From 2fdaa0aa3c454aa3ee36e267e80f324170685a56 Mon Sep 17 00:00:00 2001
From: Lukas Ettel <34522828+LukasEttel@users.noreply.github.com>
Date: Mon, 8 Jun 2020 11:37:11 +0200
Subject: [PATCH] release
---
pom.xml | 6 +-
.../ba/yoshikoWrapper/core/ParameterSet.java | 8 +-
.../cytoUtil/GraphAnalyzer.java | 89 +++++++++++++++++++
.../graphModel/YoshikoCluster.java | 4 +-
.../swing/components/EditCostPanel.java | 18 +++-
.../swing/components/MainPanel.java | 23 +++--
.../swing/components/ResultPanel.java | 13 +--
.../taskFactories/CommandTaskFactory.java | 6 +-
.../yoshikoWrapper/tasks/AlgorithmTask.java | 4 +-
.../yoshikoAlgorithm/ClusteringAlgorithm.java | 1 -
.../yoshikoAlgorithm/GraphTranslator.java | 67 +++++++++++++-
.../YoshikoAlgoritmController.java | 1 +
12 files changed, 204 insertions(+), 36 deletions(-)
diff --git a/pom.xml b/pom.xml
index 8c1c573..1fbd33d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -32,8 +32,8 @@
</properties>
<groupId>de.hhu.ba</groupId>
- <artifactId>yoshikoStandalone</artifactId>
- <version>0.1.1</version>
+ <artifactId>YoshikoStandalone</artifactId>
+ <version>1.0.0</version>
<name>YoshikoStandalone</name>
@@ -130,7 +130,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.8.2</version>
+ <version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
index 48f1639..f267e05 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -54,6 +54,8 @@ public class ParameterSet implements TunableValidator
public double defaultInsertionCost = -1;
@Tunable(description="The default deletion cost that is to be used for edges without an associated weight",context="nogui")
public double defaultDeletionCost = 1;
+ @Tunable(description="The threshold to tackle the problem of a completly poitive graph", context="nogui")
+ public double threshold = 0;
@Tunable(description="A bitmask representing which reduction rules should be used",context="nogui")
public String reductionRulesBitMask = "000000";
@@ -80,7 +82,11 @@ public class ParameterSet implements TunableValidator
@Tunable(description="Determines the number of clusters that are to be generated. -1 generates the optimal amount of clusters in the sense of WCE",context="nogui")
public int clusterCount = -1;
-
+
+
+ //ugly passing of variables
+ public boolean containsOnlyPositiveEdges;
+ public double recomendetTreshold;
/**
* Default constructor, initializes the column mappings to provide a selection of fitting columns
*/
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
index 24ca2d5..a6b8a07 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -2,6 +2,8 @@ package de.hhu.ba.yoshikoWrapper.cytoUtil;
import java.util.List;
+import de.hhu.ba.yoshikoWrapper.core.NetworkParsingException;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
@@ -160,4 +162,91 @@ public class GraphAnalyzer {
}
return false;
}
+
+ public static double recommendThreshold(CyNetwork net, ParameterSet parameterSet) throws NetworkParsingException{
+ double threshold = parameterSet.threshold;
+ double maxEdgeWeight = Double.NEGATIVE_INFINITY;
+ double minEdgeWeight = Double.POSITIVE_INFINITY;
+
+ for (CyEdge edge : net.getEdgeList()){
+ double weight;
+ weight = extractValue(edge,net, parameterSet);
+ weight -= threshold;
+
+
+ if (weight < minEdgeWeight){
+ minEdgeWeight = weight;
+ }
+ if (weight > maxEdgeWeight){
+ maxEdgeWeight = weight;
+ }
+ }
+
+ if (minEdgeWeight == maxEdgeWeight){
+ return 0;
+ }
+
+ if (minEdgeWeight >= 0){
+ return (maxEdgeWeight+minEdgeWeight)/2;
+ }
+ return 0;
+ }
+
+ private static double extractValue(CyEdge edge, CyNetwork network,ParameterSet parameterSet) throws NetworkParsingException {
+ CyColumn weightColumn = parameterSet.getWeightColumn();
+
+ //Parse editing costs
+ double weight = parameterSet.defaultDeletionCost;
+
+ //Fetch entry and check if it exists
+ CyRow edgeEntry = network.getRow(edge);
+
+ //Check if the column contains an entry for the respective edge
+ //It is possible, that there are missing entries
+ if (parameterSet.weightColumn != null){
+ if (edgeEntry.get(weightColumn.getName(), weightColumn.getType()) != null){
+ if (weightColumn.getType() == Integer.class) {
+ weight = 1.0*edgeEntry.get(weightColumn.getName(), Integer.class);
+ }
+ else if (weightColumn.getType() == Double.class) {
+ weight = edgeEntry.get(weightColumn.getName(), Double.class);
+ }
+ }
+ }
+
+
