Better handling of X,Y coordinates and node Depth.

Author: mikekucera

Cy3D/src/main/java/org/baderlab/cy3d/internal/cytoscape/view/Cy3DVisualLexicon.java

@@ -11,6 +11,7 @@
 import static org.cytoscape.view.presentation.property.NodeShapeVisualProperty.RECTANGLE;
 import static org.cytoscape.view.presentation.property.NodeShapeVisualProperty.TRIANGLE;
 
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -81,6 +82,15 @@ private void initSupportedProps() {
 		supportedValuesMap.put(DETAIL_LEVEL, asList(DETAIL_LOW, DETAIL_MED, DETAIL_HIGH));
 	}
 
+	@Override
+	public Collection<VisualProperty<?>> getNonClearableVisualProperties() {
+		return Arrays.asList(
+			BasicVisualLexicon.NODE_X_LOCATION,
+			BasicVisualLexicon.NODE_Y_LOCATION,
+			BasicVisualLexicon.NODE_Z_LOCATION
+		);
+	}
+	
 	@Override
 	public boolean isSupported(VisualProperty<?> vp) {
 		return supportedProps.contains(vp) && super.isSupported(vp);

Cy3D/src/main/java/org/baderlab/cy3d/internal/data/GraphicsData.java

@@ -7,11 +7,8 @@
 import org.baderlab.cy3d.internal.cytoscape.edges.EdgeAnalyser;
 import org.baderlab.cy3d.internal.geometric.ViewingVolume;
 import org.baderlab.cy3d.internal.task.TaskFactoryListener;
-import org.cytoscape.model.CyNode;
 import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
 import org.cytoscape.view.model.VisualLexicon;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
 import org.cytoscape.work.swing.DialogTaskManager;
 
 import com.google.common.eventbus.EventBus;
@@ -88,13 +85,6 @@ public void setGlContext(GL2 glContext) {
 
 	public void setNetworkSnapshot(CyNetworkView networkView) {
 		this.networkSnapshot = networkView;
-		
-		for(View<CyNode> node : networkView.getNodeViews()) {
-			Double x = node.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
-			System.out.println("node:" + node.getSUID() + " x' = " + x);
-		}
-		
-		
 	}
 
 	public void setPixelConverter(PixelConverter pixelConverter) {

Cy3D/src/main/java/org/baderlab/cy3d/internal/graphics/RenderEventListener.java

@@ -107,7 +107,7 @@ public void init(GLAutoDrawable drawable) {
 	 */
 	@Override
 	public void display(GLAutoDrawable drawable) {
-		System.out.println("RenderEventListener.display() " + System.currentTimeMillis());
+//		System.out.println("RenderEventListener.display() " + System.currentTimeMillis());
 		GL2 gl = drawable.getGL().getGL2();
 		graphicsData.setGlContext(gl);
 		graphicsData.setNetworkSnapshot(networkView.createSnapshot());

Cy3D/src/main/java/org/baderlab/cy3d/internal/rendering/RenderNodesProcedure.java

@@ -91,6 +91,11 @@ public void execute(GraphicsData graphicsData) {
 			Double height = nodeView.getVisualProperty(BasicVisualLexicon.NODE_HEIGHT);
 			Double depth  = nodeView.getVisualProperty(BasicVisualLexicon.NODE_DEPTH);
 
+			// Avoid flat pancake nodes
+			if(depth == null || depth.doubleValue() == 0.0) {
+				depth = width;
+			}
+			
 			// Draw it only if the visual property says it is visible
 			if (nodeView.getVisualProperty(BasicVisualLexicon.NODE_VISIBLE) && graphicsData .getViewingVolume().inside(new Vector3(x, y, z), 1)) {
 

Cy3D/src/main/java/org/baderlab/cy3d/internal/tools/NetworkToolkit.java

@@ -275,8 +275,8 @@ public static void setNodeSelected(long suid, CyNetworkView networkView, boolean
 
 		row.set(SELECTED_COLUMN_NAME, selected);
 
-		networkView.getNodeView(network.getNode(suid)).setVisualProperty(
-				BasicVisualLexicon.NODE_SELECTED, selected);
+//		networkView.getNodeView(network.getNode(suid)).setVisualProperty(
+//				BasicVisualLexicon.NODE_SELECTED, selected);
 	}
 
 	public static boolean checkNodeSelected(long index, CyNetworkView networkView) {
@@ -317,8 +317,8 @@ public static void setEdgeSelected(long suid, CyNetworkView networkView, boolean
 
 		row.set(SELECTED_COLUMN_NAME, selected);
 
-		networkView.getEdgeView(network.getEdge(suid)).setVisualProperty(
-				BasicVisualLexicon.EDGE_SELECTED, selected);
+//		networkView.getEdgeView(network.getEdge(suid)).setVisualProperty(
+//				BasicVisualLexicon.EDGE_SELECTED, selected);
 	}
 
 	public static boolean checkEdgeSelected(long index, CyNetworkView networkView) {