Uses of Class
biouml.model.Diagram

Packages that use Diagram

biouml.model
biouml.model.dynamics
biouml.model.htmlgen
biouml.model.util
biouml.plugins.cellml
biouml.plugins.ginsim
biouml.plugins.gxl
biouml.plugins.jgraph
biouml.plugins.sbml
biouml.plugins.simulation
biouml.plugins.svg
biouml.standard
biouml.standard.diagram
biouml.standard.filter
biouml.workbench.diagram

Uses of Diagram in biouml.model

Methods in biouml.model that return Diagram

Diagram	Module.getDiagram(java.lang.String name)
static Diagram	Diagram.createDiagram(DiagramType type, java.lang.String diagramName, DataCollection origin)

Methods in biouml.model with parameters of type Diagram

NodeInfo[]	QueryEngineSupport.searchLinked(Diagram diagram, Node node, QueryOptions options)
protected java.util.Set	QueryEngineSupport.searchLinked(Diagram diagram, java.util.Set lastNodes, java.util.Set linkedNodes, QueryOptions options)
NodeInfo[]	QueryEngineSupport.addLinked(Diagram diagram, Node start, NodeInfo[] linked) Appends linked nodes to the diagram.
abstract NodeInfo[]	QueryEngineSupport.getLinked(Diagram diagram, NodeInfo node, QueryOptions opt)
NodeInfo[]	QueryEngine.searchLinked(Diagram diagram, Node node, QueryOptions options)
NodeInfo[]	QueryEngine.addLinked(Diagram diagram, Node start, NodeInfo[] nodeInfoArr)
void	Node.setRelativeLocation(Diagram diagram, java.awt.Point location)
void	Module.putDiagram(Diagram diagram)
CompositeView	DiagramViewBuilder.createDiagramView(Diagram diagram, java.awt.Graphics g)
DiagramFilter	DiagramTypeSupport.getDiagramFilter(Diagram diagram)
void	DiagramTypeConverter.convert(Diagram diagram, java.lang.Class type)
void	DiagramTypeConverter.YesConverter.convert(Diagram diagram, java.lang.Class type)
void	DiagramTypeConverter.NoConverter.convert(Diagram diagram, java.lang.Class type)
void	DiagramTypeConverter.ConditionalConverter.convert(Diagram diagram, java.lang.Class type)
protected void	DiagramTypeConverter.ConditionalConverter.message(java.lang.StringBuffer buf, DiagramElement de, Diagram diagram)
DiagramFilter	DiagramType.getDiagramFilter(Diagram diagram)
boolean	DiagramExporter.accept(Diagram diagram) Returns true if the specified diagram can be exported in this format and false otherwise.
void	DiagramExporter.doExport(Diagram diagram, java.io.File file) Exports the specified diagram into the specified file or directory.
protected void	Diagram.doClone(Diagram diagram)
CompositeView	DefaultDiagramViewBuilder.createDiagramView(Diagram diagram, java.awt.Graphics g) Creates the diagram view

Uses of Diagram in biouml.model.dynamics

Methods in biouml.model.dynamics with parameters of type Diagram

protected java.util.Properties	VariablesDataCollection.createCollectionProperties(Diagram diagram)
protected static java.util.Properties	VariablesDataCollection.createProperties(Diagram diagram) Creates some properties required by DerivedDataCollection.

Constructors in biouml.model.dynamics with parameters of type Diagram

VariablesDataCollection(DataCollection parent, Diagram diagram)

Uses of Diagram in biouml.model.htmlgen

Fields in biouml.model.htmlgen declared as Diagram

protected Diagram

GenerateHTMLDialog.diagram

Methods in biouml.model.htmlgen with parameters of type Diagram

static void

GenerateHTMLDialog.genHTML(Diagram diagram, java.io.File outputFolder, java.io.File templateFile, org.apache.log4j.Category cat)

Constructors in biouml.model.htmlgen with parameters of type Diagram

GenerateHTMLDialog(javax.swing.JDialog dialog, java.lang.String title, Module module, Diagram diagram)

GenerateHTMLDialog(javax.swing.JFrame frame, java.lang.String title, Module module, Diagram diagram)

