diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 507a0bfb2985b6404ed1ea2ae54718d413ec6b39..82ae5ea73b193238f2f624ad9f77aa92a97e65fd 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -3,22 +3,20 @@ package de.hhu.ba.yoshikoWrapper;
import java.util.Properties;
import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.application.swing.CyAction;
-import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.work.swing.DialogTaskManager;
import org.osgi.framework.BundleContext;
import de.hhu.ba.yoshikoWrapper.core.ConfigurationManager;
-import de.hhu.ba.yoshikoWrapper.core.Core;
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
-import de.hhu.ba.yoshikoWrapper.gui.MainPanelAction;
import de.hhu.ba.yoshikoWrapper.gui.SolutionsPanel;
public class CyActivator extends AbstractCyActivator {
-
+
public CyActivator() {
super();
}
@@ -38,14 +36,12 @@ public class CyActivator extends AbstractCyActivator {
YoshikoLoader.loadLibrary(cm.getProperties().getProperty("pathToYoshiko"));
}
- CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
- Core.setApplicationManager(cyApplicationManager);
-
- CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
-
+ //Create symbolic links to give other classes access
+ CyCore.cy = getService(context, CyApplicationManager.class);
+ CyCore.dialogTaskManager = getService(context, DialogTaskManager.class);
//main panel and result panel
- MainPanel mainPanel = new MainPanel();
SolutionsPanel solutionsPanel = new SolutionsPanel();
+ MainPanel mainPanel = new MainPanel(solutionsPanel);
registerService(context,mainPanel,CytoPanelComponent.class, new Properties());
registerService(context,solutionsPanel,CytoPanelComponent.class, new Properties());
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
similarity index 68%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
index 7fb128424d4b5922e08200058cf02885a9048315..e910feb81a7cb62139861ed42ab3f9aeb684eedf 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
@@ -1,10 +1,11 @@
package de.hhu.ba.yoshikoWrapper.core;
//TODO: ADD LOGGER SYSTEM
-import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
@@ -13,14 +14,23 @@ import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_std__vectorT_int_t;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_ysk__ClusterEditingSolutions;
-public class Core {
+public class AlgorithmTask extends AbstractTask {
//Symbolic links
- private static CyApplicationManager cy;
private static Logger logger = YoshikoLogger.getInstance().getLogger();
- public static void performYoshiko(
+ //Parameters
+ private double insertionCostDefault;
+ private double deletionCostDefault;
+ private CyColumn permanentColumn;
+ private CyColumn forbiddenColumn;
+ private CyColumn weightColumn;
+ private int timeLimit;
+ private CyNetwork net;
+
+ public AlgorithmTask(
+ CyNetwork net,
int timeLimit,
CyColumn weightColumn,
CyColumn permanentColumn,
@@ -29,10 +39,22 @@ public class Core {
double deletionCostDefault
)
{
+ this.net = net;
+ this.timeLimit = timeLimit;
+ this.weightColumn = weightColumn;
+ this.permanentColumn = permanentColumn;
+ this.forbiddenColumn = forbiddenColumn;
+ this.insertionCostDefault = insertionCostDefault;
+ this.deletionCostDefault = deletionCostDefault;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setTitle(LocalizationManager.yoshikoStrings().getString("yoshTask"));
+ taskMonitor.setProgress(0.0);
//Get current network
- CyNetwork currentNetwork = cy.getCurrentNetwork();
- if (currentNetwork == null) {
- logger.warn("There is no network loaded. You need to load a network first!");
+ if (net == null) {
+ logger.warn("CoreAlgorithm called on a net that is NULL!");
return;
}
@@ -40,24 +62,27 @@ public class Core {
LibraryInterface.setTimeLimit(timeLimit);
//Create a node map to identify nodes and eges in the solution
- NodeMap nodeMap = new NodeMap(currentNetwork);
+ NodeMap nodeMap = new NodeMap(net);
+ taskMonitor.setProgress(0.1);
//Generate an input instance from the network
SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(
- currentNetwork,
+ net,
nodeMap,
weightColumn,
permanentColumn,
forbiddenColumn,
deletionCostDefault
);
-
+ taskMonitor.setProgress(0.2);
+
//Set the default value for insertion cost
LibraryInterface.LibraryInput_setDefaultInsertionCost(input, insertionCostDefault);
//Call Yoshiko <<< Algorithm is performed here
SWIGTYPE_p_ysk__ClusterEditingSolutions solutions = LibraryInterface.processLibraryInput(input);
-
+ taskMonitor.setProgress(0.9);
+
long numberOfSolutions = LibraryInterface.ClusterEditingSolutions_getNumberOfSolutions(solutions);
System.out.println("Found: "+numberOfSolutions+" solutions!");
@@ -66,8 +91,8 @@ public class Core {
for (long i=0;i<numberOfSolutions;i++) {
