Improved style handling

src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java

@@ -38,7 +38,6 @@ import org.cytoscape.service.util.AbstractCyActivator;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.session.events.SessionLoadedListener;
 import org.cytoscape.task.create.CloneNetworkTaskFactory;
-import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.model.CyNetworkViewFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewManager;
@@ -93,7 +92,6 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class);
 		CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
 		CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
-		CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
 		//Not sure how to correctly infer arguments here
 		CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
 		CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class);

src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java

@@ -29,7 +29,6 @@ import org.cytoscape.model.CyNetworkManager;
 import org.cytoscape.model.subnetwork.CyRootNetworkManager;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.task.create.CloneNetworkTaskFactory;
-import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewFactory;
 import org.cytoscape.view.model.CyNetworkViewManager;
@@ -61,7 +60,6 @@ public class CyCore {
 	public static VisualStyleFactory visualStyleFactory;
 	public static VisualMappingFunctionFactory continuousMappingFactory;
 	public static CyRootNetworkManager rootNetworkManager;
-	public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
 	public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
 	public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
 	//

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java

+package de.hhu.ba.yoshikoWrapper.cytoUtil;
+
+import java.util.List;
+
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.view.vizmap.mappings.BoundaryRangeValues;
+import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+
+public class StyleManager {
+
+	public static final String CLUSTERSIZE_COLUMN_NAME = "clusterSize";
+	public static final String EDGESTRENGTH_COLUMN_NAME = "edgeStrength";
+
+	public static final double MIN_EDGE_SIZE = 1.0;
+	public static final double MAX_EDGE_SIZE = 10.0;
+
+	public static final double MIN_NODE_SIZE = 5.0;
+	public static final double MAX_NODE_SIZE = 30.0;
+
+
+	private static void apply (CyNetworkView view, VisualStyle style) {
+		CyCore.visualMappingManager.setVisualStyle(style,view);
+		style.apply(view);
+		view.updateView();
+	}
+
+	public static void style(CyNetworkView view, VisualStyle style) {
+		apply(view,style);
+	}
+
+	public static void styleWithMapping(CyNetworkView view, VisualStyle style) {
+
+		style = CyCore.visualStyleFactory.createVisualStyle(style);
+
+		//Define style for solution
+		ContinuousMapping<Integer, Double> contMapNodes = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
+				CLUSTERSIZE_COLUMN_NAME,
+				Integer.class,
+				BasicVisualLexicon.NODE_SIZE
+			);
+
+		ContinuousMapping<Integer, Double> contMapEdges = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
+				EDGESTRENGTH_COLUMN_NAME,
+				Integer.class,
+				BasicVisualLexicon.EDGE_WIDTH
+			);
+
+		//Calculate size range and scale accordingly
+		List<Integer> sizes = view.getModel().getDefaultNodeTable().getColumn(CLUSTERSIZE_COLUMN_NAME).getValues(Integer.class);
+		int min = Integer.MAX_VALUE;
+		int max = Integer.MIN_VALUE;
+		for (Integer i : sizes) {
+			if (i < min) {
+				min = i;
+			}
+			if (i > max) {
+				max = i;
+			}
+		}
+		contMapNodes.addPoint(min, new BoundaryRangeValues<Double>(MIN_NODE_SIZE,MIN_NODE_SIZE,MIN_NODE_SIZE));
+		contMapNodes.addPoint(max, new BoundaryRangeValues<Double>(MAX_NODE_SIZE,MAX_NODE_SIZE,MAX_NODE_SIZE));
+
+		sizes = view.getModel().getDefaultEdgeTable().getColumn(EDGESTRENGTH_COLUMN_NAME).getValues(Integer.class);
+		min = Integer.MAX_VALUE;
+		max = Integer.MIN_VALUE;
+		for (Integer i : sizes) {
+			if (i < min) {
+				min = i;
+			}
+			if (i > max) {
+				max = i;
+			}
+		}
+
+		contMapEdges.addPoint(min, new BoundaryRangeValues<Double>(MIN_EDGE_SIZE,MIN_EDGE_SIZE,MIN_EDGE_SIZE));
+		contMapEdges.addPoint(max, new BoundaryRangeValues<Double>(MAX_EDGE_SIZE,MAX_EDGE_SIZE,MAX_EDGE_SIZE));
+
+		style.addVisualMappingFunction(contMapNodes);
+		style.addVisualMappingFunction(contMapEdges);
+		apply(view,style);
+
+	}
+
+}

