diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index d1862a67d71841823a52278522ac68f08fc02950..6af2730eaf81f62175294b854635388ce4a43fd0 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -127,5 +127,7 @@ public class CyActivator extends AbstractCyActivator {
MainPanel mainPanel = new MainPanel();
registerService(context,mainPanel,CytoPanelComponent.class, new Properties());
+ CyCore.mainPanel = mainPanel;
+
}
}
\ No newline at end of file
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 aee7b04da8bb48932c1368dc1539d9965c2167f0..e050180f8e2b1be2cf860ef0eb3276b5c93d7cf8 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -23,6 +23,7 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.util.concurrent.CountDownLatch;
+import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.command.CommandExecutorTaskFactory;
@@ -70,6 +71,7 @@ public class CyCore {
public static CommandExecutorTaskFactory commandExecutorTaskFactory;
//
+ public static MainPanel mainPanel;
//Convenience
// public static String getConfig(String key) {
// return cm.getProperties().getProperty(key);
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 8d2ddfbab332f3a914a46b5fd137c4545005430e..df98a8c01bd1749417a047aeeddad61860313a1b 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
@@ -306,7 +306,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
* Fetches all the parameters from the various swing components and packs them into a neat abstract wrapper class
* @return The currently selected parameter wrapped in a ParameterSet
*/
- private ParameterSet fetchParameters(CyNetwork net) {
+ public ParameterSet fetchParameters(CyNetwork net) {
ParameterSet ret = new ParameterSet();
ret.net = net;
ret.timeLimit = opModePanel.getTimeLimit();
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
index ebd95002c5446435990241db14abeee6ce3b0b02..4d3135cab4cc1ef47e8bceecf9e688596c27471c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -1,5 +1,6 @@
package de.hhu.ba.yoshikoWrapper.taskFactories;
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
@@ -46,7 +47,7 @@ public class CommandTaskFactory implements TaskFactory{
return new TaskIterator(
new AlgorithmTask(
null,
- new ParameterSet()
+ CyCore.mainPanel.fetchParameters(CyCore.cy.getCurrentNetwork())
)
);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index daedf67b38cc1f8c3411ac3a37eee812ff0d17d4..64712e16f638b101c9f423f8fbf59f67d8347d0c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -22,16 +22,25 @@
package de.hhu.ba.yoshikoWrapper.tasks;
import java.awt.Window;
+import java.util.Properties;
+import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
import de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm.YoshikoAlgoritmController;
+import org.cytoscape.application.swing.CytoPanel;
+import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
+import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ContainsTunables;
import org.cytoscape.work.ObservableTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.TunableValidator;
+import org.osgi.framework.Bundle;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.ServiceReference;
import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -83,8 +92,6 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
- CyNetwork networkToBeProcessed = CyCore.cy.getCurrentNetwork();
-
//TODO: Improve setProgress values
taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
@@ -99,8 +106,6 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
YoshikoAlgoritmController yoshikoAlgoritmController = new YoshikoAlgoritmController(parameterSet);
yoshikoAlgoritmController.controllAlgorithm();
- CyTable table = networkToBeProcessed.getDefaultEdgeTable();
-
/*
//Create a node map to identify nodes and eges in the solution
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
index 19625141bb846ebd751666fcc0e81b04237addfc..e8f99a56dda218f5244c5670e3225942738356c9 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
@@ -3,9 +3,12 @@ package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
import org.cytoscape.model.*;
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 java.util.*;
@@ -104,6 +107,8 @@ public final class GraphTranslator {
addNodesToResultNetwork(resultNetwork);
addEdgesToResultNetwork(clusters, resultNetwork);
+
+ // createNetworkView(resultNetwork);
}
private CySubNetwork createNewGaph(){
@@ -145,4 +150,12 @@ public final class GraphTranslator {
resultNetwork.addEdge(network.getEdge(yoshikoEdge.suid));
}
}
+
+ private CyNetworkView createNetworkView(CyNetwork resultNetwork){
+
+ CyNetworkView view = CyCore.networkViewFactory.createNetworkView(resultNetwork);
+
+ CyCore.networkViewManager.addNetworkView(view,false);
+ return view;
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
index 12c2a44403c51b05cf82be2d32aa0326f766c138..8bec067ef5febf51b2a5d6e7a8c4505c6dc2e028 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
@@ -7,13 +7,14 @@ import java.util.List;
public class YoshikoAlgoritmController {
- private int k = 19;
+ private int k;
private CyNetwork network;
private ParameterSet parameterSet;
public YoshikoAlgoritmController(ParameterSet parameterSet){
this.parameterSet = parameterSet;
this.network = parameterSet.net;
+ this.k = parameterSet.clusterCount;
}
public void controllAlgorithm(){
@@ -28,8 +29,6 @@ public class YoshikoAlgoritmController {
clusters = clusteringAlgorithm.runClusteringAlgorithm();
translator.makeCytoscapeGraph(clusters);
-
- System.out.println("asdadasd");
}