+ CyColumn permanentColumn = parameterSet.getPermanentColumn();
+ CyColumn forbiddenColumn = parameterSet.getForbiddenColumn();
+
+ //Parse Forbidden/Permanent markers
+ boolean forbidden = false;
+ boolean permanent = false;
+
+ if (permanentColumn != null) {
+ //Additional check as it is not required to have a value in every row
+ if (edgeEntry.get(permanentColumn.getName(), Boolean.class) != null) {
+ permanent = (boolean)edgeEntry.get(permanentColumn.getName(), Boolean.class);
+ }
+ }
+ if (forbiddenColumn != null) {
+ //Additional check as it is not required to have a value in every row
+ if (edgeEntry.get(forbiddenColumn.getName(), Boolean.class) != null) {
+ forbidden = (boolean)edgeEntry.get(forbiddenColumn.getName(), Boolean.class);
+ }
+ }
+
+ //Check for edges that are forbidden AND permanent -> Throw exception
+ if (forbidden && permanent) {
+ throw new NetworkParsingException("dualInfinityError");
+ }
+
+
+ if(permanent){
+ return Double.POSITIVE_INFINITY;
+ }else if (forbidden){
+ return Double.NEGATIVE_INFINITY;
+ }
+
+ return weight;
+ }
}
\ 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 57c4563..40beaed 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -164,8 +164,8 @@ public class YoshikoCluster {
)
);
- view.setVisualProperty(NETWORK_WIDTH, new Double(width));
- view.setVisualProperty(NETWORK_HEIGHT, new Double(height));
+ view.setVisualProperty(NETWORK_WIDTH, (double) width);
+ view.setVisualProperty(NETWORK_HEIGHT, (double) height);
view.fitContent();
StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
index 257ff59..d86de66 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
@@ -42,11 +42,13 @@ public class EditCostPanel extends JPanel {
private final DoubleInputField icField;
private final DoubleInputField dcField;
+ private final DoubleInputField threshholdField;
private final JSeparator separator;
private final JLabel icLabel;
private final JLabel dcLabel;
+ private final JLabel threshholdLable;
//private final HelpButton helpButton;
@@ -59,18 +61,21 @@ public class EditCostPanel extends JPanel {
icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
+ threshholdField = new DoubleInputField(Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY);
icField.setText("-1.0");
icField.setToolTipText(LocalizationManager.get("icTooltip"));
dcField.setText("1.0");
+ threshholdField.setText("0.0");
separator = new JSeparator(JSeparator.HORIZONTAL);
icLabel = new JLabel(LocalizationManager.get("defaultInsertion"));
- dcLabel = new JLabel(LocalizationManager.get("defaultDeletion"));
+ dcLabel = new JLabel("Default deletion cost:");
+ threshholdLable = new JLabel("Threshold for weight:");
//Add components
- SwingUtil.addAll(this,columnMapper,separator,icLabel,icField,dcLabel,dcField);
+ SwingUtil.addAll(this,columnMapper,separator,icLabel,icField,dcLabel,dcField, threshholdLable, threshholdField);
//SwingUtil.addAll(helpButton);
@@ -86,11 +91,13 @@ public class EditCostPanel extends JPanel {
.addGroup(layout.createParallelGroup(Alignment.LEADING)
.addComponent(icLabel)
.addComponent(dcLabel)
+ .addComponent(threshholdLable)
)
.addGap(4)
.addGroup(layout.createParallelGroup(Alignment.LEADING)
.addComponent(icField)
.addComponent(dcField)
+ .addComponent(threshholdField)
)
)
);
@@ -109,6 +116,11 @@ public class EditCostPanel extends JPanel {
.addGap(4)
.addComponent(dcField)
)
+ .addGroup(layout.createParallelGroup(Alignment.BASELINE)
+ .addComponent(threshholdLable)
+ .addGap(4)
+ .addComponent(threshholdField)
+ )
);
this.setLayout(layout);
@@ -124,6 +136,8 @@ public class EditCostPanel extends JPanel {
return dcField.getValueAsDouble();
}
+ public double getThreshold() {return threshholdField.getValueAsDouble();}
+
public ColumnMapper getColumnMapper() {
return columnMapper;
}
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 190eab5..a6eeb5e 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
@@ -23,6 +23,7 @@ package de.hhu.ba.yoshikoWrapper.swing.components;
import static javax.swing.GroupLayout.DEFAULT_SIZE;
import static javax.swing.GroupLayout.PREFERRED_SIZE;
+import static javax.swing.JOptionPane.showMessageDialog;
import java.awt.Component;
import java.awt.Dialog.ModalExclusionType;
@@ -49,7 +50,6 @@ import javax.swing.ScrollPaneConstants;
import de.hhu.ba.yoshikoWrapper.taskFactories.CommandTaskFactory;
