diff --git a/pom.xml b/pom.xml
index 34a0ed52a57a7f8ea3ec7f7c251eafcd820b1d68..8cee3140f295e25628a57a43a7da096333407220 100644
--- a/pom.xml
+++ b/pom.xml
@@ -157,6 +157,11 @@
<artifactId>swing-util-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>group-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </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 14967895edce8fb4bc906035114e91f5c3f97409..0a088f54021c7bf0cf2362aacc42e23a75987b6b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -38,6 +38,7 @@ 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.create.CloneNetworkTaskFactory;
import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
@@ -87,6 +88,7 @@ public class CyActivator extends AbstractCyActivator {
CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
+ CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.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 1bb46b7a0e44e9f6153264c5e631ca1594dec37a..50887d924d89f05fdb3108aa2833a61511e394f9 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
@@ -30,7 +30,6 @@ import org.cytoscape.application.swing.CytoPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.AbstractTask;
@@ -58,19 +57,8 @@ public class AlgorithmTask extends AbstractTask {
private Window statusWindow;
//Parameters
- private final double insertionCostDefault;
- private final double deletionCostDefault;
- private final CyColumn permanentColumn;
- private final CyColumn forbiddenColumn;
- private CyColumn weightColumn;
- private int timeLimit;
- private CyNetwork net;
- private String bitMaskRules;
- private double multiplicativeFactor;
- private boolean separatePartitionCuts;
- private boolean separateTriangles;
- private boolean useHeuristic;
- private int numberOfSolutions;
+ private final ParameterSet parameterSet;
+ private final CyNetwork net;
//Temps, need to be freed in C++
private LibraryInput input;
@@ -82,34 +70,12 @@ public class AlgorithmTask extends AbstractTask {
public AlgorithmTask(// <<< Too many variables here, some should be grouped later TODO:
Window statusWindow,
CyNetwork net,
- int timeLimit,
- CyColumn weightColumn,
- CyColumn permanentColumn,
- CyColumn forbiddenColumn,
- double insertionCostDefault,
- double deletionCostDefault,
- String bitMaskRules,
- double multiplicativeFactor,
- boolean separatePartitionCuts,
- boolean separateTriangles,
- boolean useHeuristic,
- int numberOfSolutions
+ ParameterSet parameterSet
)
{
this.statusWindow = statusWindow;
this.net = net;
- this.timeLimit = timeLimit;
- this.weightColumn = weightColumn;
- this.permanentColumn = permanentColumn;
- this.forbiddenColumn = forbiddenColumn;
- this.insertionCostDefault = insertionCostDefault;
- this.deletionCostDefault = deletionCostDefault;
- this.bitMaskRules = bitMaskRules;
- this.multiplicativeFactor = multiplicativeFactor;
- this.separatePartitionCuts = separatePartitionCuts;
- this.separateTriangles = separateTriangles;
- this.useHeuristic = useHeuristic;
- this.numberOfSolutions = numberOfSolutions;
+ this.parameterSet = parameterSet;
}
@Override
@@ -125,7 +91,7 @@ public class AlgorithmTask extends AbstractTask {
}
//Set time limit
- LibraryInterface.setTimeLimit(timeLimit);
+ LibraryInterface.setTimeLimit(parameterSet.timeLimit);
//Create a node map to identify nodes and eges in the solution
NodeMap nodeMap = new NodeMap(net);
@@ -135,24 +101,24 @@ public class AlgorithmTask extends AbstractTask {
input = NetworkParser.parseNetwork(
net,
nodeMap,
- weightColumn,
- permanentColumn,
- forbiddenColumn,
- deletionCostDefault
+ parameterSet.weightColumn,
+ parameterSet.permanentColumn,
+ parameterSet.forbiddenColumn,
+ parameterSet.defaultDeletionCost
);
taskMonitor.setProgress(0.2);
//Set the default value for insertion cost
- input.setDefaultInsertionCost(insertionCostDefault);
+ input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
//Call Yoshiko <<< Algorithm is performed here
ca = LibraryInterface.getRun(input,
- numberOfSolutions,
- bitMaskRules,
- multiplicativeFactor,
- separatePartitionCuts,
- separateTriangles,
- useHeuristic
+ parameterSet.solCount,
+ parameterSet.reductionRulesBitMask,
+ parameterSet.snrMultFactor,
+ parameterSet.usePartitionCuts,
+ parameterSet.useTriangleCuts,
+ parameterSet.useHeuristic
);
class CallbackHandler extends CplexInformer{
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 ab7cefae60d41026fe780f4caaa54cfec85aee52..803d3ee74546377edfc4b2bd82ee2c3a8d8ed81e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -28,6 +28,7 @@ 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.create.CloneNetworkTaskFactory;
import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -62,5 +63,7 @@ public class CyCore {
public static CyRootNetworkManager rootNetworkManager;
public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
+ public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
