http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphController.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphController.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphController.java
deleted file mode 100644
index bc1b7cf..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphController.java
+++ /dev/null
@@ -1,1276 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-import static javax.swing.JOptionPane.PLAIN_MESSAGE;
-import static javax.swing.JOptionPane.showInputDialog;
-import static javax.swing.JOptionPane.showMessageDialog;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Point;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.apache.taverna.lang.observer.Observable;
-import org.apache.taverna.lang.observer.Observer;
-import net.sf.taverna.t2.ui.menu.MenuManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.CompoundEdit;
-import net.sf.taverna.t2.workbench.edits.Edit;
-import net.sf.taverna.t2.workbench.edits.EditException;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.models.graph.Graph.Alignment;
-import net.sf.taverna.t2.workbench.models.graph.GraphEdge.ArrowStyle;
-import net.sf.taverna.t2.workbench.models.graph.GraphElement.LineStyle;
-import net.sf.taverna.t2.workbench.models.graph.GraphShapeElement.Shape;
-import net.sf.taverna.t2.workbench.selection.DataflowSelectionModel;
-import net.sf.taverna.t2.workbench.selection.events.DataflowSelectionMessage;
-import net.sf.taverna.t2.workflow.edits.AddDataLinkEdit;
-import net.sf.taverna.t2.workflow.edits.RemoveDataLinkEdit;
-
-import org.apache.log4j.Logger;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.common.NamedSet;
-import org.apache.taverna.scufl2.api.common.Scufl2Tools;
-import org.apache.taverna.scufl2.api.common.WorkflowBean;
-import org.apache.taverna.scufl2.api.core.BlockingControlLink;
-import org.apache.taverna.scufl2.api.core.ControlLink;
-import org.apache.taverna.scufl2.api.core.DataLink;
-import org.apache.taverna.scufl2.api.core.Processor;
-import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.port.InputActivityPort;
-import org.apache.taverna.scufl2.api.port.InputPort;
-import org.apache.taverna.scufl2.api.port.InputProcessorPort;
-import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.OutputActivityPort;
-import org.apache.taverna.scufl2.api.port.OutputPort;
-import org.apache.taverna.scufl2.api.port.OutputProcessorPort;
-import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.Port;
-import org.apache.taverna.scufl2.api.port.ProcessorPort;
-import org.apache.taverna.scufl2.api.port.ReceiverPort;
-import org.apache.taverna.scufl2.api.port.SenderPort;
-import org.apache.taverna.scufl2.api.port.WorkflowPort;
-import org.apache.taverna.scufl2.api.profiles.ProcessorBinding;
-import org.apache.taverna.scufl2.api.profiles.Profile;
-
-/**
- * @author David Withers
- */
-public abstract class GraphController implements
-               Observer<DataflowSelectionMessage> {
-       public enum PortStyle {
-               ALL {
-                       @Override
-                       Shape inputShape() {
-                               return Shape.INVHOUSE;
-                       }
-
-                       @Override
-                       Shape outputShape() {
-                               return Shape.HOUSE;
-                       }
-
-                       @Override
-                       Shape processorShape() {
-                               return Shape.RECORD;
-                       }
-               },
-               BOUND {
-                       @Override
-                       Shape inputShape() {
-                               return Shape.INVHOUSE;
-                       }
-
-                       @Override
-                       Shape outputShape() {
-                               return Shape.HOUSE;
-                       }
-
-                       @Override
-                       Shape processorShape() {
-                               return Shape.RECORD;
-                       }
-               },
-               NONE {
-                       @Override
-                       Shape inputShape() {
-                               return Shape.BOX;
-                       }
-
-                       @Override
-                       Shape outputShape() {
-                               return Shape.BOX;
-                       }
-
-                       @Override
-                       Shape processorShape() {
-                               return Shape.BOX;
-                       }
-               },
-               BLOB {
-                       @Override
-                       Shape inputShape() {
-                               return Shape.CIRCLE;
-                       }
-
-                       @Override
-                       Shape outputShape() {
-                               return Shape.CIRCLE;
-                       }
-
-                       @Override
-                       Shape processorShape() {
-                               return Shape.CIRCLE;
-                       }
-               };
-
-               abstract Shape inputShape();
-
-               abstract Shape outputShape();
-
-               abstract Shape processorShape();
-
-               Shape mergeShape() {
-                       return Shape.CIRCLE;
-               }
-       }
-
-       private static Logger logger = Logger.getLogger(GraphController.class);
-
-       private Map<String, GraphElement> idToElement = new HashMap<>();
-       private Map<WorkflowBean, GraphElement> workflowToGraph = new 
HashMap<>();
-       private Map<Port, GraphNode> ports = new HashMap<>();
-       private Map<Graph, GraphNode> inputControls = new HashMap<>();
-       private Map<Graph, GraphNode> outputControls = new HashMap<>();
-       private Map<Port, Port> nestedWorkflowPorts = new HashMap<>();
-       private Map<WorkflowPort, ProcessorPort> workflowPortToProcessorPort = 
new HashMap<>();
-       private Map<Port, Processor> portToProcessor = new HashMap<>();
-
-       private EditManager editManager;
-       private final Workflow workflow;
-       private final Profile profile;
-       private DataflowSelectionModel dataflowSelectionModel;
-       private GraphEventManager graphEventManager;
-       private Component componentForPopups;
-
-       // graph settings
-       private PortStyle portStyle = PortStyle.NONE;
-       private Map<Processor, PortStyle> processorPortStyle = new HashMap<>();
-       private Alignment alignment = Alignment.VERTICAL;
-       private boolean expandNestedDataflows = true;
-       private Map<Activity, Boolean> dataflowExpansion = new HashMap<>();
-       protected Map<String, GraphElement> graphElementMap = new HashMap<>();
-       protected GraphElement edgeCreationSource, edgeCreationSink;
-       protected GraphEdge edgeMoveElement;
-       protected boolean edgeCreationFromSource = false;
-       protected boolean edgeCreationFromSink = false;
-       private Graph graph;
-       private boolean interactive;
-       private final ColourManager colourManager;
-
-       private Scufl2Tools scufl2Tools = new Scufl2Tools();
-
-       public GraphController(Workflow workflow, Profile profile,
-                       boolean interactive, Component componentForPopups,
-                       EditManager editManager, MenuManager menuManager,
-                       ColourManager colourManager) {
-               this(workflow, profile, interactive, componentForPopups,
-                               Alignment.VERTICAL, PortStyle.NONE, 
editManager, menuManager,
-                               colourManager);
-       }
-
-       public GraphController(Workflow workflow, Profile profile,
-                       boolean interactive, Component componentForPopups,
-                       Alignment alignment, PortStyle portStyle, EditManager 
editManager,
-                       MenuManager menuManager, ColourManager colourManager) {
-               this.workflow = workflow;
-               this.profile = profile;
-               this.interactive = interactive;
-               this.componentForPopups = componentForPopups;
-               this.alignment = alignment;
-               this.portStyle = portStyle;
-               this.editManager = editManager;
-               this.colourManager = colourManager;
-               this.graphEventManager = new DefaultGraphEventManager(this,
-                               componentForPopups, menuManager);
-               graph = generateGraph();
-       }
-
-       public abstract Graph createGraph();
-
-       public abstract GraphNode createGraphNode();
-
-       public abstract GraphEdge createGraphEdge();
-
-       public void mapElement(String id, GraphElement element) {
-               idToElement.put(id, element);
-       }
-
-       public GraphElement getElement(String id) {
-               return idToElement.get(id);
-       }
-
-       public Graph getGraph() {
-               return graph;
-       }
-
-       public abstract void redraw();
-
-       /**
-        * Generates a graph model of a dataflow.