import de.hhu.ba.yoshikoWrapper.taskFactories.YoshikoCommand;
-import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.model.CyNetwork;
@@ -59,12 +59,9 @@ import org.cytoscape.work.TaskIterator;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
-import de.hhu.ba.yoshikoWrapper.cytoUtil.CommandExecutor;
import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
-import de.hhu.ba.yoshikoWrapper.help.HelpLinks;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
-import org.cytoscape.work.TaskManager;
/**This class describes the Swing Panel that the user interacts with in cytoscape
*
@@ -93,6 +90,8 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
private final JButton runButton;
+ public ParameterSet parameterSet;
+
/**
* Main constructor, creates a new Panel and initializes subcomponents
*/
@@ -214,6 +213,8 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
CyNetwork networkToBeProcessed = CyCore.cy.getCurrentNetwork();
+ parameterSet = fetchParameters(networkToBeProcessed);
+
//WARNINGS FOR FEATURES THAT ARE NOT RESEARCHED
//TODO: (Obviously) research!
if (GraphAnalyzer.isMultiGraph(networkToBeProcessed)) {
@@ -225,7 +226,14 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
);
}
-
+ try {
+ double recommendedThreshold = GraphAnalyzer.recommendThreshold(networkToBeProcessed, parameterSet);
+ if (!(recommendedThreshold==0)) {
+ showMessageDialog(null, "The provided graph only consists of edges with \n positive weight and will likely not yield a good result. \n Adjusting the threshold might be necessary. \n"+recommendedThreshold+" might be a good Threshold" , "Threshold-Warning",JOptionPane.WARNING_MESSAGE);
+ }
+ }catch (Exception exception){
+ exception.printStackTrace();
+ }
//SWING BLACK MAGIC
Window noWindow = null;
JDialog statusWindow = new JDialog(noWindow);
@@ -239,6 +247,8 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
CyCore.statusWindow = statusWindow;
//SWING BLACK MAGIC
+
+
CommandTaskFactory commandTaskFactory = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM);
TaskIterator taskIterator = commandTaskFactory.createTaskIterator();
@@ -247,8 +257,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
} catch (InterruptedException ex) {
ex.printStackTrace();
}
-
- System.out.println();
}
};
@@ -263,6 +271,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
ret.setWeightColumn(ecPanel.getWeightColumn());
ret.setPermanentColumn(ecPanel.getPermanentColumn());
ret.setForbiddenColumn(ecPanel.getForbiddenColumn());
+ ret.threshold = ecPanel.getThreshold();
ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
ret.useHeuristic = opModePanel.useHeuristic();
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 9d39b11..920b58d 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
@@ -31,18 +31,10 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Properties;
-import javax.swing.BoxLayout;
-import javax.swing.GroupLayout;
+import javax.swing.*;
import javax.swing.GroupLayout.ParallelGroup;
import javax.swing.GroupLayout.SequentialGroup;
-import javax.swing.Icon;
-import javax.swing.JButton;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTabbedPane;
-import javax.swing.LayoutStyle;
-import javax.swing.SwingConstants;
+import javax.swing.event.ChangeListener;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
@@ -275,5 +267,4 @@ NetworkAboutToBeDestroyedListener
public void handleEvent(AboutToRemoveEdgesEvent e) {
invalidateIfRelevant(e);
}
-
}
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 4d3135c..a4a294f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -45,11 +45,7 @@ public class CommandTaskFactory implements TaskFactory{
}
else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
return new TaskIterator(
- new AlgorithmTask(
- null,
- CyCore.mainPanel.fetchParameters(CyCore.cy.getCurrentNetwork())
- )
- );
+ new AlgorithmTask(null, CyCore.mainPanel.parameterSet));
}
else return null; //TODO: Might be useful to generate an error/ throw an exception here as this should never be invoked
}
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 934d74c..ea0f96d 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -112,7 +112,6 @@ public class AlgorithmTask extends AbstractTask {
//Generate solutionsPanel
resultPanel = new ResultPanel(result);
-
//Show solution panel
CyCore.registrar.registerService(resultPanel, CytoPanelComponent.class, new Properties());
