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## Uses of Class
biouml.model.Compartment

Packages that use Compartment
biouml.model |
biouml.model.dynamics |
biouml.model.util |
biouml.plugins.ginsim |
biouml.plugins.gxl |
biouml.plugins.jgraph |
biouml.plugins.sbml |
biouml.standard.diagram |
biouml.standard.filter |

Uses of Compartment in biouml.model

Subclasses of Compartment in biouml.model
`class` | `Diagram`
`class` | `EquivalentNodeGroup` Group of equivalent nodes.

Methods in biouml.model that return Compartment
`Compartment` | `QueryEngineSupport.getCompartment(Node start, Base kernel)` Should return the most suitable compartment where new node should be located.

Methods in biouml.model with parameters of type Compartment
`boolean` | `SemanticController.canAccept(Compartment compartment, java.lang.Class c)`
`boolean` | `SemanticController.canAccept(Compartment compartment, DiagramElement de)`
`java.awt.Dimension` | `SemanticController.move(Node node, Compartment parent, java.awt.Dimension offset)` Moves the specified node to the specified position.
`DiagramElement` | `SemanticController.createInstance(Compartment compartment, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)`
`protected void` | `QueryEngineSupport.createEdges(Node start, Node reaction, Compartment c, NodeInfo[] linked, java.util.Set added)`
`protected java.util.Map` | `QueryEngineSupport.getCompartmentKernels(Compartment c)`
`protected Node` | `QueryEngineSupport.findNearestNode(Compartment c, Node node, Base kernel)`
`DiagramElement` | `Node.clone(Compartment newParent, java.lang.String newName)`
`DiagramElement` | `Edge.clone(Compartment newParent, java.lang.String newName)`
`CompositeView` | `DiagramViewBuilder.createCompartmentView(Compartment compartment, DiagramViewOptions options, java.awt.Graphics g)`
`void` | `DiagramTypeConverter.ConditionalConverter.checkElements(java.util.List list, Compartment compartment, DiagramType type)`
`void` | `DiagramFilter.apply(Compartment diagram)` Hides or highlights diagram elements according to filter settings.
`void` | `DiagramFilter.restoreView(Compartment diagram)` Restores original diagram view.
`DiagramElement` | `DiagramElement.clone(Compartment newParent, java.lang.String newName)`
`boolean` | `DefaultSemanticController.canAccept(Compartment compartment, java.lang.Class c)`
`boolean` | `DefaultSemanticController.canAccept(Compartment compartment, DiagramElement de)`
`DiagramElement` | `DefaultSemanticController.createInstance(Compartment compartment, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor)`
`java.awt.Dimension` | `DefaultSemanticController.move(Node node, Compartment newParent, java.awt.Dimension offset)` Moves the specified diagram node to the specified position.
`protected void` | `DefaultSemanticController.moveEdges(Compartment root, Compartment oldCompartment, Compartment newCompartment, java.lang.String oldCompartmentName)`
`protected void` | `DefaultSemanticController.remapEdge(Edge edge, Compartment oldCompartment, Compartment newCompartment, java.lang.String oldCompartmentName)`
`protected Node` | `DefaultSemanticController.findNewNode(Node oldNode, Compartment oldCompartment, Compartment newCompartment)`
`CompositeView` | `DefaultDiagramViewBuilder.createCompartmentView(Compartment compartment, DiagramViewOptions options, java.awt.Graphics g)`
`protected CompositeView` | `DefaultDiagramViewBuilder.doCreateCompartmentView(Compartment compartment, DiagramViewOptions options, java.awt.Graphics g)` Creates compartment view.
`protected void` | `DefaultDiagramViewBuilder.buildNodes(Compartment compartment, DiagramViewOptions options, java.awt.Graphics g)` built all nodes and add them into compartment
`DiagramElement` | `Compartment.clone(Compartment newParent, java.lang.String newName)`
`protected void` | `Compartment.doClone(Compartment compartment)`
`protected boolean` | `Compartment.contains(Compartment compartment, java.lang.String name)`
`void` | `AbstractFilter.apply(Compartment diagram)` Hides or highlights diagram elements according to filter settings.
`void` | `AbstractFilter.restoreView(Compartment diagram)` Restores original diagram view.

