diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs
index abdea9ac032d4655898933f93050f48bf9581d14..839d647eef851c560a9854ff81d9caa1df594ced 100644
--- a/.settings/org.eclipse.core.resources.prefs
+++ b/.settings/org.eclipse.core.resources.prefs
@@ -1,4 +1,5 @@
eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
encoding/<project>=UTF-8
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 63e208af500eddd9c62d90a8dd1d64f18821276c..d9eb0bb43fe679776a1dc773319d45cfa4d75027 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -59,6 +59,8 @@ public class YoshikoCluster {
private ArrayList<CyNode> nodes;
private CySubNetwork net;
+ private Image img;
+
//SYMBOLIC LINKS
private final CyNetwork originalGraph;
private Logger logger = YoshikoLogger.getInstance().getLogger();
@@ -70,28 +72,26 @@ public class YoshikoCluster {
this.nodes = new ArrayList<CyNode>();
}
- private void createSubNetwork() {
+ public void createSubNetwork() {
- if (net == null) {
- CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
-
- //Create nested graph and cluster subnet
- ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
- for (CyNode n: nodes) {
- //Sadly Cytoscape doesnt provide a comfort function here
- List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
- for (CyEdge e: adjacentEdges) {
- if (nodes.contains(e.getSource()) && nodes.contains(e.getTarget())) {
- inducedEdges.add(e);
- }
+ CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
+
+ //Create nested graph and cluster subnet
+ ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
+ for (CyNode n: nodes) {
+ //Sadly Cytoscape doesnt provide a comfort function here
+ List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
+ for (CyEdge e: adjacentEdges) {
+ if (nodes.contains(e.getSource()) && nodes.contains(e.getTarget())) {
+ inducedEdges.add(e);
}
}
- CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(nodes ,inducedEdges);
+ }
+ CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(nodes ,inducedEdges);
- subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(id+1));
+ subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(id+1));
- net = subnet; //Save for further reference
- }
+ net = subnet; //Save for further reference
}
/**
@@ -114,12 +114,20 @@ public class YoshikoCluster {
}
- public void generateImage(JLabel label, int width, int height) {
+ public void applyImage(JLabel label, int width, int height) {
if (net == null) {
- createSubNetwork();
+ return;
+ }
+
+ if (img != null) {
+ getImage(width,height,label);
+ label.setIcon(new ImageIcon(img));
+ return;
}
+ }
+ private void getImage(int width, int height,JLabel label) {
final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
//layout cluster
@@ -150,7 +158,7 @@ public class YoshikoCluster {
@Override
public void run() {
- Image img = renderingEngine.createImage(width,height);
+ img = renderingEngine.createImage(width,height);
label.setIcon(new ImageIcon(img));
renderingEngine.dispose();
@@ -161,11 +169,8 @@ public class YoshikoCluster {
}
-
@Override
- public void cancel() {
- //Nothing to do as GC is handled by JAVA
- }
+ public void cancel() {}
}
);
@@ -173,8 +178,6 @@ public class YoshikoCluster {
CyCore.dialogTaskManager.execute(
createLayout
);
-
-
}
public int getSize() {
@@ -186,9 +189,6 @@ public class YoshikoCluster {
}
public CySubNetwork getSubNetwork() {
- if (net == null) {
- createSubNetwork();
- }
return net;
}
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 bd705af8c5f56118a560ff77295127622dcaea19..f351f01c9191cf03ad899f59aa5c6819a2bc697d 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -46,130 +46,33 @@ public class YoshikoSolution {
* The original Graph from which the solution was generated.
* NOTE: This can be destroyed or modified during runtime while the solution still exists and may become invalid
*/
- private CyNetwork originalGraph;
+ private final CyNetwork originalGraph;
public ArrayList<YoshikoCluster> cluster;
- public int id;
- public YoshikoSolution(CyNetwork originalGraph) {
+ private final long id;
+
+ public YoshikoSolution(CyNetwork originalGraph, long id) {
cluster = new ArrayList<YoshikoCluster>();
this.originalGraph = originalGraph;
+ this.id = id;
}
- /**
- * Transforms this solution in a meta-graph where each cluster is represented by one node
- * The nodes are linked to subgraphs representing the cluster and also their size is scaled relative to cluster size
- */
- public void exportMetaGraph() {
-
- CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
-
- metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
-
- metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
- metaGraph.getDefaultEdgeTable().createColumn("edgeStrength", Integer.class, false);
-
- CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
-
-
- //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();
- CySubNetwork subnet = c.getSubNetwork();
- CyCore.networkManager.addNetwork(subnet);
- //Create network view and register it
- CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
- //layout cluster
- CyCore.dialogTaskManager.execute(
- layout.createTaskIterator(
- subnetView,
- layout.getDefaultLayoutContext(),
- CyLayoutAlgorithm.ALL_NODE_VIEWS,
- null
- )
- );
-
- StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+ //_____________GETTER / SETTER ________________//
- CyCore.networkViewManager.addNetworkView(subnetView);
-
- clusterNode.setNetworkPointer(subnet);
- //Set node attributes
- metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
- metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
- 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;
- }
- for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
- for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