+
//
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..863c86959a06f4113adb80f8b100fded4e81380c
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -0,0 +1,20 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import org.cytoscape.model.CyColumn;
+
+public class ParameterSet {
+
+ public int timeLimit;
+ public CyColumn weightColumn;
+ public CyColumn permanentColumn;
+ public CyColumn forbiddenColumn;
+ public double defaultInsertionCost;
+ public double defaultDeletionCost;
+ public String reductionRulesBitMask;
+ public double snrMultFactor;
+ public boolean useTriangleCuts;
+ public boolean usePartitionCuts;
+ public boolean useHeuristic;
+ public int solCount;
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..6897d9a8757c9cddf4f889b75048e6de555cdb96
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author Philipp Spohr, Sep 5, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.cytoUtil;
\ No newline at end of file
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 40b3878452055c7a7b5131e3d62aa3464cc510e8..2e1f1d1e1059feb3a394b1eefd8ee6570cec2afc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -94,8 +94,11 @@ public class YoshikoCluster {
}
}
+ /**
+ * Attempt to select the nodes belonging to this cluster in the original Graph given that they still exist
+ */
public void select() {
- if (originalGraph.getDefaultNodeTable() != null) {
+ try {
List<CyRow> allRows = originalGraph.getDefaultNodeTable().getAllRows();
for (CyRow r: allRows) {
r.set("selected", false);
@@ -105,21 +108,23 @@ public class YoshikoCluster {
originalGraph.getRow(n).set("selected", true);
}
}
- else {
+ catch (Exception e) {
logger.warn("The graph doesn't exist anymore, can't highlight nodes!");
}
}
public void generateImage(JLabel label, int width, int height) {
+
if (net == null) {
createSubNetwork();
}
- CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
+
+ final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
//layout cluster
- CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
- TaskIterator createLayout = layout.createTaskIterator(
+ final CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+ final TaskIterator createLayout = layout.createTaskIterator(
view,
layout.getDefaultLayoutContext(),
CyLayoutAlgorithm.ALL_NODE_VIEWS,
@@ -161,7 +166,7 @@ public class YoshikoCluster {
@Override
public void cancel() {
- // TODO Auto-generated method stub
+ //Nothing to do as GC is handled by JAVA
}
}
@@ -197,6 +202,4 @@ public class YoshikoCluster {
return originalGraph.getRow(n).get("name", String.class);
}
-
-
}
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 bb1a5e5b92af9db4219ed6ee67c54ce6d2175444..ed2227917e664819a54d953e8e40e32f5eaaf860 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -28,17 +28,23 @@ 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.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 {
+ /**
+ * 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;
public ArrayList<YoshikoCluster> cluster;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
index 4fe0d95f0c611eeb39fc65b9e982fea289ae76db..0ce16d3353256cea0d0d6aa10404054f79118edc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -53,6 +53,7 @@ import de.hhu.ba.yoshikoWrapper.core.AlgorithmTask;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
/**This class describes the Swing Panel that the user interacts with in cytoscape
@@ -212,18 +213,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
AbstractTask yoshiko = new AlgorithmTask(
popupLevel,
CyCore.cy.getCurrentNetwork(),
- opModePanel.getTimeLimit(),
- ecPanel.getWeightColumn(),
- ecPanel.getPermanentColumn(),
- ecPanel.getForbiddenColumn(),
- ecPanel.getDefaultInsertionCost(),
- ecPanel.getDefaultDeletionCost(),
- reductionRulesChooser.getBitMask(),
- reductionRulesChooser.getMultFactor(),
- opModePanel.useTriangleCuts(),
- opModePanel.usePartitionCuts(),
- opModePanel.useHeuristic(),
- opModePanel.getSolCount()
+ fetchParameter()
);
/**
* Don't queue multiple runs at once because that will get messy
@@ -247,6 +237,26 @@ 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 fetchParameter() {
+ ParameterSet ret = new ParameterSet();
+ ret.timeLimit = opModePanel.getTimeLimit();
+ ret.weightColumn = ecPanel.getWeightColumn();
+ ret.permanentColumn = ecPanel.getPermanentColumn();
+ ret.forbiddenColumn = ecPanel.getForbiddenColumn();
+ ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
+ ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
+ ret.reductionRulesBitMask = reductionRulesChooser.getBitMask();
+ ret.snrMultFactor = reductionRulesChooser.getMultFactor();
+ ret.useTriangleCuts = opModePanel.useTriangleCuts();
+ ret.usePartitionCuts = opModePanel.usePartitionCuts();
+ ret.useHeuristic = opModePanel.useHeuristic();
+ ret.solCount = opModePanel.getSolCount();
+ return ret;
+ }
//GETTER / SETTER