as DiagramElement
`protected DiagramElement` | `ClipboardView.exploredDiagramElement`

Methods in biouml.workbench.diagram that return DiagramElement
`DiagramElement` | `DiagramElementInfo.getDiagramElement()`

Constructors in biouml.workbench.diagram with parameters of type DiagramElement
`DiagramElementInfo(DiagramElement diagramElement)`

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