Uses of Diagram in biouml.model.util

Fields in biouml.model.util declared as Diagram

protected Diagram

DiagramXmlSupport.diagram

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

static java.awt.image.BufferedImage	ImageGenerator.generateDiagramImage(Diagram diagram)
static java.awt.image.BufferedImage	ImageGenerator.generateDiagramImage(Diagram diagram, java.awt.Graphics graphics)
void	DiagramXmlWriter.write(Diagram sourceDiagram, Module module)
void	DiagramXmlWriter.write(Diagram sourceDiagram, Module module, javax.xml.transform.Transformer transformer)
protected org.w3c.dom.Element	DiagramXmlWriter.createDiagramInfo(Diagram diagram)
protected void	DiagramXmlWriter.createEventList(org.w3c.dom.Element element, Diagram diagram)
protected void	DiagramXmlWriter.createStateList(org.w3c.dom.Element element, Diagram diagram)
protected org.w3c.dom.Element	DiagramXmlWriter.createState(State state, Diagram diagram)
protected void	DiagramXmlWriter.createTransitionList(org.w3c.dom.Element element, Diagram diagram)
protected org.w3c.dom.Element	DiagramXmlWriter.createTransition(Transition transition, Diagram diagram)
protected org.w3c.dom.Element	DiagramXmlWriter.createEvent(Event event, Diagram diagram)
protected org.w3c.dom.Element	DiagramXmlWriter.createAssignment(Assignment action, Diagram diagram)
protected void	DiagramXmlReader.readVariables(org.w3c.dom.Element modelElement, Diagram diagram)

Uses of Diagram in biouml.plugins.cellml

Fields in biouml.plugins.cellml declared as Diagram

protected Diagram

CellMLSupport.diagram

Methods in biouml.plugins.cellml that return Diagram

Diagram	CellMLModelReader.read(DataCollection origin, Module module)
protected Diagram	CellMLModelReader.readDiagram(org.w3c.dom.Element element, DataCollection origin)

Methods in biouml.plugins.cellml with parameters of type Diagram

void	CellMLModelWriter.write(Diagram sourceDiagram)
void	CellMLModelWriter.write(Diagram sourceDiagram, javax.xml.transform.Transformer transformer)

Uses of Diagram in biouml.plugins.ginsim

Fields in biouml.plugins.ginsim declared as Diagram

protected Diagram

GinSimReader.diagram

Methods in biouml.plugins.ginsim with parameters of type Diagram

boolean	GinMLExporter.accept(Diagram diagram)
void	GinMLExporter.doExport(Diagram diagram, java.io.File file)

Uses of Diagram in biouml.plugins.gxl

Fields in biouml.plugins.gxl declared as Diagram

protected Diagram

GxlReader.diagram

Methods in biouml.plugins.gxl that return Diagram

protected Diagram	GxlReader.createDiagram(java.lang.String name, DataCollection origin)
Diagram	GxlReader.readDiagram(java.io.File file, DataCollection origin)

Methods in biouml.plugins.gxl with parameters of type Diagram

void	GxlWriter.writeDiagram(java.io.File file, Diagram diagram)
protected void	GxlWriter.writeGXL(java.io.Writer out, Diagram diagram)
protected void	GxlWriter.writeGXLExtension(java.io.Writer out, Diagram diagram)
protected void	GxlWriter.writeGraph(java.io.Writer out, Diagram diagram)
boolean	GxlExporter.accept(Diagram diagram)
void	GxlExporter.doExport(Diagram diagram, java.io.File file)

Uses of Diagram in biouml.plugins.jgraph

Methods in biouml.plugins.jgraph with parameters of type Diagram

static void

DiagramToJGraphTransformer.layout(Diagram diagram, ru.biosoft.graph.Layouter layouter, java.awt.Graphics g)

Uses of Diagram in biouml.plugins.sbml

Fields in biouml.plugins.sbml declared as Diagram

protected Diagram	SbmlSupport.diagram
protected Diagram	CreateDiagramElementDialog.diagram

Methods in biouml.plugins.sbml that return Diagram

Diagram	SbmlModelReader.read(org.w3c.dom.Document document, java.lang.String name, DataCollection origin)
static Diagram	SbmlModelFactory.readDiagram(java.io.File file, DataCollection origin, java.lang.String diagramName)