-        * 
-        * @return
-        */
-       public Graph generateGraph() {
-               workflowToGraph.clear();
-               ports.clear();
-               inputControls.clear();
-               outputControls.clear();
-               nestedWorkflowPorts.clear();
-               workflowPortToProcessorPort.clear();
-               graphElementMap.clear();
-               portToProcessor.clear();
-               return generateGraph(workflow, "", workflow.getName(), 0);
-       }
-
-       private Graph generateGraph(Workflow dataflow, String prefix, String 
name,
-                       int depth) {
-               Graph graph = createGraph();
-               graph.setId(prefix + name);
-               graph.setAlignment(getAlignment());
-               if (getPortStyle().equals(PortStyle.BLOB) || depth == 0)
-                       graph.setLabel("");
-               else
-                       graph.setLabel(name);
-               
graph.setFillColor(GraphColorManager.getSubGraphFillColor(depth));
-               if (depth == 0)
-                       graph.setLineStyle(LineStyle.NONE);
-               else
-                       graph.setLineStyle(LineStyle.SOLID);
-               graph.setColor(Color.BLACK);
-               graph.setShape(Shape.BOX);
-
-               if (depth == 0)
-                       graph.setWorkflowBean(dataflow);
-               if (interactive)
-                       graph.setWorkflowBean(dataflow);
-
-               // processors
-               for (Processor processor : dataflow.getProcessors())
-                       graph.addNode(generateProcessorNode(processor, 
graph.getId(), depth));
-
-               // dataflow outputs
-               NamedSet<OutputWorkflowPort> outputPorts = 
dataflow.getOutputPorts();
-               if (outputPorts.size() > 0 || depth > 0)
-                       graph.addSubgraph(generateOutputsGraph(outputPorts, 
graph.getId(),
-                                       graph, depth));
-
-               // dataflow inputs
-               NamedSet<InputWorkflowPort> inputPorts = 
dataflow.getInputPorts();
-               if (inputPorts.size() > 0 || depth > 0)
-                       graph.addSubgraph(generateInputsGraph(inputPorts, 
graph.getId(),
-                                       graph, depth));
-
-               // datalinks
-               for (DataLink datalink : dataflow.getDataLinks()) {
-                       GraphEdge edge = generateDataLinkEdge(datalink, depth);
-                       if (edge != null)
-                               graph.addEdge(edge);
-               }
-
-               // controlLinks
-               for (ControlLink controlLink : dataflow.getControlLinks())
-                       if (controlLink instanceof BlockingControlLink) {
-                               GraphEdge edge = generateControlLinkEdge(
-                                               (BlockingControlLink) 
controlLink, depth);
-                               if (edge != null)
-                                       graph.addEdge(edge);
-                       }
-
-               graphElementMap.put(graph.getId(), graph);
-               return graph;
-       }
-
-       public void transformGraph(Graph oldGraph, Graph newGraph) {
-               oldGraph.setAlignment(newGraph.getAlignment());
-               transformGraphElement(oldGraph, newGraph);
-               List<GraphEdge> oldEdges = new ArrayList<>(oldGraph.getEdges());
-               List<GraphEdge> newEdges = new ArrayList<>(newGraph.getEdges());
-               for (GraphEdge oldEdge : oldEdges) {
-                       int index = newEdges.indexOf(oldEdge);
-                       if (index >= 0) {
-                               GraphEdge newEdge = newEdges.remove(index);
-                               oldEdge.setPath(newEdge.getPath());
-                               workflowToGraph.put(oldEdge.getWorkflowBean(), 
oldEdge);
-                       } else
-                               oldGraph.removeEdge(oldEdge);
-               }
-               List<GraphNode> newNodes = new ArrayList<>(newGraph.getNodes());
-               List<GraphNode> oldNodes = new ArrayList<>(oldGraph.getNodes());
-               for (GraphNode oldNode : oldNodes) {
-                       int index = newNodes.indexOf(oldNode);
-                       if (index >= 0) {
-                               GraphNode newNode = newNodes.remove(index);
-                               oldNode.setExpanded(newNode.isExpanded());
-                               List<GraphNode> newSourceNodes = new 
ArrayList<>(
-                                               newNode.getSourceNodes());
-                               List<GraphNode> oldSourceNodes = new 
ArrayList<>(
-                                               oldNode.getSourceNodes());
-                               for (GraphNode oldSourceNode : oldSourceNodes) {
-                                       int sourceNodeIndex = 
newSourceNodes.indexOf(oldSourceNode);
-                                       if (sourceNodeIndex >= 0) {
-                                               GraphNode newSourceNode = 
newSourceNodes
-                                                               
.remove(sourceNodeIndex);
-                                               
transformGraphElement(oldSourceNode, newSourceNode);
-                                       } else
-                                               
oldNode.removeSourceNode(oldSourceNode);
-                               }
-                               for (GraphNode sourceNode : newSourceNodes)
-                                       oldNode.addSourceNode(sourceNode);
-                               List<GraphNode> newSinkNodes = new ArrayList<>(
-                                               newNode.getSinkNodes());
-                               List<GraphNode> oldSinkNodes = new ArrayList<>(
-                                               oldNode.getSinkNodes());
-                               for (GraphNode oldSinkNode : oldSinkNodes) {
-                                       int sinkNodeIndex = 
newSinkNodes.indexOf(oldSinkNode);
-                                       if (sinkNodeIndex >= 0) {
-                                               GraphNode newSinkNode = 
newSinkNodes
-                                                               
.remove(sinkNodeIndex);
-                                               
transformGraphElement(oldSinkNode, newSinkNode);
-                                       } else
-                                               
oldNode.removeSinkNode(oldSinkNode);
-                               }
-                               for (GraphNode sinkNode : newSinkNodes)
-                                       oldNode.addSinkNode(sinkNode);
-                               Graph oldSubGraph = oldNode.getGraph();
-                               Graph newSubGraph = newNode.getGraph();
-                               if (oldSubGraph != null && newSubGraph != null)
-                                       transformGraph(oldSubGraph, 
newSubGraph);
-                               transformGraphElement(oldNode, newNode);
-                       } else
-                               oldGraph.removeNode(oldNode);
-               }
-               List<Graph> newSubGraphs = new 
ArrayList<>(newGraph.getSubgraphs());
-               List<Graph> oldSubGraphs = new 
ArrayList<>(oldGraph.getSubgraphs());
-               for (Graph oldSubGraph : oldSubGraphs) {
-                       int index = newSubGraphs.indexOf(oldSubGraph);
-                       if (index >= 0) {
-                               Graph newSubGraph = newSubGraphs.remove(index);
-                               transformGraph(oldSubGraph, newSubGraph);
-                       } else
-                               oldGraph.removeSubgraph(oldSubGraph);
-               }
-               for (GraphNode node : newNodes)
-                       oldGraph.addNode(node);
-               for (Graph graph : newSubGraphs)
-                       oldGraph.addSubgraph(graph);
-               for (GraphEdge newEdge : newEdges)
-                       oldGraph.addEdge(newEdge);
-       }
-
-       public void transformGraphElement(GraphShapeElement oldGraphElement,
-                       GraphShapeElement newGraphElement) {
-               
oldGraphElement.setWorkflowBean(newGraphElement.getWorkflowBean());
-               oldGraphElement.setShape(newGraphElement.getShape());
-               oldGraphElement.setSize(newGraphElement.getSize());
-               oldGraphElement.setPosition(newGraphElement.getPosition());
-               oldGraphElement.setLabel(newGraphElement.getLabel());
-               
oldGraphElement.setLabelPosition(newGraphElement.getLabelPosition());
-               oldGraphElement.setLineStyle(newGraphElement.getLineStyle());
-               oldGraphElement.setOpacity(newGraphElement.getOpacity());
-               oldGraphElement.setVisible(newGraphElement.isVisible());
-               oldGraphElement.setColor(newGraphElement.getColor());
-               oldGraphElement.setFillColor(newGraphElement.getFillColor());
-               workflowToGraph.put(oldGraphElement.getWorkflowBean(), 
oldGraphElement);
-       }
-
-       public void filterGraph(Set<?> dataflowEntities) {
-               Set<GraphElement> graphElements = new HashSet<>();
-               for (Entry<WorkflowBean, GraphElement> entry : workflowToGraph
-                               .entrySet())
-                       if (!dataflowEntities.contains(entry.getKey()))
-                               graphElements.add(entry.getValue());
-               filterGraph(getGraph(), graphElements);
-       }
-
-       private void filterGraph(Graph graph, Set<GraphElement> graphElements) {
-               for (GraphNode node : graph.getNodes()) {
-                       node.setFiltered(graphElements.contains(node));
-                       Graph subgraph = node.getGraph();
-                       if (subgraph != null)
-                               if (graphElements.contains(subgraph)) {
-                                       removeFilter(subgraph);
-                                       subgraph.setFiltered(true);
-                               } else {
-                                       subgraph.setFiltered(false);
-                                       filterGraph(subgraph, graphElements);
-                               }
-               }
-               for (GraphEdge edge : graph.getEdges())
-                       edge.setFiltered(graphElements.contains(edge));
-               for (Graph subgraph : graph.getSubgraphs())
-                       if (graphElements.contains(subgraph)) {
-                               removeFilter(subgraph);
-                               subgraph.setFiltered(true);
-                       } else {
-                               subgraph.setFiltered(false);
-                               filterGraph(subgraph, graphElements);
-                       }
-       }
-
-       public void removeFilter() {
-               for (Entry<WorkflowBean, GraphElement> entry : workflowToGraph
-                               .entrySet())
-                       entry.getValue().setFiltered(false);
-       }
-
-       private void removeFilter(Graph graph) {
-               for (GraphNode node : graph.getNodes()) {
-                       node.setOpacity(1f);
-                       Graph subgraph = node.getGraph();
-                       if (subgraph != null) {
-                               subgraph.setFiltered(false);
-                               removeFilter(subgraph);
-                       }
-               }
-               for (GraphEdge edge : graph.getEdges())
-                       edge.setFiltered(false);
-               for (Graph subgraph : graph.getSubgraphs()) {
-                       subgraph.setFiltered(false);
-                       removeFilter(subgraph);
-               }
-       }
-
-       private GraphEdge generateControlLinkEdge(BlockingControlLink condition,
-                       int depth) {
-               GraphEdge edge = null;
-               GraphElement source = 
workflowToGraph.get(condition.getUntilFinished());
-               GraphElement sink = workflowToGraph.get(condition.getBlock());
-               if (source != null && sink != null) {
-                       edge = createGraphEdge();
-                       if (source instanceof Graph)
-                               edge.setSource(outputControls.get(source));
-                       else if (source instanceof GraphNode)
-                               edge.setSource((GraphNode) source);
-                       if (sink instanceof Graph)
-                               edge.setSink(inputControls.get(sink));
-                       else if (sink instanceof GraphNode)
-                               edge.setSink((GraphNode) sink);
-                       String sourceId = edge.getSource().getId();
-                       String sinkId = edge.getSink().getId();
-                       edge.setId(sourceId + "->" + sinkId);
-                       edge.setLineStyle(LineStyle.SOLID);
-                       edge.setColor(Color.decode("#505050"));
-                       edge.setFillColor(null);
-                       edge.setArrowHeadStyle(ArrowStyle.DOT);
-                       if (depth == 0)
-                               edge.setWorkflowBean(condition);
-                       if (interactive)
-                               edge.setWorkflowBean(condition);
-                       workflowToGraph.put(condition, edge);
-                       graphElementMap.put(edge.getId(), edge);
-               }
-               return edge;
-       }
-
-       private GraphEdge generateDataLinkEdge(DataLink datalink, int depth) {
-               GraphEdge edge = null;