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java

@@ -38,7 +38,6 @@ import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.view.presentation.RenderingEngine;
-import org.cytoscape.view.vizmap.VisualStyle;
 import org.cytoscape.work.Task;
 import org.cytoscape.work.TaskIterator;
 import org.cytoscape.work.TaskMonitor;
@@ -46,6 +45,7 @@ import org.slf4j.Logger;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
 import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
 
 import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_HEIGHT;
@@ -138,9 +138,7 @@ public class YoshikoCluster {
 				public void run(TaskMonitor taskMonitor) throws Exception {
 					taskMonitor.setStatusMessage("Generating cluster view for C:"+id);
 
-					VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle(CyCore.visualMappingManager.getCurrentVisualStyle());
-					CyCore.visualMappingManager.setVisualStyle(vs, view);
-					vs.apply(view);
+					StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
 
 					view.setVisualProperty(NETWORK_WIDTH, new Double(width));
 					view.setVisualProperty(NETWORK_HEIGHT, new Double(height));

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java

@@ -32,12 +32,10 @@ import org.cytoscape.model.CyEdge.Type;
 import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
-import org.cytoscape.view.vizmap.VisualStyle;
-import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
 
 public class YoshikoSolution {
 
@@ -78,7 +76,6 @@ public class YoshikoSolution {
 		//Add nodes
 		for (YoshikoCluster c: cluster) {
 
-			VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle(CyCore.visualMappingManager.getCurrentVisualStyle());
 
 
 			CyNode clusterNode = metaGraph.addNode();
@@ -96,13 +93,13 @@ public class YoshikoSolution {
 						null
 				)
 			);
-			CyCore.visualMappingManager.setVisualStyle(vs, subnetView);
-			vs.apply(subnetView);
-			subnetView.updateView();
+
+			StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+
 			clusterNode.setNetworkPointer(subnet);
 			//Set node attributes
 			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
-			metaGraph.getRow(clusterNode).set("clusterSize",c.getSize());
+			metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
 			map.put(c, clusterNode);
 		}
 
@@ -120,12 +117,12 @@ public class YoshikoSolution {
 						if (originalGraph.containsEdge(c1n, c2n) || originalGraph.containsEdge(c2n, c1n)) {
 							if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
 								CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
-								metaGraph.getRow(edge).set("edgeStrength",1);
+								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
 							}
 							else {
 								CyEdge edge = metaGraph.getConnectingEdgeList(map.get(c1), map.get(c2), Type.ANY).get(0);
-								metaGraph.getRow(edge).set("edgeStrength",
-								metaGraph.getRow(edge).get("edgeStrength", Integer.class)+1
+								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,
+								metaGraph.getRow(edge).get(StyleManager.EDGESTRENGTH_COLUMN_NAME, Integer.class)+1
 										);
 							}
 						}
@@ -145,7 +142,6 @@ public class YoshikoSolution {
 			)
 		);
 
-		VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle(CyCore.visualMappingManager.getCurrentVisualStyle());
 
 
 		CyCore.networkManager.addNetwork(metaGraph);
@@ -153,25 +149,7 @@ public class YoshikoSolution {
 				view
 		);
 
-		//define style for solution
-		ContinuousMapping<Integer, Double> contMap = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
-				"clusterSize",
-				Integer.class,
-				BasicVisualLexicon.NODE_SIZE
-			);
-		
-		ContinuousMapping<Integer, Double> contMapEdges = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
-				"edgeStrength",
-				Integer.class,
-				BasicVisualLexicon.EDGE_WIDTH
-			);
-
-		//Apply visual style
-		CyCore.visualMappingManager.setVisualStyle(vs, view);
-		vs.addVisualMappingFunction(contMap);
-		vs.addVisualMappingFunction(contMapEdges);
-		vs.apply(view);
-		view.updateView();
+		StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
 
 		CyCore.cy.setCurrentNetworkView(view);
 	}