diff --git a/pom.xml b/pom.xml
index 477aafb5707e5e418c432049e7607bddcfca23ea..e253b54b5d68ef31abc25ff496d06925eefd82e6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,8 +24,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<configuration>
- <source>1.6</source>
- <target>1.6</target>
+ <source>1.8</source>
+ <target>1.8</target>
<optimize>true</optimize>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
index e00c591e94797e2febaebbeb268c211c1be63dda..89b5f2675e5dc4fb406185476f75ada0c9c864fc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
@@ -2,9 +2,12 @@ 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.slf4j.Logger;
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_std__vectorT_int_t;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
@@ -12,22 +15,47 @@ import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_ysk__ClusterEditingSolutions;
public class Core {
- private static CyApplicationManager cy;
+ //Symbolic links
+ private static CyApplicationManager cy;
+ private static Logger logger = YoshikoLogger.getInstance().getLogger();
- public static void performYoshiko(int timeLimit) {
+ public static void performYoshiko(
+ int timeLimit,
+ CyColumn weightColumn,
+ double insertionCostDefault,
+ double deletionCostDefault
+ )
+ {
+ //Get current network
CyNetwork currentNetwork = cy.getCurrentNetwork();
if (currentNetwork == null) {
- //TODO
+ logger.warn("There is no network loaded. You need to load a network first!");
return;
}
+ //Set time limit
LibraryInterface.setTimeLimit(timeLimit);
-
+
+ //Create a node map to identify nodes and eges in the solution
NodeMap nodeMap = new NodeMap(currentNetwork);
- SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(currentNetwork,nodeMap);
+ //Generate an input instance from the network
+ SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(
+ currentNetwork,
+ nodeMap,
+ weightColumn,
+ deletionCostDefault
+ );
+
+ //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);
+
+
+
long numberOfSolutions = LibraryInterface.ClusterEditingSolutions_getNumberOfSolutions(solutions);
System.out.println("Found: "+numberOfSolutions+" solutions!");
double modificationCost = LibraryInterface.ClusterEditingSolutions_getTotalCost(solutions);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
index 7602223b14ad08acd1309505b127fae91c80795a..f5f3e92229f6f11e75aa5569dbc805b5875b71eb 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
@@ -2,35 +2,54 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.util.List;
+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 de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
public class NetworkParser {
- //**TODO MAKE DYNAMIC
- private static String weightIndex = "Weight";
-
+ //Symbolic Links
+ private static Logger logger = YoshikoLogger.getInstance().getLogger();
-
-
- public static SWIGTYPE_p_yskInput__LibraryInput parseNetwork(CyNetwork net,NodeMap nodeMap) {
+ public static SWIGTYPE_p_yskInput__LibraryInput parseNetwork(
+ CyNetwork net,
+ NodeMap nodeMap,
+ CyColumn weightColumn,
+ double deletionCostDefault
+ )
+ {
+ //Create an empty instance / fetch C++ object pointer
SWIGTYPE_p_yskInput__LibraryInput generatedInput = LibraryInterface.new_LibraryInput();
- if (net != null){
+ if (net != null){
+ //Create an empty full graph with a given size
LibraryInterface.LibraryInput_setSize(generatedInput, net.getNodeCount());
+ //Fetch edges
List<CyEdge> edges = net.getEdgeList();
- Class<?> weightType = net.getDefaultEdgeTable().getColumn(weightIndex).getType();
- System.out.println("Column has type:"+weightType.getName());
+
+ //Find out if the weights are double or int
+ @SuppressWarnings("unchecked")
+ Class<? extends Number> weightType = (Class<? extends Number>) weightColumn.getType();
+
+ logger.info("Column has type: "+weightType.getName());
+ //Loop over edges
for (CyEdge e : edges) {
CyRow edgeEntry = net.getRow(e);
- double weight = 0.0;
- if (weightType == Integer.class) {
- weight = (double)edgeEntry.get(weightIndex, Integer.class);
+ double weight = deletionCostDefault;
+ try {
+ weight = (double)edgeEntry.get(weightColumn.getName(), weightType);
}
- System.out.println("Found Edge: "+edgeEntry.get("name", String.class)+ "with weight:"+weight);
+ catch(Exception ex) {
+ //Invalid entry (no entry)
+ logger.info("No valid edit costs defined for: "+edgeEntry.get("name", String.class)+", falling back to default value!");
+ }
+
+ logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ "with weight:"+weight);
LibraryInterface.LibraryInput_addEdge(generatedInput,
nodeMap.get(e.getSource()),
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
index aea51813d9a33391133ae3390dc8f7eadac3bf8b..80e89e20be5714c8c8a13cf52f6eba603fe83563 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
@@ -13,7 +13,7 @@ public class DoubleInputField extends JFormattedTextField{
this.setColumns(8);
}
- public int getTimeLimit() {
- return Integer.parseInt(getText());
+ public double getValueAsDouble() {
+ return Double.parseDouble(getText());
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
index d131859a83dc17ea639add21c47b6fad3efa752f..54bd7474f9f96bb176f22c7e141df7d8f15b1a60 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
@@ -1,6 +1,10 @@
package de.hhu.ba.yoshikoWrapper.gui;
+import javax.swing.BorderFactory;
import javax.swing.JLabel;
+import javax.swing.border.EtchedBorder;
+
+import org.cytoscape.model.CyColumn;
@SuppressWarnings("serial") //Will never be serialized
public class EditCostPanel extends ComfortPanel {
@@ -13,14 +17,35 @@ public class EditCostPanel extends ComfortPanel {
private JLabel dcLabel;
public EditCostPanel() {
+
+ //Initialize components
modCostMapper = new ModificationCostMapper();
- icField = new DoubleInputField(0,Double.NEGATIVE_INFINITY);
+ icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
