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| 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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