System.out.println("Processing solution "+(i+1)+" of "+numberOfSolutions);
String columnName = "YOSHIKO_SOLUTION_"+(i+1);
- currentNetwork.getDefaultNodeTable().deleteColumn(columnName);
- currentNetwork.getDefaultNodeTable().createColumn(columnName, String.class, false);
+ net.getDefaultNodeTable().deleteColumn(columnName);
+ net.getDefaultNodeTable().createColumn(columnName, String.class, false);
long numberOfClusters = LibraryInterface.ClusterEditingSolutions_getNumberOfClusters(solutions, i);
for (long k=0;k<numberOfClusters;k++) {
System.out.println("Processing cluster "+(k+1)+" of "+numberOfClusters);
@@ -81,23 +106,12 @@ public class Core {
System.out.println("FATAL ERROR: Node was not previously mapped!");
return;
}
- currentNetwork.getRow(node).set(columnName, ""+(k+1));
+ net.getRow(node).set(columnName, ""+(k+1));
}
}
}
LibraryInterface.delete_LibraryInput(input);
+ taskMonitor.setProgress(1.0);
}
-
-
- //SETTER / GETTER METHODS
-
- public static void setApplicationManager(CyApplicationManager cyApplicationManager) {
- cy = cyApplicationManager;
- }
-
- public static CyApplicationManager getApplicationManager() {
- return cy;
- }
-
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
new file mode 100644
index 0000000000000000000000000000000000000000..47fac47bd1342b3cdda37ab605ca00b4deb44e83
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -0,0 +1,9 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.work.swing.DialogTaskManager;
+
+public class CyCore {
+ public static CyApplicationManager cy;
+ public static DialogTaskManager dialogTaskManager;
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
index 6744a35ae3980ffe826ed6161ad7ecda2961c028..f87c73981536d8b1dc260540794c851a1268d658 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
@@ -8,18 +8,15 @@ import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
-import de.hhu.ba.yoshikoWrapper.core.Core;
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
@SuppressWarnings("serial") //will never be serialized
public class ColumnMapper extends ComfortPanel{
- //Symbolic links
- private CyApplicationManager cy;
-
+
//Swing components
private JComboBox<CyColumn> editingCostMapper;
private JComboBox<CyColumn> permanentMapper;
@@ -33,7 +30,6 @@ public class ColumnMapper extends ComfortPanel{
public ColumnMapper() {
this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
- cy = Core.getApplicationManager();
//SWING COMPONENTS
editingCostMapper = new JComboBox<CyColumn>();
@@ -64,7 +60,7 @@ public class ColumnMapper extends ComfortPanel{
public void updateValues() {
- CyNetwork net = cy.getCurrentNetwork();
+ CyNetwork net = CyCore.cy.getCurrentNetwork();
if (net != null) { //Check if a network is loaded
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 ac0b3fbbaac9cac320d48cab213a95d4e02261ae..f3705081dfdfe04c91e7bc4fb9e53d82dd81a14f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -13,7 +13,11 @@ import javax.swing.JRadioButton;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
-import de.hhu.ba.yoshikoWrapper.core.Core;
+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.YoshikoLoader;
/**This class describes the Swing Panel that the user interacts with in cytoscape
@@ -41,13 +45,18 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
private final JCheckBox useTriangleCutsBox;
private final JCheckBox usePartitionCutsBox;
-
-
+ //SYMBOLIC LINKS
+ private final SolutionsPanel solutionsPanel;
+
/**
* Main constructor, creates a new Panel and initializes subcomponents
+ * @param solPanel
*/
- public MainPanel() {
+ public MainPanel(SolutionsPanel solPanel) {
+
+ this.solutionsPanel = solPanel;
+ //SWING INIT
this.setLayout(new BoxLayout(this,BoxLayout.PAGE_AXIS));
//Initialize Swing components
@@ -71,7 +80,8 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
if (YoshikoLoader.isLibraryLoaded()){
- Core.performYoshiko(
+ AbstractTask yoshiko = new AlgorithmTask(
+ CyCore.cy.getCurrentNetwork(),
timeLimitSetter.getTimeLimit(),
ecPanel.getWeightColumn(),
ecPanel.getPermanentColumn(),
@@ -79,7 +89,8 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
ecPanel.getDefaultInsertionCost(),
ecPanel.getDefaultDeletionCost()
);
-
+ CyCore.dialogTaskManager.execute(new TaskIterator(1,yoshiko));
+ solutionsPanel.setVisible(true);
}
}
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 9d773a7796479c3d758c9bc4b19244b128f537b0..b919c85a9d2e7916543055251f88a188ff472d25 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -1,3 +1,4 @@
resultsPanelTitle = Yoshiko Results
yoshVersion = Yoshiko Version
-resolveLibPath = Resolve Yoshiko Library Path
\ No newline at end of file
+resolveLibPath = Resolve Yoshiko Library Path
+yoshTask = Performing Yoshiko Algorithm
\ No newline at end of file