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## Uses of Class
biouml.model.Diagram

Packages that use Diagram
biouml.editor |
biouml.editor.graphlayout |
biouml.model |
biouml.model.dynamics |
biouml.model.htmlgen |
biouml.model.util |
biouml.modules.genenet |
biouml.modules.kegg |
biouml.modules.kegg.type.access |
biouml.modules.transpath |
biouml.standard |
biouml.standard.diagram.pathway |
biouml.standard.filter |

Uses of Diagram in biouml.editor

Constructors in biouml.editor with parameters of type Diagram
`DiagramDocument.DiagramDocument(Diagram diagram)`
`DiagramEditorHelper.DiagramEditorHelper(Diagram diagram)`
`NewDiagramElementDialog.NewDiagramElementDialog(JFrame frame, String title, DataCollection parent, Diagram diagram, Class clazz)`
`ViewerDiagramFilter.ViewerDiagramFilter(Diagram diagram)`

Methods in biouml.editor that return Diagram
`Diagram` | `DiagramDocument.getDiagram()`
`static Diagram` | `NewDiagramDialog.createDiagram(DiagramType type, String diagramName, DataCollection origin)`
`static Diagram` | `NewDiagramDialog.createDiagram(String diagramTypeClassName, String diagramName, DataCollection origin)`
`Diagram` | `ViewerDiagramFilter.getDiagram()`

Methods in biouml.editor with parameters of type Diagram
`ViewPane` | `BioUMLApplication.createViewPane(Diagram diagram)`
`ViewPane` | `BioUMLEditor.createViewPane(Diagram diagram)`
`static Image` | `SaveAsImageAction.generateDiagramImage(Diagram diagram)`
`void` | `SearchLinkedPanel.setDiagram(Diagram diagram)`

Uses of Diagram in biouml.editor.graphlayout

Methods in biouml.editor.graphlayout with parameters of type Diagram
`void` | `CellLayoutManager.layout(Diagram diagram, Node root, Node[] addedNodes, Node selectedNode)`
`void` | `ForceDirectedLayoutManager.layout(Diagram diagram, Node center, Node selectedNode)`
`void` | `ForceDirectedLayoutManager.layout(Diagram diagram, Node root, Node[] addedNodes, Node selectedNode)`
`void` | `GraphLayout.layout(Diagram diagram, Node center, Node selectedNode)`
`void` | `GraphLayout.layout(Diagram diagram, Node center, Node[] nodes, Node selectedNode)`
`void` | `LayeredLayoutManager.layout(Diagram diagram, Node center, Node selectedNode)`
`void` | `LayeredLayoutManager.layout(Diagram diagram, Node root, Node[] addedNodes, Node selectedNode)`
`void` | `LayeredOptimizedLayoutManager.layout(Diagram diagram, Node center, Node selectedNode)`
`void` | `LayeredOptimizedLayoutManager.layout(Diagram diagram, Node root, Node[] addedNodes, Node selectedNode)`

Uses of Diagram in biouml.model

Methods in biouml.model that return Diagram
`Diagram` | `Module.getDiagram(String name)`

Methods in biouml.model with parameters of type Diagram
`CompositeView` | `DefaultDiagramViewBuilder.createDiagramView(Diagram diagram, Graphics g)` Creates the diagram view
`Action[]` | `DefaultDiagramViewBuilder.getInsertActions(Diagram diagram)`
`DiagramFilter` | `DiagramType.getDiagramFilter(Diagram diagram)`
`CompositeView` | `DiagramViewBuilder.createDiagramView(Diagram diagram, Graphics g)`
`Action[]` | `DiagramViewBuilder.getInsertActions(Diagram diagram)`
`void` | `Module.putDiagram(Diagram diagram)`
`Node[]` | `QueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller, Set elements)`
`Node[]` | `QueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller)`
`Node[]` | `QueryEngine.searchLinked(Diagram diagram, Node node, int direction, int depth, SemanticController controller)`