-               Port sourcePort = datalink.getReceivesFrom();
-               Port sinkPort = datalink.getSendsTo();
-               if (nestedWorkflowPorts.containsKey(sourcePort))
-                       sourcePort = nestedWorkflowPorts.get(sourcePort);
-               if (nestedWorkflowPorts.containsKey(sinkPort))
-                       sinkPort = nestedWorkflowPorts.get(sinkPort);
-               GraphNode sourceNode = ports.get(sourcePort);
-               GraphNode sinkNode = ports.get(sinkPort);
-               if (sourceNode != null && sinkNode != null) {
-                       edge = createGraphEdge();
-                       edge.setSource(sourceNode);
-                       edge.setSink(sinkNode);
-
-                       StringBuilder id = new StringBuilder();
-                       if (sourceNode.getParent() instanceof GraphNode) {
-                               id.append(sourceNode.getParent().getId());
-                               id.append(":");
-                               id.append(sourceNode.getId());
-                       } else
-                               id.append(sourceNode.getId());
-                       id.append("->");
-                       if (sinkNode.getParent() instanceof GraphNode) {
-                               id.append(sinkNode.getParent().getId());
-                               id.append(":");
-                               id.append(sinkNode.getId());
-                       } else
-                               id.append(sinkNode.getId());
-                       edge.setId(id.toString());
-                       edge.setLineStyle(LineStyle.SOLID);
-                       edge.setColor(Color.BLACK);
-                       edge.setFillColor(Color.BLACK);
-                       if (depth == 0)
-                               edge.setWorkflowBean(datalink);
-                       if (interactive)
-                               edge.setWorkflowBean(datalink);
-                       workflowToGraph.put(datalink, edge);
-                       graphElementMap.put(edge.getId(), edge);
-               }
-               return edge;
-       }
-
-       private Graph generateInputsGraph(NamedSet<InputWorkflowPort> 
inputPorts,
-                       String prefix, Graph graph, int depth) {
-               Graph inputs = createGraph();
-               inputs.setId(prefix + "sources");
-               inputs.setColor(Color.BLACK);
-               inputs.setFillColor(null);
-               inputs.setShape(Shape.BOX);
-               inputs.setLineStyle(LineStyle.DOTTED);
-               if (getPortStyle().equals(PortStyle.BLOB))
-                       inputs.setLabel("");
-               else
-                       inputs.setLabel("Workflow input ports");
-
-               GraphNode triangle = createGraphNode();
-               triangle.setId(prefix + "WORKFLOWINTERNALSOURCECONTROL");
-               triangle.setLabel("");
-               triangle.setShape(Shape.TRIANGLE);
-               triangle.setSize(new Dimension((int) (0.2f * 72), (int) 
((Math.sin(Math
-                               .toRadians(60)) * 0.2) * 72)));
-               triangle.setFillColor(Color.decode("#ff4040"));
-               triangle.setColor(Color.BLACK);
-               triangle.setLineStyle(LineStyle.SOLID);
-               inputs.addNode(triangle);
-               inputControls.put(graph, triangle);
-
-               for (InputWorkflowPort inputWorkflowPort : inputPorts) {
-                       GraphNode inputNode = createGraphNode();
-                       inputNode.setId(prefix + "WORKFLOWINTERNALSOURCE_"
-                                       + inputWorkflowPort.getName());
-                       if (getPortStyle().equals(PortStyle.BLOB)) {
-                               inputNode.setLabel("");
-                               inputNode.setSize(new Dimension((int) (0.3f * 
72),
-                                               (int) (0.3f * 72)));
-                       } else
-                               inputNode.setLabel(inputWorkflowPort.getName());
-                       inputNode.setShape(getPortStyle().inputShape());
-                       inputNode.setColor(Color.BLACK);
-                       inputNode.setLineStyle(LineStyle.SOLID);
-                       inputNode.setFillColor(Color.decode("#8ed6f0"));
-                       if (depth == 0)
-                               inputNode.setInteractive(true);
-                       if (interactive)
-                               inputNode.setInteractive(true);
-                       if (depth < 2) {
-                               inputNode.setWorkflowBean(inputWorkflowPort);
-                               if 
(workflowPortToProcessorPort.containsKey(inputWorkflowPort)) {
-                                       ProcessorPort port = 
workflowPortToProcessorPort
-                                                       .get(inputWorkflowPort);
-                                       inputNode.setWorkflowBean(port);
-                                       workflowToGraph.put(port, inputNode);
-                               } else {
-                                       
inputNode.setWorkflowBean(inputWorkflowPort);
-                                       workflowToGraph.put(inputWorkflowPort, 
inputNode);
-                               }
-                       }
-                       ports.put(inputWorkflowPort, inputNode);
-                       inputs.addNode(inputNode);
-                       graphElementMap.put(inputNode.getId(), inputNode);
-               }
-               return inputs;
-       }
-
-       private Graph generateOutputsGraph(
-                       NamedSet<OutputWorkflowPort> outputPorts, String prefix,
-                       Graph graph, int depth) {
-               Graph outputs = createGraph();
-               outputs.setId(prefix + "sinks");
-               outputs.setColor(Color.BLACK);
-               outputs.setFillColor(null);
-               outputs.setShape(Shape.BOX);
-               outputs.setLineStyle(LineStyle.DOTTED);
-               if (getPortStyle().equals(PortStyle.BLOB))
-                       outputs.setLabel("");
-               else
-                       outputs.setLabel("Workflow output ports");
-
-               GraphNode triangle = createGraphNode();
-               triangle.setId(prefix + "WORKFLOWINTERNALSINKCONTROL");
-               triangle.setLabel("");
-               triangle.setShape(Shape.INVTRIANGLE);
-               triangle.setSize(new Dimension((int) (0.2f * 72), (int) 
((Math.sin(Math
-                               .toRadians(60)) * 0.2) * 72)));
-               triangle.setFillColor(Color.decode("#66cd00"));
-               triangle.setColor(Color.BLACK);
-               triangle.setLineStyle(LineStyle.SOLID);
-               outputs.addNode(triangle);
-               outputControls.put(graph, triangle);
-
-               for (OutputWorkflowPort outputWorkflowPort : outputPorts) {
-                       GraphNode outputNode = createGraphNode();
-                       outputNode.setId(prefix + "WORKFLOWINTERNALSINK_"
-                                       + outputWorkflowPort.getName());
-                       if (getPortStyle().equals(PortStyle.BLOB)) {
-                               outputNode.setLabel("");
-                               outputNode.setSize(new Dimension((int) (0.3f * 
72),
-                                               (int) (0.3f * 72)));
-                       } else
-                               
outputNode.setLabel(outputWorkflowPort.getName());
-                       outputNode.setShape(getPortStyle().outputShape());
-                       outputNode.setColor(Color.BLACK);
-                       outputNode.setLineStyle(LineStyle.SOLID);
-                       outputNode.setFillColor(Color.decode("#8ed6f0"));
-                       if (depth == 0)
-                               outputNode.setInteractive(true);
-                       if (interactive)
-                               outputNode.setInteractive(true);
-                       if (depth < 2) {
-                               if 
(workflowPortToProcessorPort.containsKey(outputWorkflowPort)) {
-                                       ProcessorPort port = 
workflowPortToProcessorPort
-                                                       
.get(outputWorkflowPort);
-                                       outputNode.setWorkflowBean(port);
-                                       workflowToGraph.put(port, outputNode);
-                               } else {
-                                       
outputNode.setWorkflowBean(outputWorkflowPort);
-                                       workflowToGraph.put(outputWorkflowPort, 
outputNode);
-                               }
-                       }
-                       ports.put(outputWorkflowPort, outputNode);
-                       outputs.addNode(outputNode);
-                       graphElementMap.put(outputNode.getId(), outputNode);
-               }
-               return outputs;
-       }
-
-       private GraphNode generateProcessorNode(Processor processor, String 
prefix,
-                       int depth) {
-               // Blatantly ignoring any other activities for now
-               ProcessorBinding processorBinding = scufl2Tools
-                               .processorBindingForProcessor(processor, 
profile);
-               Activity activity = processorBinding.getBoundActivity();
-               @SuppressWarnings("unused")
-               URI activityType = activity.getType();
-
-               GraphNode node = createGraphNode();
-               node.setId(prefix + processor.getName());
-               if (getPortStyle().equals(PortStyle.BLOB)) {
-                       node.setLabel("");
-                       node.setSize(new Dimension((int) (0.3f * 72), (int) 
(0.3f * 72)));
-               } else
-                       node.setLabel(processor.getName());
-               node.setShape(getPortStyle(processor).processorShape());
-               node.setColor(Color.BLACK);
-               node.setLineStyle(LineStyle.SOLID);
-               // if 
(activityType.equals(URI.create(NonExecutableActivity.URI))) {
-               // if (activityType.equals(URI.create(DisabledActivity.URI))) {
-               // node.setFillColor(GraphColorManager
-               // .getFillColor(((DisabledActivity) activity)
-               // .getActivity(), colourManager));
-               // } else {
-               // node.setFillColor(GraphColorManager
-               // .getFillColor(activityType, colourManager));
-               // }
-               // node.setOpacity(0.3f);
-               // } else
-               node.setFillColor(GraphColorManager.getFillColor(activity,
-                               colourManager));
-
-               // check whether the nested workflow processors should be 
clickable or
-               // not, if top level workflow then should be clickable 
regardless
-               if (depth == 0) {
-                       node.setInteractive(true);
-                       node.setWorkflowBean(processor);
-               }
-               if (interactive) {
-                       node.setInteractive(true);
-                       node.setWorkflowBean(processor);
-               }
-
-               if (scufl2Tools.containsNestedWorkflow(processor, profile)
-                               && expandNestedDataflow(activity)) {
-                       Workflow subDataflow = 
scufl2Tools.nestedWorkflowForProcessor(
-                                       processor, profile);
-
-                       NamedSet<InputWorkflowPort> inputWorkflowPorts = 
subDataflow
-                                       .getInputPorts();
-                       for (InputActivityPort inputActivityPort : 
activity.getInputPorts()) {
-                               InputWorkflowPort inputWorkflowPort = 
inputWorkflowPorts
-                                               
.getByName(inputActivityPort.getName());
-                               InputProcessorPort inputProcessorPort = 
scufl2Tools
-                                               
.processorPortBindingForPort(inputActivityPort, profile)
-                                               .getBoundProcessorPort();
-                               nestedWorkflowPorts.put(inputProcessorPort, 
inputWorkflowPort);
-                               
workflowPortToProcessorPort.put(inputWorkflowPort,
-                                               inputProcessorPort);
-                               processorBinding.getInputPortBindings();
-                       }
-
-                       NamedSet<OutputWorkflowPort> outputWorkflowPorts = 
subDataflow
-                                       .getOutputPorts();
-                       for (OutputActivityPort outputActivityPort : activity
-                                       .getOutputPorts()) {
-                               OutputWorkflowPort outputWorkflowPort = 
outputWorkflowPorts
-                                               
.getByName(outputActivityPort.getName());
-                               OutputProcessorPort outputProcessorPort = 
scufl2Tools
-                                               
.processorPortBindingForPort(outputActivityPort,
-                                                               
profile).getBoundProcessorPort();
-                               nestedWorkflowPorts
-                                               .put(outputProcessorPort, 
outputWorkflowPort);
-                               
workflowPortToProcessorPort.put(outputWorkflowPort,
-                                               outputProcessorPort);
-                       }
-
-                       Graph subGraph = generateGraph(subDataflow, prefix,
-                                       processor.getName(), depth + 1);
-                       // TODO why does this depth matter?
