diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 63a875a892451124e8448f3e953d9332c45cda54..1652fedf579aeec507609e441553917764bda682 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -117,7 +117,6 @@ public class CyActivator extends AbstractCyActivator {
props.setProperty(COMMAND, YoshikoCommand.PERFORM_ALGORITHM.toString());
props.setProperty(COMMAND_DESCRIPTION,"TEST PERFORM ALGORITHM");
registerService(context, commandTaskFactory, TaskFactory.class, props);
- System.out.println(props.toString());
//Initialize and register main panel
MainPanel mainPanel = new MainPanel();
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 f74c050263309cbab89cc8419dc0a8c830ee2555..87da79a3c3a696e288a56a4ae30390e1f11bf963 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -1,11 +1,16 @@
package de.hhu.ba.yoshikoWrapper.core;
+
import org.cytoscape.model.CyColumn;
+import org.cytoscape.work.Tunable;
public class ParameterSet {
- public int timeLimit;
+ @Tunable(description="Time Limit for the ILP mode", context="nogui")
+ public int timeLimit = -1;
+ @Tunable(description="A column in the edge table containing weights", context="nogui")
public CyColumn weightColumn;
+
public CyColumn permanentColumn;
public CyColumn forbiddenColumn;
public double defaultInsertionCost;
@@ -17,5 +22,5 @@ public class ParameterSet {
public boolean useHeuristic;
public int solCount;
public boolean disableMultiThreading;
-
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
index 4a970c02730b55d2dbdc1e57c4c8e64b16a8a246..1eec501cc0181d32d458f117094ce12adc009dae 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
@@ -39,7 +39,6 @@ public class YoshikoLoader {
private static Logger logger = YoshikoLogger.getInstance().getLogger();
public static void loadLibrary(String libPath) {
-
//Attempt to load from a previously stored path
File f = new File (libPath);
if (!f.exists()) {
@@ -49,15 +48,19 @@ public class YoshikoLoader {
try {
logger.info("Attempting to load library @: "+libPath);
+ //Verify version ending
if (!libPath.substring(0,libPath.lastIndexOf(".")).endsWith(REQUIRED_VERSION)) {
- throw new Exception(LocalizationManager.get("libFail")+" "+REQUIRED_VERSION);
+ logger.info(LocalizationManager.get("libFail")+" "+REQUIRED_VERSION);
+ return;
}
+ //Perform actual loading
System.load(libPath);
+
}
- catch(Exception e) {
+ catch(UnsatisfiedLinkError e) {
+ //This might happen as Java doesn't unload native libs
+ //One such case might be reloading the Cytoscape app on-the-fly
logger.error(e.getMessage());
- logger.info(LocalizationManager.get("libFail")+" "+REQUIRED_VERSION);
-
return;
}
LibraryInterface.setVerbosity(3);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
index 1b175e4f3eaf153c37fb3700e858bfe7eeab9aa7..8848647483717eb9963010d7fef1a247f6261b8a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
@@ -37,7 +37,7 @@ public class LanguageSwitcherPanel extends BasicCollapsiblePanel{
super(LocalizationManager.get("switchLanguage"));
final LanguageSwitcher switcher;
//final BasicCollapsiblePanel ret = new BasicCollapsiblePanel();
- getContentPane().setLayout(new BoxLayout(getContentPane(),BoxLayout.X_AXIS));
+ //getContentPane().setLayout(new BoxLayout(getContentPane(),BoxLayout.X_AXIS));
//SWING COMPONENTS INIT
switcher = new LanguageSwitcher();
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
index 0a964ecd2d1a98ee7f11490def7ea976b7a41ad7..812564310a916ea70ad7a2f0f044e710c2087e0e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
@@ -11,5 +11,15 @@ public enum YoshikoCommand {
*/
CREATE_CLUSTER_VIEW,
CREATE_META_GRAPH,
- PERFORM_ALGORITHM
+ PERFORM_ALGORITHM;
+
+ @Override
+ public String toString() {
+ if (this==PERFORM_ALGORITHM) {
+ return "cluster"; //TODO: Dynamic
+ }
+ return "null";
+ }
}
+
+
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 c3a0af7cf9d43f7ed73d7a696a075fa918513e82..80bc8ae8049c5af37f7acf8d45d79d9e2ac2159b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -31,6 +31,7 @@ import org.cytoscape.application.swing.CytoPanelState;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.ContainsTunables;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.slf4j.Logger;
@@ -65,11 +66,15 @@ public class AlgorithmTask extends AbstractTask {
private final Window statusWindow; //TODO: Make tunable?
//Parameters
- @Tunable(description="Parameter Set determining the operation mode for Yoshiko", context="nogui")
- private final ParameterSet parameterSet;
+
+ /**The ParameterSet specifying how the algorithm is to be performed
+ *
+ */
+ @ContainsTunables
+ public ParameterSet parameterSet = null;
@Tunable(description="Network to analyze for clusters", context="nogui")
- private final CyNetwork net;
+ public CyNetwork net;
//Temps, pointing to and need to be freed in C++
private LibraryInput input;
@@ -78,6 +83,12 @@ public class AlgorithmTask extends AbstractTask {
private ResultPanel resultPanel;
+ /**
+ * Default constructor, creates a new AlgorithmTask
+ * @param statusWindow The Window in which the status-bar is to be shown, can be null
+ * @param net The network that is to be clustered
+ * @param parameterSet The parameter set specifying the clustering mode
+ */
public AlgorithmTask(
Window statusWindow,
CyNetwork net,
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
index 103d03c1d7f44689433c8e3c1c70aa757be47b26..a5674a7ab6dff36f5f5e70afee44af3280afb41a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
@@ -10,6 +10,7 @@ import org.cytoscape.work.ObservableTask;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.TaskObserver;
+import org.cytoscape.work.Tunable;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -18,9 +19,8 @@ import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
public class CreateClusterViews implements Task {
- //TODO: Merge redundant code with CreateMetaGraphTask
-
- private ArrayList<YoshikoCluster> clusters;
+ @Tunable
+ public ArrayList<YoshikoCluster> clusters;
private boolean isTerminated;