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## Uses of Class
biouml.model.Node

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

Uses of Node in biouml.model

Subclasses of Node in biouml.model
`class` | `Compartment` General definition of the compartment as a container for nodes and edges between them.
`class` | `Diagram`
`class` | `EquivalentNodeGroup` Group of equivalent nodes.

Methods in biouml.model that return Node
`protected Node` | `QueryEngineSupport.findNearestNode(Compartment c, Node node, Base kernel)`
`Node` | `EquivalentNodeGroup.getRepresentative()`
`Node` | `Edge.getInput()`
`Node` | `Edge.getOutput()`
`protected Node` | `DefaultSemanticController.findNewNode(Node oldNode, Compartment oldCompartment, Compartment newCompartment)`
`Node` | `Compartment.findNode(java.lang.String id)`

Methods in biouml.model with parameters of type Node
`java.awt.Dimension` | `SemanticController.move(Node node, Compartment parent, java.awt.Dimension offset)` Moves the specified node to the specified position.
`NodeInfo[]` | `QueryEngineSupport.searchLinked(Diagram diagram, Node node, QueryOptions options)`
`NodeInfo[]` | `QueryEngineSupport.addLinked(Diagram diagram, Node start, NodeInfo[] linked)` Appends linked nodes to the diagram.
`Compartment` | `QueryEngineSupport.getCompartment(Node start, Base kernel)` Should return the most suitable compartment where new node should be located.
`protected void` | `QueryEngineSupport.createEdges(Node start, Node reaction, Compartment c, NodeInfo[] linked, java.util.Set added)`
`protected Node` | `QueryEngineSupport.findNearestNode(Compartment c, Node node, Base kernel)`
`NodeInfo[]` | `QueryEngine.searchLinked(Diagram diagram, Node node, QueryOptions options)`
`NodeInfo[]` | `QueryEngine.addLinked(Diagram diagram, Node start, NodeInfo[] nodeInfoArr)`
`protected void` | `Node.doClone(Node node)`
`CompositeView` | `DiagramViewBuilder.createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)`
`void` | `DiagramViewBuilder.moveNode(Node node, java.awt.Point newLocation)`
`java.awt.Dimension` | `DefaultSemanticController.move(Node node, Compartment newParent, java.awt.Dimension offset)` Moves the specified diagram node to the specified position.
`void` | `DefaultSemanticController.moveNode(Node oldNode, Node newNode)`
`void` | `DefaultSemanticController.moveEdges(Node oldNode, Node newNode)`
`protected Node` | `DefaultSemanticController.findNewNode(Node oldNode, Compartment oldCompartment, Compartment newCompartment)`
`protected void` | `DefaultSemanticController.moveEdge(Edge oldEdge, Node inNode, Node outNode)`
`CompositeView` | `DefaultDiagramViewBuilder.createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `DefaultDiagramViewBuilder.createNodeCoreView(CompositeView container, Node node, DiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `DefaultDiagramViewBuilder.createNoteView(CompositeView container, Node node, DiagramViewOptions options, java.awt.Graphics g)`
`void` | `DefaultDiagramViewBuilder.moveNode(Node node, java.awt.Point newLocation)`
`protected void` | `Compartment.remapEdge(DataCollection newParent, Edge edge, Node inNode, Node outNode)`
`protected abstract void` | `AbstractFilter.processNode(Node node)` Should high or highlight node depending on filter settings.

Constructors in biouml.model with parameters of type Node
`Edge(DataCollection parent, java.lang.String id, Base kernel, Node input, Node output)`
`Edge(DataCollection parent, Base kernel, Node input, Node output)`

Uses of Node in biouml.model.dynamics

Methods in biouml.model.dynamics with parameters of type Node
`CompositeView` | `EModelDiagramViewBuilder.createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)` Adds vriable value to node view.

Uses of Node in biouml.model.util

Methods in biouml.model.util with parameters of type Node
`static void` | `DiagramXmlWriter.writeNodeInfo(org.w3c.dom.Element element, Node node, org.w3c.dom.Document doc)`
`protected static void` | `DiagramXmlWriter.setLocation(org.w3c.dom.Element element, Node node)`
`static void` | `DiagramXmlReader.readNodeInfo(org.w3c.dom.Element element, Node node, java.lang.String diagramName)`
`protected static void` | `DiagramXmlReader.readLocation(org.w3c.dom.Element element, Node node, java.lang.String diagramName)`

Uses of Node in biouml.plugins.cellml

Methods in biouml.plugins.cellml that return Node
`protected Node` | `CellMLModelReader.createSpecies(biouml.plugins.cellml.CellMLModelReader.ComponentInfo speciesInfo)` Creates node for species.