-                       if (depth == 0)
-                               subGraph.setWorkflowBean(processor);
-                       if (interactive)
-                               subGraph.setWorkflowBean(processor);
-                       node.setGraph(subGraph);
-                       node.setExpanded(true);
-
-                       workflowToGraph.put(processor, subGraph);
-               } else {
-                       graphElementMap.put(node.getId(), node);
-                       workflowToGraph.put(processor, node);
-               }
-
-               NamedSet<InputProcessorPort> inputPorts = 
processor.getInputPorts();
-               if (inputPorts.size() == 0) {
-                       GraphNode portNode = createGraphNode();
-                       portNode.setShape(Shape.BOX);
-                       portNode.setColor(Color.BLACK);
-                       portNode.setFillColor(node.getFillColor());
-                       portNode.setLineStyle(LineStyle.SOLID);
-                       node.addSinkNode(portNode);
-               } else
-                       for (InputPort inputPort : inputPorts) {
-                               GraphNode portNode = createGraphNode();
-                               portNode.setId("i" + 
inputPort.getName().replaceAll("\\.", ""));
-                               portNode.setLabel(inputPort.getName());
-                               portNode.setShape(Shape.BOX);
-                               portNode.setColor(Color.BLACK);
-                               portNode.setFillColor(node.getFillColor());
-                               portNode.setLineStyle(LineStyle.SOLID);
-                               if (depth == 0)
-                                       portNode.setWorkflowBean(inputPort);
-                               if (interactive)
-                                       portNode.setWorkflowBean(inputPort);
-                               if (!node.isExpanded())
-                                       workflowToGraph.put(inputPort, 
portNode);
-                               ports.put(inputPort, portNode);
-                               node.addSinkNode(portNode);
-                               graphElementMap.put(portNode.getId(), portNode);
-                               // portToActivity.put(inputPort, activity);
-                               portToProcessor.put(inputPort, processor);
-                       }
-
-               NamedSet<OutputProcessorPort> outputPorts = 
processor.getOutputPorts();
-               if (outputPorts.size() == 0) {
-                       GraphNode portNode = createGraphNode();
-                       portNode.setShape(Shape.BOX);
-                       portNode.setColor(Color.BLACK);
-                       portNode.setFillColor(node.getFillColor());
-                       portNode.setLineStyle(LineStyle.SOLID);
-                       node.addSourceNode(portNode);
-               } else
-                       for (OutputPort outputPort : outputPorts) {
-                               GraphNode portNode = createGraphNode();
-                               portNode.setId("o" + 
outputPort.getName().replaceAll("\\.", ""));
-                               portNode.setLabel(outputPort.getName());
-                               portNode.setShape(Shape.BOX);
-                               portNode.setColor(Color.BLACK);
-                               portNode.setFillColor(node.getFillColor());
-                               portNode.setLineStyle(LineStyle.SOLID);
-                               if (depth == 0)
-                                       portNode.setWorkflowBean(outputPort);
-                               if (interactive)
-                                       portNode.setWorkflowBean(outputPort);
-                               if (!node.isExpanded())
-                                       workflowToGraph.put(outputPort, 
portNode);
-                               ports.put(outputPort, portNode);
-                               node.addSourceNode(portNode);
-                               graphElementMap.put(portNode.getId(), portNode);
-                               // portToActivity.put(outputPort, activity);
-                               portToProcessor.put(outputPort, processor);
-                       }
-
-               return node;
-       }
-
-       /**
-        * Returns the dataflow.
-        * 
-        * @return the dataflow
-        */
-       public Workflow getWorkflow() {
-               return workflow;
-       }
-
-       public Profile getProfile() {
-               return profile;
-       }
-
-       /**
-        * Returns the dataflowSelectionModel.
-        * 
-        * @return the dataflowSelectionModel
-        */
-       public DataflowSelectionModel getDataflowSelectionModel() {
-               return dataflowSelectionModel;
-       }
-
-       /**
-        * Sets the dataflowSelectionModel.
-        * 
-        * @param dataflowSelectionModel
-        *            the new dataflowSelectionModel
-        */
-       public void setDataflowSelectionModel(
-                       DataflowSelectionModel dataflowSelectionModel) {
-               if (this.dataflowSelectionModel != null)
-                       this.dataflowSelectionModel.removeObserver(this);
-               this.dataflowSelectionModel = dataflowSelectionModel;
-               this.dataflowSelectionModel.addObserver(this);
-       }
-
-       /**
-        * Sets the proportion of the node's jobs that have been completed.
-        * 
-        * @param nodeId
-        *            the id of the node
-        * @param complete
-        *            the proportion of the nodes's jobs that have been 
completed, a
-        *            value between 0.0 and 1.0
-        */
-       public void setNodeCompleted(String nodeId, float complete) {
-               if (graphElementMap.containsKey(nodeId)) {
-                       GraphElement graphElement = graphElementMap.get(nodeId);
-                       graphElement.setCompleted(complete);
-               }
-       }
-
-       public void setEdgeActive(String edgeId, boolean active) {
-       }
-
-       /**
-        * Returns the alignment.
-        * 
-        * @return the alignment
-        */
-       public Alignment getAlignment() {
-               return alignment;
-       }
-
-       /**
-        * Returns the portStyle.
-        * 
-        * @return the portStyle
-        */
-       public PortStyle getPortStyle() {
-               return portStyle;
-       }
-
-       /**
-        * Returns the portStyle for a processor.
-        * 
-        * @return the portStyle for a processor
-        */
-       public PortStyle getPortStyle(Processor processor) {
-               if (processorPortStyle.containsKey(processor))
-                       return processorPortStyle.get(processor);
-               return portStyle;
-       }
-
-       /**
-        * Sets the alignment.
-        * 
-        * @param alignment
-        *            the new alignment
-        */
-       public void setAlignment(Alignment alignment) {
-               this.alignment = alignment;
-       }
-
-       /**
-        * Sets the portStyle.
-        * 
-        * @param style
-        *            the new portStyle
-        */
-       public void setPortStyle(PortStyle portStyle) {
-               this.portStyle = portStyle;
-               processorPortStyle.clear();
-       }
-
-       /**
-        * Sets the portStyle for a processor.
-        * 
-        * @param style
-        *            the new portStyle for the processor
-        */
-       public void setPortStyle(Processor processor, PortStyle portStyle) {
-               processorPortStyle.put(processor, portStyle);
-       }
-
-       /**
-        * Shut down any processing and update threads related to this 
controller.
-        * 
-        */
-       public void shutdown() {
-       }
-
-       /**
-        * Returns true if the default is to expand nested workflows.
-        * 
-        * @return true if the default is to expand nested workflows
-        */
-       public boolean expandNestedDataflows() {
-               return expandNestedDataflows;
-       }
-
-       /**
-        * Returns true if the nested dataflow should be expanded.
-        * 
-        * @param dataflow
-        * @return true if the nested dataflow should be expanded
-        */
-       public boolean expandNestedDataflow(Activity dataflow) {
-               if (dataflowExpansion.containsKey(dataflow))
-                       return dataflowExpansion.get(dataflow);
-               return expandNestedDataflows;
-       }
-
-       /**
-        * Sets the default for expanding nested workflows.
-        * 
-        * @param expand
-        *            the default for expanding nested workflows
-        */
-       public void setExpandNestedDataflows(boolean expand) {
-               dataflowExpansion.clear();
-               this.expandNestedDataflows = expand;
-       }
-
-       /**
-        * Sets whether the nested dataflow should be expanded.