+ icField.setText("-1.0");
+ dcField.setText("1.0");
icLabel = new JLabel("Insertion Cost:");
dcLabel = new JLabel("Deletion Cost:");
icLabel.setLabelFor(icField);
dcLabel.setLabelFor(dcField);
this.addAll(modCostMapper,icField,dcField,icLabel,dcLabel);
+
+ //
+ this.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+ }
+
+ //SETTER / GETTER
+
+ public CyColumn getWeightColumn() {
+ return modCostMapper.getValue();
+ }
+
+ public double getDefaultInsertionCost() {
+ return icField.getValueAsDouble();
+ }
+
+ public double getDefaultDeletionCost() {
+ return dcField.getValueAsDouble();
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
index 770d241c3bf5523b33b3485339a1def29f354495..df06a396d5ba02c37be745d6988c335d077954d3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
@@ -21,7 +21,7 @@ public class FormatHelper {
public static NumberFormatter getDoubleFormatter(double minValue, double maxValue) {
NumberFormat format = NumberFormat.getInstance();
NumberFormatter formatter = new NumberFormatter(format);
- formatter.setValueClass(Integer.class);
+ formatter.setValueClass(Double.class);
formatter.setMinimum(minValue);
formatter.setMaximum(maxValue);
formatter.setAllowsInvalid(false);
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 403ceb434d38d05b4666fe5239aef9ed34ac1281..f870b9c5e3f945b27aa46eaa258c0c16dbf949b5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -97,7 +97,12 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
if (YoshikoLoader.isLibraryLoaded()){
- Core.performYoshiko(timeLimitSetter.getTimeLimit());
+ Core.performYoshiko(
+ timeLimitSetter.getTimeLimit(),
+ ecPanel.getWeightColumn(),
+ ecPanel.getDefaultInsertionCost(),
+ ecPanel.getDefaultDeletionCost()
+ );
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
index 78c74b132d987aa541c512b7c4e09926df50fec9..fb110698557223cfcd19a9f27362d30190c745a3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
@@ -10,11 +10,13 @@ import javax.swing.JComboBox;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnDeletedListener;
import de.hhu.ba.yoshikoWrapper.core.Core;
@SuppressWarnings("serial") //will never be serialized
-public class ModificationCostMapper extends ComfortPanel {
+public class ModificationCostMapper extends ComfortPanel{
//Symbolic links
private CyApplicationManager cy;
@@ -36,8 +38,7 @@ public class ModificationCostMapper extends ComfortPanel {
//Initial call to get table values
updateValues();
//Add a focus listener to update values
- //TODO: This might be a bit inelegant but there is no way to get a callback from CS when a table changes values
- tableFields.addFocusListener(new FocusListener() {
+ tableFields.addFocusListener (new FocusListener() {
@Override
public void focusGained(FocusEvent e) {
@@ -57,7 +58,10 @@ public class ModificationCostMapper extends ComfortPanel {
CyNetwork net = cy.getCurrentNetwork();
if (net != null) { //Check if a network is loaded
for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
- tableFields.addItem(c);
+ //Only add columns with numeric values
+ if (c.getType() == Integer.class || c.getType() == Double.class) {
+ tableFields.addItem(c);
+ }
}
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
index e87817e26c40e022a279327dd52f622d1a80a1b0..f56afd8bdced6a150e4a94d555dfe4b40776de0c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
@@ -93,10 +93,6 @@ public class LibraryInterface {
LibraryInterfaceJNI.delete_LibraryInput(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self));
}
- public static void LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput self, long id) {
- LibraryInterfaceJNI.LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), id);
- }
-
public static void LibraryInput_addEdge(SWIGTYPE_p_yskInput__LibraryInput self, long sourceID, long targetID, double cost) {
LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_0(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), sourceID, targetID, cost);
}
@@ -105,6 +101,14 @@ public class LibraryInterface {
LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_1(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), sourceID, targetID, cost, permanent, forbidden);
}
+ public static void LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput self, long id) {
+ LibraryInterfaceJNI.LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), id);
+ }
+
+ public static void LibraryInput_setDefaultInsertionCost(SWIGTYPE_p_yskInput__LibraryInput self, double cost) {
+ LibraryInterfaceJNI.LibraryInput_setDefaultInsertionCost(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), cost);
+ }
+
public static String getVersionString() {
return LibraryInterfaceJNI.getVersionString();
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
index 2ed424470bdf7d750edba86d06739cc5bbb82178..8332626738495dffb9f5e66702299f8fd10f0d18 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
@@ -29,9 +29,10 @@ public class LibraryInterfaceJNI {
public final static native void delete_ClusterEditingSolutions(long jarg1);
public final static native long new_LibraryInput();
public final static native void delete_LibraryInput(long jarg1);
- public final static native void LibraryInput_setSize(long jarg1, long jarg2);
public final static native void LibraryInput_addEdge__SWIG_0(long jarg1, long jarg2, long jarg3, double jarg4);
public final static native void LibraryInput_addEdge__SWIG_1(long jarg1, long jarg2, long jarg3, double jarg4, boolean jarg5, boolean jarg6);
+ public final static native void LibraryInput_setSize(long jarg1, long jarg2);
+ public final static native void LibraryInput_setDefaultInsertionCost(long jarg1, double jarg2);
public final static native String getVersionString();
public final static native long processLibraryInput(long jarg1);
public final static native void setTimeLimit(int jarg1);