Uses of Diagram in biouml.model.dynamics

Constructors in biouml.model.dynamics with parameters of type Diagram
`VariablesDataCollection.VariablesDataCollection(DataCollection parent, Diagram diagram)`

Methods in biouml.model.dynamics with parameters of type Diagram
`DiagramFilter` | `EModelDiagramType.getDiagramFilter(Diagram diagram)`

Uses of Diagram in biouml.model.htmlgen

Constructors in biouml.model.htmlgen with parameters of type Diagram
`GenerateHTMLDialog.GenerateHTMLDialog(JDialog dialog, String title, Module module, Diagram diagram)`
`GenerateHTMLDialog.GenerateHTMLDialog(JFrame frame, String title, Module module, Diagram diagram)`

Methods in biouml.model.htmlgen with parameters of type Diagram
`static void` | `GenerateHTMLDialog.genHTML(Diagram diagram, File outputFolder, File templateFile, Category cat)`

Uses of Diagram in biouml.model.util

Methods in biouml.model.util that return Diagram
`Diagram` | `DiagramXMLReader.read()`
`Diagram` | `DiagramXMLReader.read(DataCollection origin, Module module)`

Methods in biouml.model.util with parameters of type Diagram
`void` | `DiagramXMLWriter.write(Diagram sourceDiagram, Transformer transformer)`
`void` | `DiagramXMLWriter.write(Diagram sourceDiagram)`

Uses of Diagram in biouml.modules.genenet

Methods in biouml.modules.genenet with parameters of type Diagram
`DiagramFilter` | `GeneNetDiagramType.getDiagramFilter(Diagram diagram)`
`Node[]` | `GeneNetQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller, Set elements)`
`Node[]` | `GeneNetQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller)`
`Node[]` | `GeneNetQueryEngine.searchLinked(Diagram diagram, Node node, int direction, int depth, SemanticController controller)`

Uses of Diagram in biouml.modules.kegg

Methods in biouml.modules.kegg with parameters of type Diagram
`DiagramFilter` | `KeggPathwayDiagramType.getDiagramFilter(Diagram diagram)`
`Node[]` | `KeggPathwayQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller, Set elements)`
`Node[]` | `KeggPathwayQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller)`
`Node[]` | `KeggPathwayQueryEngine.searchLinked(Diagram diagram, Node node, int direction, int depth, SemanticController controller)`

Uses of Diagram in biouml.modules.kegg.type.access

Methods in biouml.modules.kegg.type.access that return Diagram
`Diagram` | `DiagramReader.read(DataCollection origin, String name, Module module)`

Uses of Diagram in biouml.modules.transpath

Methods in biouml.modules.transpath with parameters of type Diagram
`DiagramFilter` | `TranspathDiagramType.getDiagramFilter(Diagram diagram)`
`Node[]` | `TranspathQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller, Set elements)`
`Node[]` | `TranspathQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller)`
`Node[]` | `TranspathQueryEngine.searchLinked(Diagram diagram, Node node, int direction, int depth, SemanticController controller)`

Uses of Diagram in biouml.standard

Methods in biouml.standard with parameters of type Diagram
`Node[]` | `StandardQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller, Set elements)`
`Node[]` | `StandardQueryEngine.searchLinked(Diagram diagram, Node node, int direction, SemanticController controller)`
`Node[]` | `StandardQueryEngine.searchLinked(Diagram diagram, Node node, int direction, int depth, SemanticController controller)`

Uses of Diagram in biouml.standard.diagram.pathway

Methods in biouml.standard.diagram.pathway with parameters of type Diagram
`DiagramFilter` | `PathwayDiagramType.getDiagramFilter(Diagram diagram)`

Uses of Diagram in biouml.standard.filter

Constructors in biouml.standard.filter with parameters of type Diagram
`BiopolimerDiagramFilter.BiopolimerDiagramFilter(Diagram diagram)`

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