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momeara/AddTwoNodesTask.java

Created November 10, 2015 15:43
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AddTwoNodes test case
Raw
README.rst
ISSUE:

With Cytoscape 3.3.0-SNAPSHOT, Java 1.8.0_45

From an empty network running the AddTwoNodes task creates two nodes but does not show their names Clicking and dragging on the top node gives this exception:

Exception in thread "AWT-EventQueue-0" java.lang.IllegalStateException: width of node has degenerated to zero after rounding

at org.cytoscape.ding.impl.DNodeView.setOffset(DNodeView.java:470) at org.cytoscape.ding.impl.InnerCanvas$MouseDraggedDelegator.singleLeftClick(InnerCanvas.java:1476) at org.cytoscape.ding.impl.InnerCanvas$MouseDraggedDelegator.delegateMouseEvent(InnerCanvas.java:1417) at org.cytoscape.ding.impl.InnerCanvas.mouseDragged(InnerCanvas.java:304) at org.cytoscape.ding.impl.cyannotator.listeners.CanvasMouseMotionListener.mouseDragged(CanvasMouseMotionListener.java:58) at java.awt.AWTEventMulticaster.mouseDragged(AWTEventMulticaster.java:319) at java.awt.Component.processMouseMotionEvent(Component.java:6573) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6294) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4550) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Raw
AddTwoNodesTask.java
package org.AddTwoNodes.internal.tasks;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.VisualStyle;
public class AddTwoNodesTask extends AbstractTask {
private CyNetworkView netView;
private final VisualMappingManager vmmServiceRef;
public AddTwoNodesTask(final CyNetworkView netView, final VisualMappingManager vmmServiceRef){
this.netView = netView;
this.vmmServiceRef =vmmServiceRef;
}
public void run(TaskMonitor monitor) {
CyNetwork network = netView.getModel();
CyNode node1 = network.addNode();
network.getDefaultNodeTable().getRow(node1.getSUID()).set("name", "Node1");
CyNode node2 = network.addNode();
network.getDefaultNodeTable().getRow(node2.getSUID()).set("name", "Node2");
// Apply the change to the view
VisualStyle style = vmmServiceRef.getCurrentVisualStyle();
style.apply(netView);
netView.updateView();
}
}
Raw
AddTwoNodesTaskFactory.java
package org.AddTwoNodes.internal.tasks;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
public class AddTwoNodesTaskFactory extends AbstractTaskFactory {
private final CyApplicationManager cyApplicationManagerServiceRef;
private final VisualMappingManager vmmServiceRef;
public AddTwoNodesTaskFactory(final CyApplicationManager cyApplicationManagerServiceRef, VisualMappingManager vmmServiceRef){
this.cyApplicationManagerServiceRef = cyApplicationManagerServiceRef;
this.vmmServiceRef = vmmServiceRef;
}
public TaskIterator createTaskIterator(){
return new TaskIterator(new AddTwoNodesTask(cyApplicationManagerServiceRef.getCurrentNetworkView(), vmmServiceRef));
}
}
Raw
CyActivator.java
package org.AddTwoNodes.internal
import org.osgi.framework.BundleContext;
import static org.cytoscape.work.ServiceProperties.COMMAND;
import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE;
import static org.cytoscape.work.ServiceProperties.IN_MENU_BAR;
import static org.cytoscape.work.ServiceProperties.MENU_GRAVITY;
import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU;
import static org.cytoscape.work.ServiceProperties.TITLE;
import org.AddTwoNodes.internal.tasks.AddTwoNodesTaskFactory;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.task.NetworkTaskFactory;
import org.cytoscape.task.NetworkViewTaskFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskFactory;
import java.util.Properties;
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
}
public void start(BundleContext bc) {
AddTwoNodesTaskFactory addTwoNodesTaskFactory = new AddTwoNodesTaskFactory(cyApplicationManagerServiceRef, vmmServiceRef);
Properties addTwoNodesTaskFactoryProps = new Properties();
addTwoNodesTaskFactoryProps.setProperty("preferredMenu","Apps.Samples");
addTwoNodesTaskFactoryProps.setProperty("title","Add two nodes");
registerService(bc,addTwoNodesTaskFactory,TaskFactory.class, addTwoNodesTaskFactoryProps);
}
}
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