- 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(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
- }
- else {
- CyEdge edge = metaGraph.getConnectingEdgeList(map.get(c1), map.get(c2), Type.ANY).get(0);
- metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,
- metaGraph.getRow(edge).get(StyleManager.EDGESTRENGTH_COLUMN_NAME, Integer.class)+1
- );
- }
- }
- }
- }
- }
- }
-
- CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
-
- //Layout and style solution
-
- TaskIterator it = layout.createTaskIterator(
- view,
- layout.getDefaultLayoutContext(),
- CyLayoutAlgorithm.ALL_NODE_VIEWS,
- null
- );
-
- it.append(new Task() {
-
- @Override
- public void run(TaskMonitor taskMonitor) throws Exception {
- StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
- }
-
- @Override
- public void cancel() {}
-
- });
-
- CyCore.dialogTaskManager.execute(
- it
- );
-
- CyCore.networkManager.addNetwork(metaGraph);
- CyCore.networkViewManager.addNetworkView(
- view
- );
+ public ArrayList<YoshikoCluster> getCluster() {
+ return cluster;
+ }
- view.updateView();
+ public CyNetwork getOriginalGraph() {
+ return originalGraph;
+ }
- CyCore.cy.setCurrentNetworkView(view);
+ /**
+ * @return the id
+ */
+ public long getId() {
+ return id;
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
index 78ec25c416f1b960ed779cd5a9d7846df582dc31..79a1fbf3bbdd8c7e76210ba0ab4db6c0a1526293 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
@@ -1,16 +1,16 @@
/*******************************************************************************
* Copyright (C) 2017 Philipp Spohr
- *
+ *
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
- *
+ *
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
- *
+ *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -42,40 +42,41 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class ClusterView extends JPanel {
-
+
private final JLabel title;
private final JLabel clusterSize;
private final JLabel icon;
private final BasicCollapsiblePanel nodeList;
-
- private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,3);
+
+ private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,1);
private final Border highlightBorder = BorderFactory.createLineBorder(GraphicsLoader.yoshikoGreen,3);
-
+ private final Border selectedBorder = BorderFactory.createLineBorder(Color.BLUE,3);
+
//SYMBOLIC LINKS
-
+
/**Simple array list containing references to the nodes that are represented by this cluster view
- *
+ *
*/
private YoshikoCluster cluster;
-
+
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.getID()+1));
clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.getSize());
icon = new JLabel();
icon.setBorder(BorderFactory.createLineBorder(Color.BLACK));
- cluster.generateImage(icon,128, 128);
+ cluster.applyImage(icon,128, 128);
SwingUtil.addAll(this,title,clusterSize,icon);
this.add(Box.createVerticalStrut(4));
-
+
nodeList = new BasicCollapsiblePanel(LocalizationManager.get("nodes"));
-
+
//Loop over nodes in the cluster and add them to the view
for (CyNode n : c.getSubNetwork().getNodeList()) {
nodeList.add(
@@ -84,15 +85,15 @@ public class ClusterView extends JPanel {
)
);
}
-
+
this.add(nodeList);
-
+
this.addMouseListener(mouseListener);
-
+
this.setBorder(regularBorder);
}
-
+
private MouseListener mouseListener = new MouseListener() {
@Override
@@ -102,7 +103,7 @@ public class ClusterView extends JPanel {
public void mousePressed(MouseEvent e) {
cluster.select();
}
-
+
@Override
public void mouseReleased(MouseEvent e) {}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 59a51fdc2ff343bdd65e6b8f9daf69ffef88d3a1..dfb5ab9f753325ec12520f00b86b17e6a01bebc3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
@@ -53,7 +53,6 @@ import org.cytoscape.util.swing.BasicCollapsiblePanel;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
-import de.hhu.ba.yoshikoWrapper.core.AlgorithmTask;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
@@ -63,6 +62,7 @@ import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanelFactory;
import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
/**This class describes the Swing Panel that the user interacts with in cytoscape
*
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index 689695db6d437282216734c7ad08d6b4944d93bb..d541c1aa21cbe80473fd9acf39f626d2c7be9efe 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
@@ -162,7 +162,7 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
private void addSolutionTab(YoshikoSolution s) {
SolutionTab tab = new SolutionTab(s);
solutionTabs.add(
- LocalizationManager.get("solution")+" "+(s.id+1),
+ LocalizationManager.get("solution")+" "+(s.getId()+1),
tab
);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
index a017efc83b95a601a4aa6218345b89df6aa3d2ef..2f593cdceb8081c1b0936b67bafa8f1960cf523f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
@@ -32,10 +32,14 @@ import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import org.cytoscape.work.TaskIterator;
+
+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;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateMetaGraphTask;
@SuppressWarnings("serial")
public class SolutionTab extends JPanel {
@@ -88,7 +92,11 @@ public class SolutionTab extends JPanel {
@Override
public void actionPerformed(ActionEvent e) {
- solution.exportMetaGraph();
+ CyCore.dialogTaskManager.execute(
+ new TaskIterator(1,
+ new CreateMetaGraphTask(solution)
+ )
+ );
}
});
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
similarity index 91%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index faccd1cc19824fd080c206284c05eff798fc2b05..787ee1c02f623a679a4695b2a3a1bb5003880209 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.core;
