biouml.standard.diagram
Class PathwayDiagramViewBuilder

java.lang.Object
  biouml.model.DefaultDiagramViewBuilder
      biouml.standard.diagram.PathwayDiagramViewBuilder

All Implemented Interfaces:

DiagramViewBuilder

Direct Known Subclasses:

GeneNetworkDiagramType.GeneNetworkDiagramViewBuilder, MetabolicPathwayDiagramType.MetabolicPathwayDiagramViewBuilder, PathwaySimulationDiagramViewBuilder, SemanticNetworkDiagramType.SemanticNetworkDiagramViewBuilder

public class PathwayDiagramViewBuilder

extends DefaultDiagramViewBuilder

Default implementation of DiagramViewBuilder.

Field Summary

Fields inherited from class biouml.model.DefaultDiagramViewBuilder

log

Constructor Summary

PathwayDiagramViewBuilder()

Method Summary

protected boolean	createCellCoreView(CompositeView container, Node node, DiagramViewOptions diagramOptions, java.awt.Graphics g)
protected boolean	createConceptCoreView(CompositeView container, java.lang.String title, PathwayDiagramViewOptions diagramOptions, java.awt.Graphics g)
DiagramViewOptions	createDefaultDiagramViewOptions()
CompositeView	createDiagramView(Diagram diagram, java.awt.Graphics g) Creates the diagram view
CompositeView	createEdgeView(Edge edge, DiagramViewOptions viewOptions, java.awt.Graphics g)
CompositeView	createEquivalentNodeGroupView(EquivalentNodeGroup group, DiagramViewOptions options, java.awt.Graphics g) Creates view for equivalent node grpoup.
protected boolean	createFunctionCoreView(CompositeView container, java.lang.String title, PathwayDiagramViewOptions diagramOptions, java.awt.Graphics g)
protected boolean	createGeneCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)
protected boolean	createNodeCoreView(CompositeView container, Node node, DiagramViewOptions viewOptions, java.awt.Graphics g)
CompositeView	createNodeView(Node node, DiagramViewOptions options, java.awt.Graphics g)
protected boolean	createProcessCoreView(CompositeView container, java.lang.String title, PathwayDiagramViewOptions diagramOptions, java.awt.Graphics g)
protected boolean	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	createReactionCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)
protected void	createReactionTitle(DiagramElement reaction, PathwayDiagramViewOptions options, java.awt.Graphics g)
void	createReactionTitles(Compartment compartment, DiagramViewOptions diagramOptions, java.awt.Graphics g)
protected boolean	createRNACoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)
CompositeView	createSemanticRelationView(Edge edge, PathwayDiagramViewOptions viewOptions, java.awt.Graphics g)
protected boolean	createStateCoreView(CompositeView container, java.lang.String title, PathwayDiagramViewOptions diagramOptions, java.awt.Graphics g)
protected boolean	createSubstanceCoreView(CompositeView container, Node node, PathwayDiagramViewOptions options, java.awt.Graphics g)
protected void	doLocateReaction(Node reactionNode, DiagramViewOptions options, java.awt.Graphics g)
protected Brush	getReactionBrush(Base reaction, PathwayDiagramViewOptions options)
protected ArrowView.Tip	getRelationEndTip(Edge edge, PathwayDiagramViewOptions options)
protected Pen	getRelationPen(Edge edge, PathwayDiagramViewOptions options)
protected ArrowView.Tip	getRelationStartTip(Edge edge, PathwayDiagramViewOptions options)
void	locateReaction(Node reactionNode, DiagramViewOptions options, java.awt.Graphics g) Locate reaction.

Methods inherited from class biouml.model.DefaultDiagramViewBuilder

buildNodes, calcAttachmentPoints, createCompartmentView, createNoteView, doCreateCompartmentView, getIcon, getIcon, hideElement, isReaction, moveNode, proportion, removeElement

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PathwayDiagramViewBuilder

public PathwayDiagramViewBuilder()

Method Detail

createDefaultDiagramViewOptions

public DiagramViewOptions createDefaultDiagramViewOptions()

Specified by:

createDefaultDiagramViewOptions in interface DiagramViewBuilder

Overrides:

createDefaultDiagramViewOptions in class DefaultDiagramViewBuilder

createDiagramView

public CompositeView createDiagramView(Diagram diagram,
                                       java.awt.Graphics g)