Methods in biouml.plugins.cellml with parameters of type Node
`protected void` | `CellMLModelReader.readRole(Node reactionNode, org.w3c.dom.Element element, java.lang.String speciesName, java.lang.String role)`
`protected void` | `CellMLModelReader.readKineticLaw(biouml.plugins.cellml.CellMLModelReader.ComponentInfo reactionInfo, Node reaction, org.w3c.dom.Element element, java.lang.String varName)`

Uses of Node in biouml.plugins.ginsim

Methods in biouml.plugins.ginsim with parameters of type Node
`protected boolean` | `GinSimDiagramViewBuilder.createNodeCoreView(CompositeView container, Node node, DiagramViewOptions options, java.awt.Graphics g)`

Uses of Node in biouml.plugins.gxl

Fields in biouml.plugins.gxl declared as Node
`protected Node` | `GxlParserContext.currentNode`

Methods in biouml.plugins.gxl that return Node
`Node` | `GxlParserContext.getNodeContext()`

Methods in biouml.plugins.gxl with parameters of type Node
`protected void` | `GxlReader.GxlHandler.processNodeExtension(Node node, org.xml.sax.Attributes attrs)` It is stub for further overriding
`void` | `GxlParserContext.enterNodeContext(Node node)`

Uses of Node in biouml.plugins.sbml

Fields in biouml.plugins.sbml declared as Node
`protected Node` | `CreateDiagramElementDialog.node`

Methods in biouml.plugins.sbml that return Node
`protected Node` | `SbmlModelReader_21.readSpecie(org.w3c.dom.Element element, java.lang.String speciesId, java.lang.String speciesName)`
`protected Node` | `SbmlModelReader.readSpecie(org.w3c.dom.Element element, java.lang.String specieId, java.lang.String specieName)`
`protected Node` | `SbmlModelReader.readReaction(org.w3c.dom.Element element, java.lang.String reactionId, java.lang.String reactionName)`
`Node` | `CreateDiagramElementDialog.getNode()`
`protected Node` | `CreateDiagramElementDialog.createDiagramElement()`

Methods in biouml.plugins.sbml with parameters of type Node
`java.lang.String` | `SbmlSupport.parseFormula(java.lang.String formula, Node reaction)` General template to cinvert SBML formula into BioUML formula.
`protected boolean` | `SbmlSupport.parseAsParameter(java.lang.String token, java.lang.StringBuffer result, Node reaction)`
`protected boolean` | `SbmlModelWriter_L1.validReaction(Node reaction)`
`protected void` | `SbmlModelWriter_L1.writeFormula(java.lang.String formula, Node reaction, org.w3c.dom.Element kineticLawElement)`
`protected void` | `SbmlModelWriter_L1.writeStoichiometry(org.w3c.dom.Element specieReferenceElement, SpecieReference species, Node reaction)`
`protected boolean` | `SbmlModelWriter_21.validReaction(Node reaction)`
`protected void` | `SbmlModelWriter_21.writeFormula(java.lang.String formula, Node reaction, org.w3c.dom.Element kineticLawElement)`
`protected void` | `SbmlModelWriter_21.writeStoichiometry(org.w3c.dom.Element specieReferenceElement, SpecieReference species, Node reaction)`
`protected abstract boolean` | `SbmlModelWriter.validReaction(Node reaction)` Returns true if reaction is valid according to given version of SBML specification.
`protected void` | `SbmlModelWriter.writeSpecie(org.w3c.dom.Element speciesListElement, Node species)`
`protected void` | `SbmlModelWriter.writeReaction(org.w3c.dom.Element reactionListElement, Node reaction)`
`protected void` | `SbmlModelWriter.writeReactants(org.w3c.dom.Element reactionElement, Node reaction)`
`protected void` | `SbmlModelWriter.writeProducts(org.w3c.dom.Element reactionElement, Node reaction)`
`protected boolean` | `SbmlModelWriter.writeSpecieReferences(org.w3c.dom.Element listElement, Node reaction, java.lang.String role)`
`protected void` | `SbmlModelWriter.writeStubReference(org.w3c.dom.Element listElement, Node reaction, java.lang.String stubName)`
`protected void` | `SbmlModelWriter.writeKineticLaw(org.w3c.dom.Element reactionElement, Node reaction)`
`protected abstract void` | `SbmlModelWriter.writeFormula(java.lang.String formula, Node reaction, org.w3c.dom.Element kineticLawElement)`
`protected Variable` | `SbmlModelReader_21.readParameter(org.w3c.dom.Element element, java.lang.String parameterId, Node reaction)`
`protected void` | `SbmlModelReader_21.validateReaction(Node reaction)`
`protected void` | `SbmlModelReader_21.readStoichiometry(org.w3c.dom.Element element, SpecieReference reference, Node reaction)`
`protected void` | `SbmlModelReader_21.readKineticLawFormula(org.w3c.dom.Element element, Node reaction, KineticLaw kineticLaw)`
`protected void` | `SbmlModelReader_21.readModifiers(org.w3c.dom.Element element, Node reaction)`
`protected void` | `SbmlModelReader_11.validateReaction(Node reaction)`
`protected void` | `SbmlModelReader_11.readKineticLawFormula(org.w3c.dom.Element kineticLawElement, Node reaction, KineticLaw law)`
`protected void` | `SbmlModelReader_11.readStoichiometry(org.w3c.dom.Element element, SpecieReference reference, Node reaction)`
`protected void` | `SbmlModelReader.validateReaction(Node reaction)`
`protected void` | `SbmlModelReader.readModifiers(org.w3c.dom.Element element, Node reaction)`
`protected abstract void` | `SbmlModelReader.readStoichiometry(org.w3c.dom.Element element, SpecieReference reference, Node reactionNode)`
`protected abstract void` | `SbmlModelReader.readKineticLawFormula(org.w3c.dom.Element element, Node reaction, KineticLaw law)`
`protected void` | `SbmlModelReader.readParameterList(org.w3c.dom.Element parent, Node reaction)` Read list of parameters for the specified element.
`protected Variable` | `SbmlModelReader.readParameter(org.w3c.dom.Element element, java.lang.String parameterId, Node reaction)`
`protected void` | `SbmlModelReader.readReactants(org.w3c.dom.Element element, Node reaction)`
`protected void` | `SbmlModelReader.readProducts(org.w3c.dom.Element element, Node reaction)`
`protected void` | `SbmlModelReader.readSpecieReference(Node reactionNode, org.w3c.dom.Element element, java.lang.String specieId, java.lang.String role)`
`protected void` | `SbmlModelReader.readKineticLaw(org.w3c.dom.Element element, Node reaction)`
`protected boolean` | `SbmlModelReader.parseAsParameter(java.lang.String token, java.lang.StringBuffer result, Node reaction)`

