diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index a228110a520fbf15eda4e4da8bb87852b7b943a4..02bcee9949ca4f8fe4bc1c4f9b0073b0a6cb36af 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -117,7 +117,7 @@ public class CyActivator extends AbstractCyActivator {
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "yoshiko");
props.setProperty(COMMAND, YoshikoCommand.PERFORM_ALGORITHM.toString());
- props.setProperty(COMMAND_DESCRIPTION,"TEST PERFORM ALGORITHM");
+ props.setProperty(COMMAND_DESCRIPTION,"Cluster a network with the Yoshiko algorithm");
registerService(context, commandTaskFactory, TaskFactory.class, props);
//Initialize and register main panel
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 753d5bb3f4ce91fe61c17142c67b0d847896a861..79d7daaa14067a70c1b07172010d8ce87a83cea9 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -8,21 +8,40 @@ public class ParameterSet {
@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;
-
+ @Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
public CyColumn permanentColumn;
+ @Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
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;
+
+ @Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
+ 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="A bitmask representing which reduction rules should be used",context="nogui") //TODO: Filter bad bitmasks
+ public String reductionRulesBitMask = "000000";
+ @Tunable(description="A value controlling the resolution of the SNR reduction rule. Higher values mean a longer running time but possibly better reduction.",context="nogui")
+ public double snrMultFactor = 1.0;
+
+ @Tunable(description="Alternative Callback for CPLEX, might be faster on certain instances",context="nogui")
+ public boolean useTriangleCuts = false;
+ @Tunable(description="Alternative Callback for CPLEX, might be faster on large instances",context="nogui")
+ public boolean usePartitionCuts = false;
+
+ @Tunable(description="Uses a heuristic instead of ILP to solve WCE, significantly faster",context="nogui")
+ public boolean useHeuristic = true;
+
+ @Tunable(description="The maximum number of (optimal) solutions that is to be calculated",context="nogui")
+ public int solCount = 1;
+
+ @Tunable(description="Disable multithreading to keep the system responsive",context="nogui")
public boolean disableMultiThreading;
+
+ @Tunable(description="Automatically choose an appopriate set of reduction rules (overrides a given bitmask)",context="nogui")
/**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
- public boolean suggestReduction;
+ public boolean suggestReduction = true;
}
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 51c1dafca4c2ad4ca4b6d1358563520ce860b464..c6003910ae939c4e7359a03d7d67f98b7ec1a207 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -6,14 +6,14 @@ import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
-import org.slf4j.Logger;
+//import org.slf4j.Logger;
-import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
+//import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
public class GraphAnalyzer {
- private static Logger logger = YoshikoLogger.getInstance().getLogger();
+ //private static Logger logger = YoshikoLogger.getInstance().getLogger();
public static boolean isMultiGraph(CyNetwork net) {
//TODO: Better algorithm?
@@ -38,6 +38,13 @@ public class GraphAnalyzer {
return false;
}
+ /**
+ * Checks whether two edges connect the same pair of nodes
+ * This function is symmetric
+ * @param e1 An arbitrary CyEdge
+ * @param e2 An arbitrary CyEdge
+ * @return true if the edges connect the same pair of nodes, false otherwise
+ */
private static boolean connectSameNodes(CyEdge e1, CyEdge e2) {
if (//Treating all edges as undirected here
(e1.getSource() == e2.getTarget() && e1.getTarget() == e2.getSource()) ||
@@ -61,7 +68,7 @@ public class GraphAnalyzer {
* Generates a fitting bitmask by choosing the reduction rules that appear to be the best choice based on current research
* @param containsRealValues
* @param heuristic
- * @return
+ * @return The bitmask as a String
*/
public static String suggestReductionRules(boolean containsRealValues, boolean heuristic) {
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 812564310a916ea70ad7a2f0f044e710c2087e0e..87fb8c9b9fdc62ef34ad6c5caf2f7a4c086fc2c2 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
@@ -18,6 +18,9 @@ public enum YoshikoCommand {
if (this==PERFORM_ALGORITHM) {
return "cluster"; //TODO: Dynamic
}
+ else if (this==CREATE_CLUSTER_VIEW) {
+ return "createcvs";
+ }
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 0535700545e8dd0835df9fc31449ddbb00bd38bf..8920a781c04170ef7bc16adc7b4e6d3918ee76d8 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -76,7 +76,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
public ParameterSet parameterSet = null;
@Tunable(description="Network to analyze for clusters", context="nogui")
- public CyNetwork net;
+ public CyNetwork net = CyCore.cy.getCurrentNetwork();
//Temps, pointing to and need to be freed in C++
private LibraryInput c_input;
@@ -289,7 +289,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
@Override
public <R> R getResults(Class<? extends R> type) {
- //TODO:
+ //TODO: Return Result in some format that is suitable for console applications
if (type.equals(YoshikoResult.class)) {
return (R) (result!=null ? result : null);
}