+package de.hhu.ba.yoshikoWrapper.tasks;
import java.awt.Window;
import java.util.Properties;
@@ -34,6 +34,11 @@ import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.core.NetworkParser;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
+import de.hhu.ba.yoshikoWrapper.core.StatusInformer;
import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
@@ -49,6 +54,7 @@ import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
public class AlgorithmTask extends AbstractTask {
+ private String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_";
//Symbolic links
private static Logger logger = YoshikoLogger.getInstance().getLogger();
@@ -137,20 +143,18 @@ public class AlgorithmTask extends AbstractTask {
long numberOfSolutions = result.getNumberOfSolutions();
-
taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO localize
YoshikoResult yoshikoResult = new YoshikoResult();
yoshikoResult.flags = result.getFlags();
- System.out.print("ILP FLAG: "+yoshikoResult.flags.getIlpGenerated());
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
- YoshikoSolution solution = new YoshikoSolution(net);
- String columnName = "YOSHIKO_SOLUTION_"+(i+1);
+ YoshikoSolution solution = new YoshikoSolution(net,i);
+ String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
net.getDefaultNodeTable().deleteColumn(columnName);
net.getDefaultNodeTable().createColumn(columnName, String.class, false);
@@ -170,16 +174,18 @@ public class AlgorithmTask extends AbstractTask {
long sizeOfCluster = clusterVector.size();
for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
- taskMonitor.setStatusMessage("Processing entry "+(l+1)+ " of "+sizeOfCluster);
+ taskMonitor.setStatusMessage("Processing node "+(l+1)+ " of "+sizeOfCluster);
int nodeID = clusterVector.get(l);
CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
cluster.addNode(node);
net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
}
- cluster.getSubNetwork();
+ cluster.createSubNetwork();
+ //Register cluster with solution for further reference
solution.cluster.add(cluster);
}
+ //Register solution with result for further reference
yoshikoResult.solutions.add(solution);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..6f75831a8157f92f61ea52be8aa7e9739c7aa7db
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
@@ -0,0 +1,143 @@
+package de.hhu.ba.yoshikoWrapper.tasks;
+
+import java.util.HashMap;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+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.work.AbstractTask;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+
+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.graphModel.YoshikoCluster;
+import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+
+public class CreateMetaGraphTask extends AbstractTask {
+
+ private final YoshikoSolution solution;
+
+ public CreateMetaGraphTask(YoshikoSolution s) {
+ this.solution = s;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
+
+ metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
+
+ metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
+ metaGraph.getDefaultEdgeTable().createColumn("edgeStrength", Integer.class, false);
+
+ CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+
+
+ //Map Cluster to Nodes for further reference
+ HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+
+
+ //Add nodes
+ for (YoshikoCluster c: solution.getCluster()) {
+
+
+
+ CyNode clusterNode = metaGraph.addNode();
+ CySubNetwork subnet = c.getSubNetwork();
+ CyCore.networkManager.addNetwork(subnet);
+ //Create network view and register it
+ CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
+ //layout cluster
+ CyCore.dialogTaskManager.execute(
+ layout.createTaskIterator(
+ subnetView,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ )
+ );
+
+ StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+
+ CyCore.networkViewManager.addNetworkView(subnetView);
+
+ clusterNode.setNetworkPointer(subnet);
+ //Set node attributes
+ metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
+ metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
+ map.put(c, clusterNode);
+ }
+
+ //Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
+ for (YoshikoCluster c1:solution.getCluster()) {
+ for (YoshikoCluster c2:solution.getCluster()) {
+ if (
+ metaGraph.containsEdge(map.get(c1),map.get(c2))
+ || c1 == c2
+ ) {
+ continue;
+ }
+ for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
+ for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
+ if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().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(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
+ }
+ else {
+ CyEdge edge = metaGraph.getConnectingEdgeList(map.get(c1), map.get(c2), Type.ANY).get(0);
+ metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,
+ metaGraph.getRow(edge).get(StyleManager.EDGESTRENGTH_COLUMN_NAME, Integer.class)+1
+ );
+ }
+ }
+ }
+ }
+ }
+ }
+
+ CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
+
+ //Layout and style solution
+
+ TaskIterator it = layout.createTaskIterator(
+ view,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ );
+
+ it.append(new Task() {
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
+ }
+
+ @Override
+ public void cancel() {}
+
+ });
+
+ CyCore.dialogTaskManager.execute(
+ it
+ );
+
+ CyCore.networkManager.addNetwork(metaGraph);
+ CyCore.networkViewManager.addNetworkView(
+ view
+ );
+
+ view.updateView();
+
+ CyCore.cy.setCurrentNetworkView(view);
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..dd84947abcf1a87b991a1337d4374131145ebb61
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author Philipp Spohr, Sep 14, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.tasks;
\ No newline at end of file