-        * 
-        * @param expand
-        *            whether the nested dataflow should be expanded
-        * @param dataflow
-        *            the nested dataflow
-        */
-       public void setExpandNestedDataflow(Activity dataflow, boolean expand) {
-               dataflowExpansion.put(dataflow, expand);
-       }
-
-       private boolean isSingleOutputProcessor(Object dataflowObject) {
-               boolean result = false;
-               if (dataflowObject instanceof Processor) {
-                       Processor processor = (Processor) dataflowObject;
-                       result = processor.getOutputPorts().size() == 1;
-               }
-               return result;
-       }
-
-       public boolean startEdgeCreation(GraphElement graphElement, Point 
point) {
-               if (!edgeCreationFromSource && !edgeCreationFromSink) {
-                       Object dataflowObject = graphElement.getWorkflowBean();
-                       if (dataflowObject instanceof ReceiverPort) {
-                               edgeCreationSink = graphElement;
-                               edgeCreationFromSink = true;
-                       } else if (dataflowObject instanceof SenderPort
-                                       || 
isSingleOutputProcessor(dataflowObject)) {
-                               edgeCreationSource = graphElement;
-                               edgeCreationFromSource = true;
-                       } else if (graphElement instanceof GraphEdge) {
-                               GraphEdge edge = (GraphEdge) graphElement;
-                               edgeCreationSource = edge.getSource();
-                               edgeCreationFromSource = true;
-                               edgeMoveElement = edge;
-                       }
-               }
-               return edgeCreationFromSource || edgeCreationFromSink;
-       }
-
-       public boolean moveEdgeCreationTarget(GraphElement graphElement, Point 
point) {
-               boolean edgeValid = false;
-               Object dataflowObject = graphElement.getWorkflowBean();
-               if (edgeCreationFromSink) {
-                       if (graphElement instanceof GraphNode) {
-                               Object sinkObject = 
edgeCreationSink.getWorkflowBean();
-                               if (dataflowObject instanceof OutputPort) {
-                                       Processor sourceProcessor = 
portToProcessor
-                                                       .get(dataflowObject);
-                                       if (sourceProcessor != null) {
-                                               Processor sinkProcessor = null;
-                                               if (sinkObject instanceof 
Processor)
-                                                       sinkProcessor = 
(Processor) sinkObject;
-                                               else if 
(portToProcessor.containsKey(sinkObject))
-                                                       sinkProcessor = 
portToProcessor.get(sinkObject);
-                                               if (sinkProcessor != null) {
-                                                       Set<Processor> 
possibleSinkProcessors = scufl2Tools
-                                                                       
.possibleDownStreamProcessors(workflow,
-                                                                               
        sourceProcessor);
-                                                       if 
(possibleSinkProcessors.contains(sinkProcessor)) {
-                                                               
edgeCreationSource = graphElement;
-                                                               edgeValid = 
true;
-                                                       }
-                                               }
-                                               if (sinkObject instanceof 
OutputWorkflowPort) {
-                                                       edgeCreationSource = 
graphElement;
-                                                       edgeValid = true;
-                                               }
-                                       }
-                               } else if (dataflowObject instanceof 
InputWorkflowPort) {
-                                       edgeCreationSource = graphElement;
-                                       edgeValid = true;
-                               } else if (dataflowObject instanceof Processor) 
{
-                                       Processor sourceProcessor = (Processor) 
dataflowObject;
-                                       Processor sinkProcessor = null;
-                                       if (sinkObject instanceof Processor)
-                                               sinkProcessor = (Processor) 
sinkObject;
-                                       else if 
(portToProcessor.containsKey(sinkObject))
-                                               sinkProcessor = 
portToProcessor.get(sinkObject);
-                                       if (sinkProcessor != null) {
-                                               Set<Processor> 
possibleSinkProcessors = scufl2Tools
-                                                               
.possibleDownStreamProcessors(workflow,
-                                                                               
sourceProcessor);
-                                               if 
(possibleSinkProcessors.contains(sinkProcessor)) {
-                                                       edgeCreationSource = 
graphElement;
-                                                       edgeValid = true;
-                                               }
-                                       }
-                                       if (sinkObject instanceof 
OutputWorkflowPort) {
-                                               edgeCreationSource = 
graphElement;
-                                               edgeValid = true;
-                                       }
-                               }
-                       }
-                       if (!edgeValid)
-                               edgeCreationSource = null;
-               } else if (edgeCreationFromSource) {
-                       if (graphElement instanceof GraphNode) {
-                               Object sourceObject = 
edgeCreationSource.getWorkflowBean();
-                               if (dataflowObject instanceof InputPort) {
-                                       Processor sinkProcessor = 
portToProcessor
-                                                       .get(dataflowObject);
-                                       if (sinkProcessor != null) {
-                                               Processor sourceProcessor = 
null;
-                                               if (sourceObject instanceof 
Processor)
-                                                       sourceProcessor = 
(Processor) sourceObject;
-                                               else if 
(portToProcessor.containsKey(sourceObject))
-                                                       sourceProcessor = 
portToProcessor.get(sourceObject);
-                                               if (sourceProcessor != null) {
-                                                       Set<Processor> 
possibleSourceProcessors = scufl2Tools
-                                                                       
.possibleUpStreamProcessors(workflow,
-                                                                               
        sinkProcessor);
-                                                       if 
(possibleSourceProcessors
-                                                                       
.contains(sourceProcessor)) {
-                                                               
edgeCreationSink = graphElement;
-                                                               edgeValid = 
true;
-                                                       }
-                                               }
-                                               if (sourceObject instanceof 
InputWorkflowPort) {
-                                                       edgeCreationSink = 
graphElement;
-                                                       edgeValid = true;
-                                               }
-                                       }
-                               } else if (dataflowObject instanceof 
OutputWorkflowPort) {
-                                       if (sourceObject != null) {
-                                               edgeCreationSink = graphElement;
-                                               edgeValid = true;
-                                       }
-                               } else if (dataflowObject instanceof Processor) 
{
-                                       Processor sinkProcessor = (Processor) 
dataflowObject;
-                                       Processor sourceProcessor = null;
-                                       if (sourceObject instanceof Processor)
-                                               sourceProcessor = (Processor) 
sourceObject;
-                                       else if 
(portToProcessor.containsKey(sourceObject))
-                                               sourceProcessor = 
portToProcessor.get(sourceObject);
-                                       if (sourceProcessor != null) {
-                                               Set<Processor> 
possibleSourceProcessors = scufl2Tools
-                                                               
.possibleUpStreamProcessors(workflow,
-                                                                               
sinkProcessor);
-                                               if 
(possibleSourceProcessors.contains(sourceProcessor)) {
-                                                       edgeCreationSink = 
graphElement;
-                                                       edgeValid = true;
-                                               }
-                                       }
-                                       if (sourceObject instanceof 
InputWorkflowPort) {
-                                               edgeCreationSink = graphElement;
-                                               edgeValid = true;
-                                       }
-                               }
-                       }
-                       if (!edgeValid)
-                               edgeCreationSink = null;
-               }
-               return edgeValid;
-       }
-
-       public boolean stopEdgeCreation(GraphElement graphElement, Point point) 
{
-               boolean edgeCreated = false;
-               if (edgeCreationSource != null && edgeCreationSink != null) {
-                       SenderPort source = null;
-                       ReceiverPort sink = null;
-                       Object sourceDataflowObject = 
edgeCreationSource.getWorkflowBean();
-                       Object sinkDataflowObject = 
edgeCreationSink.getWorkflowBean();
-                       if (sourceDataflowObject instanceof SenderPort)
-                               source = (SenderPort) sourceDataflowObject;
-                       else if (sourceDataflowObject instanceof Processor) {
-                               Processor processor = (Processor) 
sourceDataflowObject;
-                               source = 
showPortOptions(processor.getOutputPorts(), "output",
-                                               componentForPopups, point);
-                       }
-                       if (sinkDataflowObject instanceof ReceiverPort)
-                               sink = (ReceiverPort) sinkDataflowObject;
-                       else if (sinkDataflowObject instanceof Processor) {
-                               Processor processor = (Processor) 
sinkDataflowObject;
-                               sink = 
showPortOptions(processor.getInputPorts(), "input",
-                                               componentForPopups, point);
-                       }
-                       if (source != null && sink != null) {
-                               Edit<?> edit = null;
-                               if (edgeMoveElement == null) {
-                                       DataLink dataLink = new DataLink();
-                                       dataLink.setReceivesFrom(source);
-                                       dataLink.setSendsTo(sink);
-                                       edit = new AddDataLinkEdit(workflow, 
dataLink);
-                               } else {
-                                       Object existingSink = 
edgeMoveElement.getSink()
-                                                       .getWorkflowBean();
-                                       if (existingSink != sink) {
-                                               List<Edit<?>> editList = new 
ArrayList<Edit<?>>();
-                                               DataLink existingDataLink = 
(DataLink) edgeMoveElement
-                                                               
.getWorkflowBean();
-                                               DataLink newDataLink = new 
DataLink();
-                                               
newDataLink.setReceivesFrom(existingDataLink
-                                                               
.getReceivesFrom());
-                                               newDataLink.setSendsTo(sink);
-                                               editList.add(new 
RemoveDataLinkEdit(workflow,
-                                                               
existingDataLink));
-                                               editList.add(new 
AddDataLinkEdit(workflow, newDataLink));
-                                               edit = new 
CompoundEdit(editList);
-                                       }
-                               }
-                               try {
-                                       if (edit != null) {
-                                               
editManager.doDataflowEdit(workflow.getParent(), edit);
-                                               edgeCreated = true;
-                                       }
-                               } catch (EditException e) {
-                                       logger.debug("Failed to create datalink 
from '"
-                                                       + source.getName() + "' 
to '" + sink.getName()
-                                                       + "'");
-                               }
-                       }
-               }
-               edgeCreationSource = null;
-               edgeCreationSink = null;
-               edgeMoveElement = null;
-               edgeCreationFromSource = false;
-               edgeCreationFromSink = false;
-
-               return edgeCreated;
-       }
-
-       private <T extends Port> T showPortOptions(NamedSet<T> ports,
-                       String portType, Component component, Point point) {
-               T result = null;
-               if (ports.size() == 0) {
-                       showMessageDialog(component, "Service has no " + 
portType
-                                       + " ports to connect to");
-               } else if (ports.size() == 1)
-                       result = ports.first();
-               else {
-                       Object[] portNames = ports.getNames().toArray();
-                       String portName = (String) showInputDialog(component, 
"Select an "
-                                       + portType + " port", "Port Chooser", 
PLAIN_MESSAGE, null,
-                                       portNames, portNames[0]);
-                       if (portName != null)
-                               result = ports.getByName(portName);
-               }
-               return result;
-
-       }
-
-       public void resetSelection() {
-               if (dataflowSelectionModel != null)
-                       for (Object dataflowElement : 
dataflowSelectionModel.getSelection()) {
-                               GraphElement graphElement = workflowToGraph
-                                               .get(dataflowElement);
-                               if (graphElement != null)
-                                       graphElement.setSelected(true);
-                       }
-       }
-
-       public void setIteration(String nodeId, int iteration) {
-               if (graphElementMap.containsKey(nodeId)) {
-                       GraphElement graphElement = graphElementMap.get(nodeId);
-                       graphElement.setIteration(iteration);
-               }
-       }
-
-       public void setErrors(String nodeId, int errors) {
-               if (graphElementMap.containsKey(nodeId)) {
-                       GraphElement graphElement = graphElementMap.get(nodeId);
-                       graphElement.setErrors(errors);
-               }
-       }
-
-       @Override
-       public void notify(Observable<DataflowSelectionMessage> sender,
-                       DataflowSelectionMessage message) throws Exception {
-               GraphElement graphElement = 
workflowToGraph.get(message.getElement());
-               if (graphElement != null)
-                       graphElement.setSelected(message.getType().equals(
-                                       DataflowSelectionMessage.Type.ADDED));
-       }
-
-       /**
-        * Returns the GraphEventManager.
