diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index d7dd81cf1a0d9cf468d62ef61dce5d5dfecb999c..e663ccde4c3872b6b3cb56f820b16c05a56a03ae 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -12,9 +12,11 @@ import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedListener;
import org.cytoscape.model.events.NetworkAddedListener;
import org.cytoscape.model.events.RemovedEdgesListener;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.cytoscape.session.events.SessionLoadedListener;
+import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -59,6 +61,9 @@ public class CyActivator extends AbstractCyActivator {
CyCore.visualMappingManager = getService(context,VisualMappingManager.class);
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);
+
//Set language according to settings
LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
index d6ca606e47540c2998139fea4a2f5b3ed24eb47c..a07a2e9a6441444a9ed4883a647570a05d6cae66 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
@@ -149,7 +149,9 @@ public class AlgorithmTask extends AbstractTask {
//Loop over cluster
for (long k=0;k<numberOfClusters;k++) {
//Create java instance
- YoshikoCluster cluster = new YoshikoCluster(k);
+ YoshikoCluster cluster = new YoshikoCluster(k,net);
+
+
taskMonitor.setStatusMessage("Processing cluster "+(k+1)+" of "+numberOfClusters);
SWIGTYPE_p_std__vectorT_int_t clusterVector = LibraryInterface.ClusterEditingSolutions_getCluster(result, i, k);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
index 984f59c0a92cb3e4fa13540059534aab6a4ffcbf..ef06d00fedfde22a2d6ea1428615d01c94e1d62b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -4,7 +4,9 @@ import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -34,6 +36,8 @@ public class CyCore {
public static VisualMappingManager visualMappingManager;
public static VisualStyleFactory visualStyleFactory;
public static VisualMappingFunctionFactory continuousMappingFactory;
+ public static CyRootNetworkManager rootNetworkManager;
+ public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
//
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
index 50d4a292d191e5377d08d6077803d86e233c8d4c..86021ef1f56e30484283ef8524c516e4764002fd 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -2,14 +2,22 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+
public class YoshikoCluster {
- public long id;
+
+
+ public final long id;
+ public final CyNetwork originalGraph;
+
public ArrayList<CyNode> nodes;
- public YoshikoCluster(long id) {
+ public YoshikoCluster(long id, CyNetwork originalGraph) {
this.id = id;
- this.nodes = new ArrayList<CyNode>();
+ this.originalGraph = originalGraph;
+ this.nodes = new ArrayList<CyNode>();
}
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
index 083b120040ff093a9f9504a691498932d03e7c07..34394474241d8e3124cc54ffa7216c9b7dba65da 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -2,17 +2,25 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+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;
public class YoshikoSolution {
private CyNetwork originalGraph;
+
public ArrayList<YoshikoCluster> cluster;
public int id;
@@ -23,9 +31,9 @@ public class YoshikoSolution {
/**
* Transforms this solution in a meta-graph where each cluster is represented by one node
- * @return The meta-graph as CyNetwork
+ * The nodes are linked to subgraphs representing the cluster and also their size is scaled relative to cluster size
*/
- public CyNetwork toMetaGraph() {
+ public void exportMetaGraph() {
CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
@@ -33,12 +41,48 @@ public class YoshikoSolution {
metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
+ CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+
+
//Map Cluster to Nodes for further reference
HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+ //Convert original graph to root graph to allow embedding of nodes
+ CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
+
//Add nodes
for (YoshikoCluster c: cluster) {
CyNode clusterNode = metaGraph.addNode();
+ //Create nested graph and cluster subnet
+ ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
+ for (CyNode n: c.nodes) {
+ //Sadly Cytoscape doesnt provide a comfort function here
+ List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
+ for (CyEdge e: adjacentEdges) {
+ if (c.nodes.contains(e.getSource()) && c.nodes.contains(e.getTarget())) {
+ inducedEdges.add(e);
+ }
+ }
+ }
+ CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(c.nodes ,inducedEdges);
+
+ subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(c.id+1));
+
+ CyCore.networkManager.addNetwork(subnet);
+ //Create network view and register it
+ CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
+ CyCore.networkViewManager.addNetworkView(subnetView);
+ //layout cluster
+ CyCore.dialogTaskManager.execute(
+ layout.createTaskIterator(
+ subnetView,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ )
+ );
+ clusterNode.setNetworkPointer(subnet);
+ //Set node attributes
metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.id);
metaGraph.getRow(clusterNode).set("clusterSize",c.nodes.size());
map.put(c, clusterNode);
@@ -64,7 +108,38 @@ public class YoshikoSolution {
}
}
}
- return metaGraph;
+
+ CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
+ //layout solution
+ CyCore.dialogTaskManager.execute(
+ layout.createTaskIterator(
+ view,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ )
+ );
+
+ CyCore.networkManager.addNetwork(metaGraph);
+ CyCore.networkViewManager.addNetworkView(
+ view
+ );
+
+ //define style for solution
+ ContinuousMapping<Integer, Double> contMap = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
+ "clusterSize",
+ Integer.class,
+ BasicVisualLexicon.NODE_SIZE
+ );
+ VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle("Meta-Graph Style");
+ vs.addVisualMappingFunction(contMap);
+ CyCore.visualMappingManager.addVisualStyle(vs);
+ CyCore.cy.setCurrentNetworkView(view);
+ //Apply visual style
+ CyCore.visualMappingManager.setVisualStyle(vs, view);
+ vs.apply(view);
+ view.updateView();
+
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
index 629289c4a142ba35f6e267ebad8d9a7a5303a122..3dbb10f31c4bafa52f416f3bd7b1fa60db97a7c3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
@@ -11,12 +11,9 @@ import javax.swing.BoxLayout;
import javax.swing.JLabel;
import javax.swing.border.Border;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
-import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
@@ -26,10 +23,6 @@ public class ClusterView extends ComfortPanel {
private final JLabel title;
private final JLabel clusterSize;
- private final CyNetworkView clusterView;
-
- private CyNetwork clusterSubNet;
-
private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY);
private final Border highlightBorder = BorderFactory.createLineBorder(Color.RED);
@@ -42,16 +35,14 @@ public class ClusterView extends ComfortPanel {
public ClusterView(YoshikoCluster c) {
- this.cluster = c;
+ this.cluster = c;
+
//Swing init
this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
title = new JLabel(LocalizationManager.get("cluster")+" "+(c.id+1));
clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.nodes.size());
-
- this.clusterSubNet = CyCore.networkFactory.createNetwork();
- this.clusterView = CyCore.networkViewFactory.createNetworkView(this.clusterSubNet);
-
+
this.addAll(title,clusterSize);
this.add(Box.createVerticalStrut(4));
@@ -59,7 +50,7 @@ public class ClusterView extends ComfortPanel {
for (CyNode n : c.nodes) {
this.add(
new JLabel(
- CyCore.cy.getCurrentNetwork().getRow(n).get("name", String.class)
+ c.originalGraph.getRow(n).get("name", String.class)
)
);
}
@@ -79,13 +70,13 @@ public class ClusterView extends ComfortPanel {
public void mousePressed(MouseEvent e) {
//Undo previous selection
- List<CyRow> allRows = CyCore.cy.getCurrentNetwork().getDefaultNodeTable().getAllRows();
+ List<CyRow> allRows = cluster.originalGraph.getDefaultNodeTable().getAllRows();
for (CyRow r: allRows) {
r.set("selected", false);
}
//Select nodes corresponding to the cluster
for (CyNode n : cluster.nodes) {
- CyCore.cy.getCurrentNetwork().getRow(n).set("selected", true);
+ cluster.originalGraph.getRow(n).set("selected", true);
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
index 3ed940f4a0edeb6e2dbe023940d2b2c114139a4c..8a71ad1426deacb9c16b0720ed3ed5b34fd46432 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
@@ -10,14 +10,6 @@ import javax.swing.JButton;
import javax.swing.JLabel;
import javax.swing.JScrollPane;
-import org.cytoscape.model.CyNetwork;
-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.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
@@ -56,37 +48,7 @@ public class SolutionTab extends ComfortPanel {
@Override
public void actionPerformed(ActionEvent e) {
- CyNetwork metaGraph = solution.toMetaGraph();
- CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
- //layout solution
- CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
- CyCore.dialogTaskManager.execute(
- layout.createTaskIterator(
- view,
- layout.getDefaultLayoutContext(),
- CyLayoutAlgorithm.ALL_NODE_VIEWS,
- null
- )
- );
- //define style for solution
- ContinuousMapping<Integer, Double> contMap = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
- "clusterSize",
- Integer.class,
- BasicVisualLexicon.NODE_SIZE
- );
- VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle("Meta-Graph Style");
- vs.addVisualMappingFunction(contMap);
- CyCore.visualMappingManager.addVisualStyle(vs);
-
-
- CyCore.networkManager.addNetwork(metaGraph);
- CyCore.networkViewManager.addNetworkView(
- view
- );
-
- CyCore.cy.setCurrentNetworkView(view);
- vs.apply(CyCore.cy.getCurrentNetworkView());
- CyCore.cy.getCurrentNetworkView().updateView();
+ solution.exportMetaGraph();
}
});