Description copied from class: DefaultDiagramViewBuilder

Creates the diagram view

Specified by:

createDiagramView in interface DiagramViewBuilder

Overrides:

createDiagramView in class DefaultDiagramViewBuilder

createReactionTitles

public void createReactionTitles(Compartment compartment,
                                 DiagramViewOptions diagramOptions,
                                 java.awt.Graphics g)

createConceptCoreView

protected boolean createConceptCoreView(CompositeView container,
                                        java.lang.String title,
                                        PathwayDiagramViewOptions diagramOptions,
                                        java.awt.Graphics g)

createFunctionCoreView

protected boolean createFunctionCoreView(CompositeView container,
                                         java.lang.String title,
                                         PathwayDiagramViewOptions diagramOptions,
                                         java.awt.Graphics g)

createProcessCoreView

protected boolean createProcessCoreView(CompositeView container,
                                        java.lang.String title,
                                        PathwayDiagramViewOptions diagramOptions,
                                        java.awt.Graphics g)

createStateCoreView

protected boolean createStateCoreView(CompositeView container,
                                      java.lang.String title,
                                      PathwayDiagramViewOptions diagramOptions,
                                      java.awt.Graphics g)

createCellCoreView

protected boolean createCellCoreView(CompositeView container,
                                     Node node,
                                     DiagramViewOptions diagramOptions,
                                     java.awt.Graphics g)

createGeneCoreView

protected boolean createGeneCoreView(CompositeView container,
                                     Node node,
                                     PathwayDiagramViewOptions options,
                                     java.awt.Graphics g)

createRNACoreView

protected boolean createRNACoreView(CompositeView container,
                                    Node node,
                                    PathwayDiagramViewOptions options,
                                    java.awt.Graphics g)

createProteinCoreView

protected boolean createProteinCoreView(CompositeView container,
                                        Node node,
                                        PathwayDiagramViewOptions options,
                                        java.awt.Graphics g,
                                        java.lang.String functionalState,
                                        java.lang.String configuration,
                                        java.lang.String modification)

createSubstanceCoreView

protected boolean createSubstanceCoreView(CompositeView container,
                                          Node node,
                                          PathwayDiagramViewOptions options,
                                          java.awt.Graphics g)

createReactionCoreView

protected boolean createReactionCoreView(CompositeView container,
                                         Node node,
                                         PathwayDiagramViewOptions options,
                                         java.awt.Graphics g)

createReactionTitle

protected void createReactionTitle(DiagramElement reaction,
                                   PathwayDiagramViewOptions options,
                                   java.awt.Graphics g)

createNodeCoreView

protected boolean createNodeCoreView(CompositeView container,
                                     Node node,
                                     DiagramViewOptions viewOptions,
                                     java.awt.Graphics g)

Overrides:

createNodeCoreView in class DefaultDiagramViewBuilder

Returns:

indicates whether a node title should be added to node core view

createNodeView

public CompositeView createNodeView(Node node,
                                    DiagramViewOptions options,
                                    java.awt.Graphics g)

Specified by:

createNodeView in interface DiagramViewBuilder

Overrides:

createNodeView in class DefaultDiagramViewBuilder

createEquivalentNodeGroupView

public CompositeView createEquivalentNodeGroupView(EquivalentNodeGroup group,
                                                   DiagramViewOptions options,
                                                   java.awt.Graphics g)

Description copied from class: DefaultDiagramViewBuilder

Creates view for equivalent node grpoup. In view mode they are represented by one node image, in design mode they look likes compartment.

Overrides:

createEquivalentNodeGroupView in class DefaultDiagramViewBuilder

createEdgeView

public CompositeView createEdgeView(Edge edge,
                                    DiagramViewOptions viewOptions,
                                    java.awt.Graphics g)

Specified by:

createEdgeView in interface DiagramViewBuilder

Overrides:

createEdgeView in class DefaultDiagramViewBuilder

Pendung:

high take initial ports into account

createSemanticRelationView

public CompositeView createSemanticRelationView(Edge edge,
                                                PathwayDiagramViewOptions viewOptions,
                                                java.awt.Graphics g)

locateReaction

public void locateReaction(Node reactionNode,
                           DiagramViewOptions options,
                           java.awt.Graphics g)

Locate reaction.

doLocateReaction

protected void doLocateReaction(Node reactionNode,
                                DiagramViewOptions options,
                                java.awt.Graphics g)

getReactionBrush

protected Brush getReactionBrush(Base reaction,
                                 PathwayDiagramViewOptions options)

Pendung:

stub version

getRelationPen

protected Pen getRelationPen(Edge edge,
                             PathwayDiagramViewOptions options)

Pendung:

stub version

getRelationStartTip

protected ArrowView.Tip getRelationStartTip(Edge edge,
                                            PathwayDiagramViewOptions options)

getRelationEndTip

protected ArrowView.Tip getRelationEndTip(Edge edge,
                                          PathwayDiagramViewOptions options)