-        * 
-        * @return the GraphEventManager
-        */
-       public GraphEventManager getGraphEventManager() {
-               return graphEventManager;
-       }
-
-       /**
-        * Sets the GraphEventManager.
-        * 
-        * @param graphEventManager
-        *            the new GraphEventManager
-        */
-       public void setGraphEventManager(GraphEventManager graphEventManager) {
-               this.graphEventManager = graphEventManager;
-       }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEdge.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEdge.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEdge.java
deleted file mode 100644
index d1348d2..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEdge.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-import java.awt.Point;
-import java.util.List;
-
-/**
- * An edge connecting two nodes in a graph.
- *
- * @author David Withers
- */
-public class GraphEdge extends GraphElement {
-       public enum ArrowStyle {NONE, NORMAL, DOT}
-
-       private GraphNode source;
-       private GraphNode sink;
-       private ArrowStyle arrowHeadStyle = ArrowStyle.NORMAL;
-       private ArrowStyle arrowTailStyle = ArrowStyle.NONE;
-       private List<Point> path;
-
-       /**
-        * Constructs a new instance of Edge.
-        *
-        */
-       public GraphEdge(GraphController graphController) {
-               super(graphController);
-       }
-
-       /**
-        * Returns the source.
-        *
-        * @return the source
-        */
-       public GraphNode getSource() {
-               return source;
-       }
-
-       /**
-        * Sets the source.
-        *
-        * @param source the new source
-        */
-       public void setSource(GraphNode source) {
-               this.source = source;
-       }
-
-       /**
-        * Returns the sink.
-        *
-        * @return the sink
-        */
-       public GraphNode getSink() {
-               return sink;
-       }
-
-       /**
-        * Sets the sink.
-        *
-        * @param sink the new sink
-        */
-       public void setSink(GraphNode sink) {
-               this.sink = sink;
-       }
-
-       /**
-        * Returns the arrowHeadStyle.
-        *
-        * @return the arrowHeadStyle
-        */
-       public ArrowStyle getArrowHeadStyle() {
-               return arrowHeadStyle;
-       }
-
-       /**
-        * Sets the arrowHeadStyle.
-        *
-        * @param arrowHeadStyle the new arrowHeadStyle
-        */
-       public void setArrowHeadStyle(ArrowStyle arrowHeadStyle) {
-               this.arrowHeadStyle = arrowHeadStyle;
-       }
-
-       /**
-        * Returns the arrowTailStyle.
-        *
-        * @return the arrowTailStyle
-        */
-       public ArrowStyle getArrowTailStyle() {
-               return arrowTailStyle;
-       }
-
-       /**
-        * Sets the arrowTailStyle.
-        *
-        * @param arrowTailStyle the new arrowTailStyle
-        */
-       public void setArrowTailStyle(ArrowStyle arrowTailStyle) {
-               this.arrowTailStyle = arrowTailStyle;
-       }
-
-       /**
-        * Returns the path.
-        *
-        * @return the path
-        */
-       public List<Point> getPath() {
-               return path;
-       }
-
-       /**
-        * Sets the path.
-        *
-        * @param path the new path
-        */
-       public void setPath(List<Point> path) {
-               this.path = path;
-       }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphElement.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphElement.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphElement.java
deleted file mode 100644
index ea968ce..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphElement.java
+++ /dev/null
@@ -1,430 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-import java.awt.Color;
-import java.awt.Point;
-
-import org.apache.taverna.scufl2.api.common.WorkflowBean;
-
-/**
- * An element of a graph.
- * 
- * @author David Withers
- */
-public abstract class GraphElement {
-       public enum LineStyle {
-               NONE, SOLID, DOTTED
-       }
-
-       private String id;
-       private String label;
-       private Point labelPosition;
-       private LineStyle lineStyle = LineStyle.SOLID;
-       private Color color = Color.BLACK;
-       private Color fillColor;
-       private float opacity = 1f;
-       private GraphElement parent;
-       private boolean selected;
-       private boolean active;
-       private boolean interactive;
-       private boolean visible = true;
-       private boolean filtered;
-       private WorkflowBean workflowBean;
-       protected GraphController graphController;
-       protected float completed;
-       protected int iteration;
-       protected int errors;
-
-       protected GraphElement(GraphController graphController) {
-               this.graphController = graphController;
-       }
-
-       /**
-        * Returns the eventManager.
-        * 
-        * @return the eventManager
-        */
-       public GraphEventManager getEventManager() {
-               if (graphController != null) {
-                       return graphController.getGraphEventManager();
-               }
-               return null;
-       }
-
-       /**
-        * Returns the workflowBean.
-        * 
-        * @return the workflowBean
-        */
-       public WorkflowBean getWorkflowBean() {
-               return workflowBean;
-       }
-
-       /**
-        * Sets the workflowBean.
-        * 
-        * @param workflowBean
-        *            the new workflowBean
-        */
-       public void setWorkflowBean(WorkflowBean workflowBean) {
-               this.workflowBean = workflowBean;
-       }
-
-       /**
-        * Returns the parent.
-        * 
-        * @return the parent
-        */
-       public GraphElement getParent() {
-               return parent;
-       }
-
-       /**
-        * Sets the parent.
-        * 
-        * @param parent
-        *            the new parent
-        */
-       protected void setParent(GraphElement parent) {
-               this.parent = parent;
-       }
-
-       /**
-        * Returns the label.
-        * 
-        * @return the label
-        */
-       public String getLabel() {
-               return label;
-       }
-
-       /**
-        * Sets the label.
-        * 
-        * @param label
-        *            the new label
-        */
-       public void setLabel(String label) {
-               this.label = label;
-       }
-
-       /**
-        * Returns the labelPosition.
-        * 
-        * @return the labelPosition
-        */
-       public Point getLabelPosition() {
-               return labelPosition;
-       }
-
-       /**
-        * Sets the labelPosition.
-        * 
-        * @param labelPosition
-        *            the new labelPosition
-        */
-       public void setLabelPosition(Point labelPosition) {
-               this.labelPosition = labelPosition;
-       }
-
-       /**
-        * Returns the id.
-        * 
-        * @return the id
-        */
-       public String getId() {
-               return id;
-       }
-
-       /**
-        * Sets the id.
-        * 
-        * @param id
-        *            the new id
-        */
-       public void setId(String id) {
-               if (graphController != null) {
-                       graphController.mapElement(id, this);
-               }
-               this.id = id;
-       }
-
-       /**
-        * Returns the colour.
-        * 
-        * @return the colour
-        */
-       public Color getColor() {
-               return color;
-       }
-
-       /**
-        * Sets the colour.
-        * 
-        * @param color
-        *            the new colour
-        */
-       public void setColor(Color color) {
-               this.color = color;
-       }
-
-       /**
-        * Returns the fillColor.
-        * 
-        * @return the fillColor
-        */
-       public Color getFillColor() {
-               return fillColor;
-       }
-
-       /**
-        * Sets the fillColor.
-        * 
-        * @param fillColor
-        *            the new fillColor
-        */
-       public void setFillColor(Color fillColor) {
-               this.fillColor = fillColor;
-       }
-
-       /**
-        * Returns the lineStyle.
-        * 
-        * @return the lineStyle
-        */
-       public LineStyle getLineStyle() {
-               return lineStyle;
-       }
-
-       /**
-        * Sets the lineStyle.
-        * 
-        * @param lineStyle
-        *            the new lineStyle
-        */
-       public void setLineStyle(LineStyle lineStyle) {
-               this.lineStyle = lineStyle;
-       }
-
-       @Override
-       public String toString() {
-               return id + "[" + label + "]";
-       }
-
-       /**
-        * Returns the selected.
-        * 
-        * @return the selected
-        */
-       public boolean isSelected() {
-               return selected;
-       }
-
-       /**
-        * Sets the selected.
-        * 
-        * @param selected
-        *            the new selected
-        */
-       public void setSelected(boolean selected) {
-               this.selected = selected;
-       }
-
-       /**
-        * Returns the iteration.
-        * 
-        * @return the value of iteration
-        */
-       public int getIteration() {
-               return iteration;
-       }
-
-       /**
-        * Sets the iteration.
-        * 
-        * @param iteration
-        *            the new value for iteration
-        */
-       public void setIteration(int iteration) {
-               this.iteration = iteration;
-       }
-
-       /**
-        * Returns the errors.
-        * 
-        * @return the value of errors
-        */
-       public int getErrors() {
-               return errors;
-       }
-
-       /**
-        * Sets the errors.
-        * 
-        * @param errors
-        *            the new value for errors
-        */
-       public void setErrors(int errors) {
-               this.errors = errors;
-       }
-
-       /**
-        * Returns the completed.
-        * 
-        * @return the value of completed
-        */
-       public float getCompleted() {
-               return completed;
-       }
-
-       /**
-        * Sets the completed value.
-        * 
-        * @param completed
-        */
-       public void setCompleted(float completed) {
-               this.completed = completed;
-       }
-
-       /**
-        * Returns <code>true</code> if the element is active. The default 
value is
-        * <code>false</code>.
-        * 
-        * @return <code>true</code> if the element is active
-        */
-       public boolean isActive() {
-               return active;
-       }
-
-       /**
-        * Sets the value of active.
