diff --git a/pom.xml b/pom.xml
index 36149f4ac0018cdaa6f665c5c5e97624bc4b8bfd..1ef32a4f72c9c5f3af0ea3a5f2ae54a835f166df 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<properties>
<bundle.symbolicName>de.hhu.ba.yoshikoWrapper</bundle.symbolicName>
<bundle.namespace>de.hhu.ba.yoshikoWrapper</bundle.namespace>
- <cytoscape.api.version>3.0.0</cytoscape.api.version>
+ <cytoscape.api.version>3.0.1</cytoscape.api.version>
<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
<osgi.api.version>4.2.0</osgi.api.version>
@@ -12,7 +12,7 @@
<groupId>de.hhu.ba</groupId>
<artifactId>yoshikoWrapper</artifactId>
- <version>0.0.2</version>
+ <version>0.0.3</version>
<name>YoshikoWrapper</name>
@@ -125,6 +125,12 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>layout-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ <type>bundle</type>
+ </dependency>
</dependencies>
<description>A Cytoscape plugin for graph-based clustering that wraps the yoshiko algorithm.</description>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 8512ade4cf00b1180679a1c0b0d46a38c1f1e60f..d7dd81cf1a0d9cf468d62ef61dce5d5dfecb999c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -6,6 +6,7 @@ import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.events.AddedEdgesListener;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedListener;
@@ -15,6 +16,11 @@ import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.cytoscape.session.events.SessionLoadedListener;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
@@ -47,7 +53,12 @@ public class CyActivator extends AbstractCyActivator {
CyCore.networkViewFactory = getService(context, CyNetworkViewFactory.class);
CyCore.networkFactory = getService(context, CyNetworkFactory.class);
CyCore.swing = getService(context, CySwingApplication.class);
-
+ CyCore.networkViewManager = getService(context,CyNetworkViewManager.class);
+ CyCore.networkManager = getService(context,CyNetworkManager.class);
+ CyCore.layoutAlgorithmManager = getService(context,CyLayoutAlgorithmManager.class);
+ CyCore.visualMappingManager = getService(context,VisualMappingManager.class);
+ CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class);
+ CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
//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 9ce0ad48935bbc222fa3ede8fee08d9184e0da59..d6ca606e47540c2998139fea4a2f5b3ed24eb47c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
@@ -137,7 +137,7 @@ public class AlgorithmTask extends AbstractTask {
for (long i=0;i<numberOfSolutions;i++) {
taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
- YoshikoSolution solution = new YoshikoSolution();
+ YoshikoSolution solution = new YoshikoSolution(net);
String columnName = "YOSHIKO_SOLUTION_"+(i+1);
net.getDefaultNodeTable().deleteColumn(columnName);
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 48e10473143add793c89b78cbe6d12044eb8e680..984f59c0a92cb3e4fa13540059534aab6a4ffcbf 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -3,11 +3,18 @@ package de.hhu.ba.yoshikoWrapper.core;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
+
/**Simple link collection to enable access to Cytoscape instances
*
*/
@@ -21,6 +28,12 @@ public class CyCore {
public static CyNetworkViewFactory networkViewFactory;
public static CyNetworkFactory networkFactory;
public static CySwingApplication swing;
+ public static CyNetworkViewManager networkViewManager;
+ public static CyNetworkManager networkManager;
+ public static CyLayoutAlgorithmManager layoutAlgorithmManager;
+ public static VisualMappingManager visualMappingManager;
+ public static VisualStyleFactory visualStyleFactory;
+ public static VisualMappingFunctionFactory continuousMappingFactory;
//
}
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 2ff9493f3d4fcce254ab77d955aebe93a4075335..083b120040ff093a9f9504a691498932d03e7c07 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -1,14 +1,70 @@
package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
+import java.util.HashMap;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+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;
- public YoshikoSolution() {
+ public YoshikoSolution(CyNetwork originalGraph) {
cluster = new ArrayList<YoshikoCluster>();
+ this.originalGraph = originalGraph;
+ }
+
+ /**
+ * Transforms this solution in a meta-graph where each cluster is represented by one node
+ * @return The meta-graph as CyNetwork
+ */
+ public CyNetwork toMetaGraph() {
+
+ CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
+
+ metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
+
+ metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
+
+ //Map Cluster to Nodes for further reference
+ HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+
+ //Add nodes
+ for (YoshikoCluster c: cluster) {
+ CyNode clusterNode = metaGraph.addNode();
+ metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.id);
+ metaGraph.getRow(clusterNode).set("clusterSize",c.nodes.size());
+ map.put(c, clusterNode);
+ }
+
+ //Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
+ for (YoshikoCluster c1:cluster) {
+ for (YoshikoCluster c2:cluster) {
+ if (
+ metaGraph.containsEdge(map.get(c1),map.get(c2))
+ || c1 == c2
+ ) {
+ continue;
+ }
+ clusterloop:
+ for (CyNode c1n : c1.nodes) {
+ for (CyNode c2n : c2.nodes) {
+ if (originalGraph.containsEdge(c1n, c2n) || originalGraph.containsEdge(c2n, c1n)) {
+ metaGraph.addEdge(map.get(c1), map.get(c2), false);
+ break clusterloop;
+ }
+ }
+ }
+ }
+ }
+ return metaGraph;
}
}
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 3bad6d69479b188085505bfcb74e40d53620e52b..3ed940f4a0edeb6e2dbe023940d2b2c114139a4c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
@@ -1,6 +1,8 @@
package de.hhu.ba.yoshikoWrapper.gui;
import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import javax.swing.Box;
import javax.swing.BoxLayout;
@@ -8,6 +10,14 @@ 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;
@@ -42,7 +52,45 @@ public class SolutionTab extends ComfortPanel {
clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.cluster.size());
createMetaGraph = new JButton(LocalizationManager.get("createMetaGraph"));
- this.addAll(clusterCount,scrollPane);
+ createMetaGraph.addActionListener(new ActionListener() {
+
+ @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();
+ }
+
+ });
+ this.addAll(clusterCount,scrollPane,createMetaGraph);
}
}
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 0386be728defd72faa97b31dc5f02dc9fbef5d14..d443a6a175fad86114ee844cd199eeaca012a008 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -20,4 +20,5 @@ cost = Cost:
nrSolutions = Number of Solutions:
redRuleChooserTitle = Reduction Rules
discardSolution = Discard
-createMetaGraph = Create Meta-Graph
\ No newline at end of file
+createMetaGraph = Create Meta-Graph
+metaGraph = Meta Graph
\ No newline at end of file