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| 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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