-        * 
-        * @param active
-        *            the new active
-        */
-       public void setActive(boolean active) {
-               this.active = active;
-       }
-
-       /**
-        * Returns <code>true</code> if the element is interactive. The default
-        * value is <code>false</code>.
-        * 
-        * @return <code>true</code> if the element is interactive
-        */
-       public boolean isInteractive() {
-               return interactive;
-       }
-
-       /**
-        * Sets the value of interactive.
-        * 
-        * @param interactive
-        *            the new interactive
-        */
-       public void setInteractive(boolean interactive) {
-               this.interactive = interactive;
-       }
-
-       /**
-        * Returns <code>true</code> if the element is visible. The default 
value is
-        * <code>true</code>.
-        * 
-        * @return <code>true</code> if the element is visible
-        */
-       public boolean isVisible() {
-               return visible;
-       }
-
-       /**
-        * Sets whether the element is visible.
-        * 
-        * @param visible
-        *            the new value for visible
-        */
-       public void setVisible(boolean visible) {
-               this.visible = visible;
-       }
-
-       /**
-        * Returns the opacity value. The default value is 1.0
-        * 
-        * @return the opacity value
-        */
-       public float getOpacity() {
-               return opacity;
-       }
-
-       /**
-        * Sets the opacity of the element. Must be a value between 0.0 and 1.0.
-        * 
-        * @param opacity
-        *            the new opacity value
-        */
-       public void setOpacity(float opacity) {
-               this.opacity = opacity;
-       }
-
-       /**
-        * Returns <code>true</code> if the element is filtered.
-        * 
-        * @return <code>true</code> if the element is filtered
-        */
-       public boolean isFiltered() {
-               return filtered;
-       }
-
-       /**
-        * Sets the value of filtered.
-        * 
-        * @param filtered
-        *            the new value for filtered
-        */
-       public void setFiltered(boolean filtered) {
-               this.filtered = filtered;
-       }
-
-       @Override
-       public int hashCode() {
-               final int prime = 31;
-               int result = 1;
-               result = prime * result + ((id == null) ? 0 : id.hashCode());
-               return result;
-       }
-
-       @Override
-       public boolean equals(Object obj) {
-               if (this == obj)
-                       return true;
-               if (obj == null)
-                       return false;
-               if (getClass() != obj.getClass())
-                       return false;
-
-               // Equality by id
-               GraphElement other = (GraphElement) obj;
-               if (id == null)
-                       return (other.id == null);
-               return id.equals(other.id);
-       }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEventManager.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEventManager.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEventManager.java
deleted file mode 100644
index a6b9b0e..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphEventManager.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-public interface GraphEventManager {
-       void mouseClicked(GraphElement graphElement, short button, boolean 
altKey,
-                       boolean ctrlKey, boolean metaKey, int x, int y, int 
screenX,
-                       int screenY);
-
-       void mouseDown(GraphElement graphElement, short button, boolean altKey,
-                       boolean ctrlKey, boolean metaKey, int x, int y, int 
screenX,
-                       int screenY);
-
-       void mouseUp(GraphElement graphElement, short button, boolean altKey,
-                       boolean ctrlKey, boolean metaKey, final int x, final 
int y,
-                       int screenX, int screenY);
-
-       void mouseMoved(GraphElement graphElement, short button, boolean altKey,
-                       boolean ctrlKey, boolean metaKey, int x, int y, int 
screenX,
-                       int screenY);
-
-       void mouseOver(GraphElement graphElement, short button, boolean altKey,
-                       boolean ctrlKey, boolean metaKey, int x, int y, int 
screenX,
-                       int screenY);
-
-       void mouseOut(GraphElement graphElement, short button, boolean altKey,
-                       boolean ctrlKey, boolean metaKey, int x, int y, int 
screenX,
-                       int screenY);
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphNode.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphNode.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphNode.java
deleted file mode 100644
index 3f3f85f..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphNode.java
+++ /dev/null
@@ -1,153 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * A node of a graph that can optionally contain other graphs.
- * 
- * @author David Withers
- */
-public class GraphNode extends GraphShapeElement {
-       private List<GraphNode> sourceNodes = new ArrayList<>();
-       private List<GraphNode> sinkNodes = new ArrayList<>();
-       private Graph graph;
-       private boolean expanded;
-
-       /**
-        * Constructs a new instance of Node.
-        * 
-        */
-       public GraphNode(GraphController graphController) {
-               super(graphController);
-       }
-
-       /**
-        * Adds a sink node.
-        * 
-        * @param sinkNode
-        *            the sink node to add
-        */
-       public void addSinkNode(GraphNode sinkNode) {
-               sinkNode.setParent(this);
-               sinkNodes.add(sinkNode);
-       }
-
-       /**
-        * Adds a source node.
-        * 
-        * @param sourceNode
-        *            the source node to add
-        */
-       public void addSourceNode(GraphNode sourceNode) {
-               sourceNode.setParent(this);
-               sourceNodes.add(sourceNode);
-       }
-
-       /**
-        * Returns the graph that this node contains.
-        * 
-        * @return the graph that this node contains
-        */
-       public Graph getGraph() {
-               return graph;
-       }
-
-       /**
-        * Returns the sinkNodes.
-        * 
-        * @return the sinkNodes
-        */
-       public List<GraphNode> getSinkNodes() {
-               return sinkNodes;
-       }
-
-       /**
-        * Returns the sourceNodes.
-        * 
-        * @return the sourceNodes
-        */
-       public List<GraphNode> getSourceNodes() {
-               return sourceNodes;
-       }
-
-       /**
-        * Returns true if this node is expanded to show the contained graph.
-        * 
-        * @return true if this node is expanded
-        */
-       public boolean isExpanded() {
-               return expanded;
-       }
-
-       /**
-        * Removes a sink node.
-        * 
-        * @param sinkNode
-        *            the node to remove
-        * @return true if the node was removed, false otherwise
-        */
-       public boolean removeSinkNode(GraphNode sinkNode) {
-               return sinkNodes.remove(sinkNode);
-       }
-
-       /**
-        * Removes a source node.
-        * 
-        * @param sourceNode
-        *            the node to remove
-        * @return true if the node was removed, false otherwise
-        */
-       public boolean removeSourceNode(GraphNode sourceNode) {
-               return sourceNodes.remove(sourceNode);
-       }
-
-       /**
-        * Sets whether this node is expanded to show the contained graph.
-        * 
-        * @param expanded
-        *            true if this node is expanded
-        */
-       public void setExpanded(boolean expanded) {
-               this.expanded = expanded;
-       }
-
-       /**
-        * Sets the graph that this node contains.
-        * 
-        * @param graph
-        *            the new graph
-        */
-       public void setGraph(Graph graph) {
-               if (graph != null)
-                       graph.setParent(this);
-               this.graph = graph;
-       }
-
-       @Override
-       public void setSelected(boolean selected) {
-               super.setSelected(selected);
-               if (isExpanded())
-                       getGraph().setSelected(selected);
-       }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphShapeElement.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphShapeElement.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphShapeElement.java
deleted file mode 100644
index 1bb8b6d..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/GraphShapeElement.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2008 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph;
-
-import java.awt.Dimension;
-import java.awt.Point;
-
-/**
- * A Graph element that has shape, size and position properties.
- * 
- * @author David Withers
- */
-public class GraphShapeElement extends GraphElement {
-       public enum Shape {
-               BOX, RECORD, HOUSE, INVHOUSE, DOT, CIRCLE, TRIANGLE, INVTRIANGLE
-       }
-
-       private Shape shape;
-       private int x, y, width, height;
-
-       public GraphShapeElement(GraphController graphController) {
-               super(graphController);
-       }
-
-       /**
-        * Returns the height.
-        * 
-        * @return the height
-        */
-       public int getHeight() {
-               return height;
-       }
-
-       /**
-        * Returns the position.
-        * 
-        * @return the position
-        */
-       public Point getPosition() {
-               return new Point(x, y);
-       }
-
-       /**
-        * Returns the shape of the element.
-        * 
-        * @return the shape of the element
-        */
-       public Shape getShape() {
-               return shape;
-       }
-
-       /**
-        * Returns the width.
-        * 
-        * @return the width
-        */
-       public int getWidth() {
-               return width;
-       }
-
-       /**
-        * Sets the position.
-        * 
-        * @param position
-        *            the new position
-        */
-       public void setPosition(Point position) {
-               x = position.x;
-               y = position.y;
-       }
-
-       /**
-        * Sets the shape of the element.
-        * 
-        * @param shape
-        *            the new shape of the element
-        */
-       public void setShape(Shape shape) {
-               this.shape = shape;
-       }
-
-       /**
-        * Returns the size of the element.
-        * 
-        * @return the size of the element
-        */
-       public Dimension getSize() {
-               return new Dimension(width, height);
-       }
-
-       /**
-        * Sets the size of the element.
-        * 
-        * @param size
-        *            the new size of the node
-        */
-       public void setSize(Dimension size) {
-               width = size.width;
-               height = size.height;
-       }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a9a52bd5/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/dot/GraphLayout.java
----------------------------------------------------------------------
diff --git 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/dot/GraphLayout.java
 
b/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/dot/GraphLayout.java
deleted file mode 100644
index 1205953..0000000
--- 
a/taverna-graph-model/src/main/java/net/sf/taverna/t2/workbench/models/graph/dot/GraphLayout.java
+++ /dev/null
@@ -1,326 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2008 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- 
******************************************************************************/
-package net.sf.taverna.t2.workbench.models.graph.dot;
-
-import static java.lang.Float.parseFloat;
-import static 
net.sf.taverna.t2.workbench.models.graph.Graph.Alignment.HORIZONTAL;
-
-import java.awt.Dimension;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.workbench.models.graph.Graph;
-import net.sf.taverna.t2.workbench.models.graph.GraphController;
-import net.sf.taverna.t2.workbench.models.graph.GraphEdge;
-import net.sf.taverna.t2.workbench.models.graph.GraphElement;
-import net.sf.taverna.t2.workbench.models.graph.GraphNode;
-
-import org.apache.log4j.Logger;
-
-/**
- * Lays out a graph from a DOT layout.