Uses of Node in biouml.standard.diagram

Methods in biouml.standard.diagram that return Node
`protected Node` | `PathwaySemanticController.getNode(Base kernel, java.util.Set elements)`
`protected Node` | `CreateDiagramElementDialog.createDiagramElement()`
`Node` | `CreateDiagramElementDialog.getNode()`

Methods in biouml.standard.diagram with parameters of type Node
`protected void` | `ReactionPane.generateRoles(Node reactionNode)` Generates roles for reaction node and edges for pathway simulation diagram.
`protected boolean` | `PathwaySimulationDiagramViewBuilder.createNodeCoreView(CompositeView container, Node node, DiagramViewOptions options, java.awt.Graphics g)`
`CompositeView` | `PathwaySimulationDiagramViewBuilder.createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwaySimulationDiagramViewBuilder.createEventView(CompositeView eventView, Node node, PathwaySimulationDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwaySimulationDiagramViewBuilder.createEquationView(CompositeView view, Node node, PathwaySimulationDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwaySimulationDiagramViewBuilder.createStateView(CompositeView stateView, Node node, PathwaySimulationDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createCellCoreView(CompositeView container, Node node, DiagramViewOptions diagramOptions, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createGeneCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createRNACoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createProteinCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g, java.lang.String functionalState, java.lang.String configuration, java.lang.String modification)`
`protected boolean` | `PathwayDiagramViewBuilder.createSubstanceCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createReactionCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)`
`protected boolean` | `PathwayDiagramViewBuilder.createNodeCoreView(CompositeView container, Node node, DiagramViewOptions viewOptions, java.awt.Graphics g)`
`CompositeView` | `PathwayDiagramViewBuilder.createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)`
`void` | `PathwayDiagramViewBuilder.locateReaction(Node reactionNode, DiagramViewOptions options, java.awt.Graphics g)` Locate reaction.
`protected void` | `PathwayDiagramViewBuilder.doLocateReaction(Node reactionNode, DiagramViewOptions options, java.awt.Graphics g)`

Uses of Node in biouml.standard.filter

Methods in biouml.standard.filter with parameters of type Node
`protected void` | `HideAction.hideNode(Node node)`
`protected void` | `HideAction.hideNodeEdges(Node node)`
`protected void` | `BiopolimerDiagramFilter.processNode(Node node)`
`protected Action` | `BiopolimerDiagramFilter.getNodeAction(Node node)`

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