//Focus solution panel
@@ -130,8 +129,7 @@ public class AlgorithmTask extends AbstractTask {
}
}
);
- eastPanel.getThisComponent().revalidate();
-
+ //eastPanel.getThisComponent().revalidate();
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java
index 8078e78..8c9e467 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java
@@ -437,7 +437,6 @@ public class ClusteringAlgorithm {
if (edgeArray[i][j].startingWeight < 0){
clusteringCost -= edgeArray[i][j].startingWeight;
System.out.println("Insert edge:("+i+","+ j+") with cost "+edgeArray[i][j].startingWeight);
-
}
edgeArray[i][j].startingWeight = 0;
}
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 73fd93e..504d747 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
@@ -1,26 +1,43 @@
package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.NetworkParsingException;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
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 javax.swing.*;
+import java.awt.*;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
import java.util.*;
+import java.util.List;
+
+import static javax.swing.JOptionPane.*;
public final class GraphTranslator {
private CyNetwork network;
private ParameterSet parameterSet;
+ private boolean containsOnlyPositiveWeigths;
+ private double maxWeight;
+ private double minWeight;
+
private double deletionCostDefault;
private double insertionCostDefault;
+ private double threshold;
CyColumn weightColumn;
@@ -34,13 +51,19 @@ public final class GraphTranslator {
this.weightColumn = parameterSet.getWeightColumn();
this.deletionCostDefault = parameterSet.defaultDeletionCost;
this.insertionCostDefault = parameterSet.defaultInsertionCost;
+ this.threshold = parameterSet.threshold;
this.nodeMap = new HashMap<>();
+ this.containsOnlyPositiveWeigths = true;
}
public YoshikoEdge[][] translateGraph() throws NetworkParsingException {
+ containsOnlyPositiveWeigths = true;
this.makeGraph();
this.makeGraphComplete();
+ parameterSet.containsOnlyPositiveEdges = containsOnlyPositiveWeigths;
+ parameterSet.recomendetTreshold = (minWeight + maxWeight)/2;
+
return edgeArray;
}
@@ -67,6 +90,10 @@ public final class GraphTranslator {
double weight;
weight = extractValue(e);
+ weight -= threshold;
+ if (weight < 0){
+ containsOnlyPositiveWeigths = false;
+ }
YoshikoEdge yoshikoEdge = new YoshikoEdge(e.getSUID(), weight, u, v);
edgeArray[yoshikoEdge.source][yoshikoEdge.target]= yoshikoEdge;
@@ -77,7 +104,7 @@ public final class GraphTranslator {
for (int i = 1; i < edgeArray.length; i++){
for (int j = 0; j < i; j++){
if (edgeArray[i][j] == null){
- YoshikoEdge yoshikoEdge = new YoshikoEdge(-1, insertionCostDefault, i, j);
+ YoshikoEdge yoshikoEdge = new YoshikoEdge(-1, insertionCostDefault-threshold, i, j);
edgeArray[i][j] = yoshikoEdge;
}
}
@@ -153,4 +180,42 @@ public final class GraphTranslator {
}
}
+ public void writeClusters(List<List<Integer>> clusters, int k) {
+ FileWriter fileWriter = null;
+ BufferedWriter bufferedWriter = null;
+
+ String s = network.getRow(network).get(CyNetwork.NAME, String.class);
+
+ s = s.substring(0, s.indexOf("."));
+
+ if (k < 0) {
+ s = s + "yoshikoClustering";
+ } else {
+ s = s+ "k-Clustering";
+ }
+
+ try {
+ File file = new File("C:\\Users\\User\\Desktop\\relevantClustEval\\optimalThreshold\\"+s);
+ file.createNewFile();
+ fileWriter = new FileWriter(file);
+ bufferedWriter = new BufferedWriter(fileWriter);
+ for (int i = 0; i < clusters.size(); i++) {
+ List<Integer> cluster = clusters.get(i);
+ for (Integer nodeId : cluster) {
+ bufferedWriter.write(network.getRow(nodeMap.get(nodeId)).get(CyNetwork.NAME, String.class) + " " + i + "\n");
+ }
+ }
+ bufferedWriter.close();
+ fileWriter.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } finally {
+ try {
+ bufferedWriter.close();
+ fileWriter.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
}
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 e08a1de..58a1833 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
@@ -43,6 +43,7 @@ public class YoshikoAlgoritmController {
result.addSolution(solution);
taskMonitor.setStatusMessage("Processing Clusters");
+ translator.writeClusters(clusters, k);
translator.transateClusters(clusters, solution);
}
}
\ No newline at end of file
--
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