- * 
- * @author David Withers
- */
-public class GraphLayout implements DOTParserVisitor {
-       private static final Logger logger = 
Logger.getLogger(GraphLayout.class);
-       private static final int BORDER = 10;
-
-       private Rectangle bounds;
-       private Rectangle requiredBounds;
-       private GraphController graphController;
-       private int xOffset;
-       private int yOffset;
-
-       public Rectangle layoutGraph(GraphController graphController, Graph 
graph,
-                       String laidOutDot, Rectangle requiredBounds) throws 
ParseException {
-               this.graphController = graphController;
-               this.requiredBounds = requiredBounds;
-
-               bounds = null;
-               xOffset = 0;
-               yOffset = 0;
-
-               logger.debug(laidOutDot);
-               DOTParser parser = new DOTParser(new StringReader(laidOutDot));
-               parser.parse().jjtAccept(this, graph);
-
-               // int xOffset = (bounds.width - bounds.width) / 2;
-               // int yOffset = (bounds.height - bounds.height) / 2;
-
-               return new Rectangle(xOffset, yOffset, bounds.width, 
bounds.height);
-       }
-
-       @Override
-       public Object visit(SimpleNode node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTParse node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTGraph node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTStatementList node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTStatement node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTAttributeStatement node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTNodeStatement node, Object data) {
-               GraphElement element = 
graphController.getElement(removeQuotes(node
-                               .getName()));
-               if (element != null)
-                       return node.childrenAccept(this, element);
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTNodeId node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTPort node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTEdgeStatement node, Object data) {
-               StringBuilder id = new StringBuilder();
-               id.append(removeQuotes(node.getName()));
-               if (node.getPort() != null) {
-                       id.append(":");
-                       id.append(removeQuotes(node.getPort()));
-               }
-               if (node.children != null)
-                       for (Node child : node.children)
-                               if (child instanceof ASTEdgeRHS) {
-                                       NamedNode rhsNode = (NamedNode) 
child.jjtAccept(this, data);
-                                       id.append("->");
-                                       
id.append(removeQuotes(rhsNode.getName()));
-                                       if (rhsNode.getPort() != null) {
-                                               id.append(":");
-                                               
id.append(removeQuotes(rhsNode.getPort()));
-                                       }
-                               }
-               GraphElement element = 
graphController.getElement(id.toString());
-               if (element != null)
-                       return node.childrenAccept(this, element);
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTSubgraph node, Object data) {
-               GraphElement element = graphController.getElement(removeQuotes(
-                               node.getName()).substring("cluster_".length()));
-               if (element != null)
-                       return node.childrenAccept(this, element);
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTEdgeRHS node, Object data) {
-               return node;
-       }
-
-       @Override
-       public Object visit(ASTAttributeList node, Object data) {
-               return node.childrenAccept(this, data);
-       }
-
-       @Override
-       public Object visit(ASTAList node, Object data) {
-               if (data instanceof Graph) {
-                       Graph graph = (Graph) data;
-                       if ("bb".equalsIgnoreCase(node.getName())) {
-                               Rectangle rect = getRectangle(node.getValue());
-                               if (rect.width == 0 && rect.height == 0) {
-                                       rect.width = 500;
-                                       rect.height = 500;
-                               }
-                               if (bounds == null) {
-                                       bounds = calculateBounds(rect);
-                                       rect = bounds;
-                               }
-                               graph.setSize(rect.getSize());
-                               graph.setPosition(rect.getLocation());
-                       } else if ("lp".equalsIgnoreCase(node.getName())) {
-                               if (bounds != null)
-                                       
graph.setLabelPosition(getPoint(node.getValue()));
-                       }
-               } else if (data instanceof GraphNode) {
-                       GraphNode graphNode = (GraphNode) data;
-                       if ("width".equalsIgnoreCase(node.getName()))
-                               graphNode.setSize(new 
Dimension(getSize(node.getValue()),
-                                               graphNode.getHeight()));
-                       else if ("height".equalsIgnoreCase(node.getName()))
-                               graphNode.setSize(new 
Dimension(graphNode.getWidth(),
-                                               getSize(node.getValue())));
-                       else if ("pos".equalsIgnoreCase(node.getName())) {
-                               Point position = getPoint(node.getValue());
-                               position.x = position.x - (graphNode.getWidth() 
/ 2);
-                               position.y = position.y - 
(graphNode.getHeight() / 2);
-                               graphNode.setPosition(position);
-                       } else if ("rects".equalsIgnoreCase(node.getName())) {
-                               List<Rectangle> rectangles = 
getRectangles(node.getValue());
-                               List<GraphNode> sinkNodes = 
graphNode.getSinkNodes();
-                               if 
(graphController.getAlignment().equals(HORIZONTAL)) {
-                                       Rectangle rect = rectangles.remove(0);
-                                       graphNode.setSize(rect.getSize());
-                                       
graphNode.setPosition(rect.getLocation());
-                               } else {
-                                       Rectangle rect = 
rectangles.remove(sinkNodes.size());
-                                       graphNode.setSize(rect.getSize());
-                                       
graphNode.setPosition(rect.getLocation());
-                               }
-                               Point origin = graphNode.getPosition();
-                               for (GraphNode sinkNode : sinkNodes) {
-                                       Rectangle rect = rectangles.remove(0);
-                                       rect.setLocation(rect.x - origin.x, 
rect.y - origin.y);
-                                       sinkNode.setSize(rect.getSize());
-                                       
sinkNode.setPosition(rect.getLocation());
-                               }
-                               for (GraphNode sourceNode : 
graphNode.getSourceNodes()) {
-                                       Rectangle rect = rectangles.remove(0);
-                                       rect.setLocation(rect.x - origin.x, 
rect.y - origin.y);
-                                       sourceNode.setSize(rect.getSize());
-                                       
sourceNode.setPosition(rect.getLocation());
-                               }
-                       }
-               } else if (data instanceof GraphEdge) {
-                       GraphEdge graphEdge = (GraphEdge) data;
-                       if ("pos".equalsIgnoreCase(node.getName()))
-                               graphEdge.setPath(getPath(node.getValue()));
-               }
-               return node.childrenAccept(this, data);
-       }
-
-       private Rectangle calculateBounds(Rectangle bounds) {
-               bounds = new Rectangle(bounds);
-               bounds.width += BORDER;
-               bounds.height += BORDER;
-               Rectangle newBounds = new Rectangle(bounds);
-               double ratio = bounds.width / (float) bounds.height;
-               double requiredRatio = requiredBounds.width
-                               / (float) requiredBounds.height;
-               // adjust the bounds so they match the aspect ration of the 
required bounds
-               if (ratio > requiredRatio)
-                       newBounds.height = (int) (ratio / requiredRatio * 
bounds.height);
-               else if (ratio < requiredRatio)
-                       newBounds.width = (int) (requiredRatio / ratio * 
bounds.width);
-
-               xOffset = (newBounds.width - bounds.width) / 2;
-               yOffset = (newBounds.height - bounds.height) / 2;
-               // adjust the bounds and so they are not less than the required 
bounds
-               if (newBounds.width < requiredBounds.width) {
-                       xOffset += (requiredBounds.width - newBounds.width) / 2;
-                       newBounds.width = requiredBounds.width;
-               }
-               if (newBounds.height < requiredBounds.height) {
-                       yOffset += (requiredBounds.height - newBounds.height) / 
2;
-                       newBounds.height = requiredBounds.height;
-               }
-               // adjust the offset for the border
-               xOffset += BORDER / 2;
-               yOffset += BORDER / 2;
-               return newBounds;
-       }
-
-       private List<Point> getPath(String value) {
-               List<Point> path = new ArrayList<>();
-               for (String point : removeQuotes(value).split(" ")) {
-                       String[] coords = point.split(",");
-                       if (coords.length == 2) {
-                               int x = (int) parseFloat(coords[0]) + xOffset;
-                               int y = (int) parseFloat(coords[1]) + yOffset;
-                               path.add(new Point(x, flipY(y)));
-                       }
-               }
-               return path;
-       }
-
-       private int flipY(int y) {
-               return bounds.height - y;
-       }
-
-       private List<Rectangle> getRectangles(String value) {
-               List<Rectangle> rectangles = new ArrayList<>();
-               String[] rects = value.split(" ");
-               for (String rectangle : rects)
-                       rectangles.add(getRectangle(rectangle));
-               return rectangles;
-       }
-
-       private Rectangle getRectangle(String value) {
-               String[] coords = removeQuotes(value).split(",");
-               Rectangle rectangle = new Rectangle();
-               rectangle.x = (int) parseFloat(coords[0]);
-               rectangle.y = (int) parseFloat(coords[3]);
-               rectangle.width = (int) parseFloat(coords[2]) - rectangle.x;
-               rectangle.height = rectangle.y - (int) parseFloat(coords[1]);
-               rectangle.x += xOffset;
-               rectangle.y += yOffset;
-               if (bounds != null)
-                       rectangle.y = flipY(rectangle.y);
-               else
-                       rectangle.y = rectangle.height - rectangle.y;
-               return rectangle;
-       }
-
-       private Point getPoint(String value) {
-               String[] coords = removeQuotes(value).split(",");
-               return new Point(xOffset + (int) parseFloat(coords[0]), 
flipY(yOffset
-                               + (int) parseFloat(coords[1])));
-       }
-
-       private int getSize(String value) {
-               return (int) (parseFloat(removeQuotes(value)) * 72);
-       }
-
-       private String removeQuotes(String value) {
-               String result = value.trim();
-               if (result.startsWith("\""))
-                       result = result.substring(1);
-               if (result.endsWith("\""))
-                       result = result.substring(0, result.length() - 1);
-               result = result.replaceAll("\\\\", "");
-               return result;
-       }
-}

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