Methods in biouml.plugins.sbml with parameters of type Diagram

static java.lang.Object	SbmlSemanticController.resolveName(Diagram diagram, java.lang.String sname) Search SBML model element with the specified name.
java.lang.String	SbmlSemanticController.generateReactionName(Diagram diagram) Generates unique reaction name for the specified diagram.
static boolean	SbmlModelWriter_L1.isValidModel(Diagram diagram) Checks if the model represented by diagram is representable in SBML level 1 version 1 model.
static boolean	SbmlModelWriter_21.isValidModel(Diagram diagram) Checks if the model represented by diagram is representable in SBML level 1 version 1 model.
org.w3c.dom.Document	SbmlModelWriter.createDOM(Diagram sourceDiagram)
static org.w3c.dom.Document	SbmlModelFactory.createDOM(Diagram diagram)
static void	SbmlModelFactory.writeDiagram(java.io.File file, Diagram sourceDiagram)
boolean	SbmlExporter.accept(Diagram diagram)
void	SbmlExporter.doExport(Diagram diagram, java.io.File file)

Constructors in biouml.plugins.sbml with parameters of type Diagram

CreateDiagramElementDialog(Diagram diagram, Compartment parent, java.lang.Class type)

Uses of Diagram in biouml.plugins.simulation

Fields in biouml.plugins.simulation declared as Diagram

protected Diagram

SimulationEngine.diagram

Methods in biouml.plugins.simulation that return Diagram

Diagram

SimulationEngine.getDiagram()

Methods in biouml.plugins.simulation with parameters of type Diagram

void	SimulationEngine.setDiagram(Diagram diagram)

Uses of Diagram in biouml.plugins.svg

Methods in biouml.plugins.svg with parameters of type Diagram

boolean	SvgDiagramExporter.accept(Diagram diagram) Accepts any diagram.
void	SvgDiagramExporter.doExport(Diagram diagram, java.io.File file)

Uses of Diagram in biouml.standard

Methods in biouml.standard with parameters of type Diagram

NodeInfo[]

StandardQueryEngine.getLinked(Diagram diagram, NodeInfo node, QueryOptions opt)

Uses of Diagram in biouml.standard.diagram

Methods in biouml.standard.diagram that return Diagram

protected Diagram

PathwaySimulationDiagramViewBuilder.getDiagram(DiagramElement de)

Methods in biouml.standard.diagram with parameters of type Diagram

DiagramFilter	SemanticNetworkDiagramType.getDiagramFilter(Diagram diagram)
java.lang.String	PathwaySemanticController.generateReactionName(Diagram diagram) Generates unique reaction name.
CompositeView	PathwayDiagramViewBuilder.createDiagramView(Diagram diagram, java.awt.Graphics g)
DiagramFilter	PathwayDiagramType.getDiagramFilter(Diagram diagram)

Constructors in biouml.standard.diagram with parameters of type Diagram

ReactionPane(Diagram diagram, Compartment compartment, java.awt.Point point, ViewEditorPane viewEditor)

Uses of Diagram in biouml.standard.filter

Constructors in biouml.standard.filter with parameters of type Diagram

BiopolimerDiagramFilter(Diagram diagram)

Uses of Diagram in biouml.workbench.diagram

Fields in biouml.workbench.diagram declared as Diagram

protected Diagram	ProcessDiagramDialog.diagram
protected Diagram	ImportDiagramDialog.diagram
protected Diagram	ExportDiagramDialog.diagram
protected Diagram	DiagramEditorHelper.diagram

Methods in biouml.workbench.diagram that return Diagram

Diagram

DiagramDocument.getDiagram()

Methods in biouml.workbench.diagram with parameters of type Diagram

void	DiagramsPane.removeDiagram(Diagram diagram)
boolean	DiagramImageWriter.accept(Diagram diagram) Accepts any diagram.
void	DiagramImageWriter.doExport(Diagram diagram, java.io.File file)
static DiagramExporterRegistry.ExporterInfo[]	DiagramExporterRegistry.getExporterInfo(java.lang.String format, Diagram diagram) Returns suitable exporter for the specified format.

Constructors in biouml.workbench.diagram with parameters of type Diagram

ExportDiagramDialog(Diagram diagram)

DiagramEditorHelper(Diagram diagram)

DiagramDocument(Diagram diagram)

ConvertDiagramDialog(Diagram diagram)