Uses of Compartment in biouml.model.dynamics

Methods in biouml.model.dynamics with parameters of type Compartment
`void` | `EModel.fillList(Compartment compartment, java.util.List list, java.lang.Class role)`
`protected void` | `EModel.readMath(Compartment compartment)`

Uses of Compartment in biouml.model.util

Methods in biouml.model.util with parameters of type Compartment
`static void` | `DiagramXmlWriter.writeCompartmentInfo(org.w3c.dom.Element element, Compartment compartment)`
`protected void` | `DiagramXmlWriter.createFunctionList(org.w3c.dom.Element node, Compartment compartment)`
`protected void` | `DiagramXmlWriter.createEquationList(org.w3c.dom.Element node, Compartment compartment)`
`static void` | `DiagramXmlReader.readCompartmentInfo(org.w3c.dom.Element element, Compartment compartment, java.lang.String diagramName)`

Uses of Compartment in biouml.plugins.ginsim

Methods in biouml.plugins.ginsim with parameters of type Compartment
`protected CompositeView` | `GinSimDiagramViewBuilder.doCreateCompartmentView(Compartment compartment, DiagramViewOptions options, java.awt.Graphics g)` Creates compartment view.

Uses of Compartment in biouml.plugins.gxl

Methods in biouml.plugins.gxl with parameters of type Compartment
`protected void` | `GxlWriter.writeElements(java.io.Writer out, Compartment compartment)`

Uses of Compartment in biouml.plugins.jgraph

Methods in biouml.plugins.jgraph with parameters of type Compartment
`static org.jgraph.graph.GraphModel` | `DiagramToJGraphTransformer.generateGraph(Compartment diagram, Filter filter)` Generates graph for BioUML diagram or its part.
`static void` | `DiagramToJGraphTransformer.applyLayout(Compartment diagram, org.jgraph.graph.GraphModel graph)`

Uses of Compartment in biouml.plugins.sbml

Fields in biouml.plugins.sbml declared as Compartment
`protected Compartment` | `SbmlModelReader.defaultCompartment`
`protected Compartment` | `CreateDiagramElementDialog.parent`

Methods in biouml.plugins.sbml that return Compartment
`protected Compartment` | `SbmlModelReader_21.readCompartment(org.w3c.dom.Element element, java.lang.String compartmentId, java.lang.String compartmentName)`
`protected Compartment` | `SbmlModelReader.readCompartment(org.w3c.dom.Element element, java.lang.String compartmentId, java.lang.String compartmentName)`

Methods in biouml.plugins.sbml with parameters of type Compartment
`protected static void` | `SbmlSemanticController.fillNameMap(Compartment compartment, java.util.HashMap map)`
`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.
`protected void` | `SbmlModelWriter.fillCompartmentList(Compartment compartment, boolean includeItself)`
`protected void` | `SbmlModelWriter.writeCompartment(org.w3c.dom.Element compartmentListElement, Compartment compartment)`
`protected void` | `SbmlModelWriter.writeSpecieList(org.w3c.dom.Element speciesListElement, Compartment compartment)`
`protected void` | `SbmlModelWriter.writeReactionList(org.w3c.dom.Element reactionListElement, Compartment compartment)`
`void` | `SbmlModelReader.layout(Compartment compartment)` Stub implimentation for diagram layout.
`void` | `SbmlModelReader.layout(Compartment compartment, int x, int y)` Hierarchically layout compartments and species.

Constructors in biouml.plugins.sbml with parameters of type Compartment
`CreateDiagramElementDialog(Diagram diagram, Compartment parent, java.lang.Class type)`

Uses of Compartment in biouml.standard.diagram

Fields in biouml.standard.diagram declared as Compartment
`protected Compartment` | `SemanticRelationPane.parent`

Methods in biouml.standard.diagram with parameters of type Compartment
`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)`
`void` | `PathwayDiagramViewBuilder.createReactionTitles(Compartment compartment, DiagramViewOptions diagramOptions, java.awt.Graphics g)`
`static CreateEdgeDialog` | `CreateEdgeDialog.getSemanticRelationDialog(Compartment parent, java.awt.Point point, ViewEditorPane viewEditor)`
`static CreateEdgeDialog` | `CreateEdgeDialog.getNoteLinkDialog(Compartment parent, java.awt.Point point, ViewEditorPane viewEditor)`

Constructors in biouml.standard.diagram with parameters of type Compartment
`SemanticRelationPane(Compartment parent, ViewEditorPane viewEditor)`
`ReactionPane(Diagram diagram, Compartment compartment, java.awt.Point point, ViewEditorPane viewEditor)`
`NoteLinkPane(Compartment parent, ViewEditorPane viewEditor)`
`CreateEdgeDialog(Compartment parent, java.awt.Point point, ViewEditorPane viewEditor, java.lang.String title, SemanticRelationPane relationPane)`
`CreateDiagramElementDialog(Compartment parent, java.lang.Class type)`

Uses of Compartment in biouml.standard.filter

Methods in biouml.standard.filter with parameters of type Compartment
`protected void` | `BiopolimerDiagramFilter.collectDiagramInfo(Compartment comp)` Build list of all species in the diagram.

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