diff --git a/pom.xml b/pom.xml
index 47ac4958f7ebda9ee82b1adc724de7a0be4cb6af..42698a1c1b7748931a415eed0d23655fe230335b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -33,7 +33,7 @@
<groupId>de.hhu.ba</groupId>
<artifactId>yoshikoWrapper</artifactId>
- <version>0.1.4</version>
+ <version>0.1.5</version>
<name>YoshikoWrapper</name>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index b79892ee08f50af56220b59916d69d6ba2beb93d..f34df8026716566d65a387afae841db54cfa564b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -110,7 +110,7 @@ public class CyActivator extends AbstractCyActivator {
}
}
- //Register commands / CyRest
+ //Register commands / CyRest //TODO: Group shared calls for better code readability / less lines of code
TaskFactory commandTaskFactory_PERFORM_ALGORITHM = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM);
Properties props_PERFORM_ALGORITHM = new Properties();
props_PERFORM_ALGORITHM.setProperty(COMMAND_NAMESPACE, "yoshiko");
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 74fd62bc7b07e228e4ad5b788521a10a27306697..62271fab52f1c72469bfcf77ab5cfb9a3c7baafa 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -52,6 +52,9 @@ public class ParameterSet implements TunableValidator
/**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
public boolean suggestReduction = true;
+ @Tunable(description="Determines the number of clusters that are to be generated. -1 generates the optimal amount of clusters in the sense of WCE")
+ public int clusterCount = -1;
+
@Override
public ValidationState getValidationState(Appendable errMsg) {
System.out.println("DEBUG: Running VALIDATION of tunables"); //TODO: Move to logger (if it would work)
@@ -68,6 +71,11 @@ public class ParameterSet implements TunableValidator
errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)\n");
return ValidationState.INVALID;
}
+ //Checks for cluster count number
+ if ((clusterCount < 0 && clusterCount != -1)||(clusterCount == 0)) {
+ errMsg.append("Invalid cluster count number!");
+ return ValidationState.INVALID;
+ }
return ValidationState.OK;
} catch (IOException e) {
// TODO Auto-generated catch block
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 f7d349d0ca9dd87ba359202f9edf84e3cc464d9a..937bf0ec72c5a2ae81a3b0a32ad4bfb4c22dff40 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
@@ -31,7 +31,7 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
public class YoshikoLoader {
- public static final String REQUIRED_VERSION = "2.1.1";
+ public static final String REQUIRED_VERSION = "2.1.2";
private static boolean isLoaded;
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 1ef7cc8345a480edecdeadb8803c5e8634e838e4..24ca2d5df9c0002ac7ca3cf7b6d976184d6834bc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -15,6 +15,11 @@ public class GraphAnalyzer {
//private static Logger logger = YoshikoLogger.getInstance().getLogger();
+ /**
+ * Simple helper function, checks if a network contains multiple edges between a pair of nodes
+ * @param net The CyNetwork that is to be analyzed
+ * @return <b>true</b> if a pair of nodes exists that is connected with more than one edge, <b>false</b> otherwise
+ */
public static boolean isMultiGraph(CyNetwork net) {
//TODO: Better algorithm?
@@ -43,7 +48,7 @@ public class GraphAnalyzer {
* 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
+ * @return <b>true</b> if the edges connect the same pair of nodes, <b>false</b> otherwise
*/
private static boolean connectSameNodes(CyEdge e1, CyEdge e2) {
if (//Treating all edges as undirected here
@@ -98,12 +103,23 @@ public class GraphAnalyzer {
ret += (usePDRRule ? "1" : "0");
ret += (useSNRule ? "1" : "0");
+ //TODO: Spend some thoughts on logging, make a coherent design decision on logging
//logger.info("Suggesting the following reduction-rules bitmask: "+ret);
- System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
+ //System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
return ret;
}
+ /**
+ * Simple helper function that checks if a WCE instance contains real values (as opposed to only integers)
+ * @param net The network from which the WCE instance is to be derived
+ * @param weightColumn The CyColumn from which - if != null - the edge weights are taken
+ * @param permanentColumn The CyColumn from which - if != null - we derive if edges are permanent
+ * @param forbiddenColumn The CyColumn from which - if != null - we derive if edges are forbidden
+ * @param defaultInsertionCost The insertion cost used for non-existing edges or ones with no mapping associated
+ * @param defaultDeletionCost The deletion cost for edges with no mapping associated
+ * @return true if the WCE instance is real-valued, false otherwise
+ */
public static boolean containsRealValues(
CyNetwork net,
CyColumn weightColumn,
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java
new file mode 100644
index 0000000000000000000000000000000000000000..24932a0f2663aec9cbecf6059ca4afe8d7071e48
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java
@@ -0,0 +1,50 @@
+/*******************************************************************************
+ * Copyright (C) 2017 Philipp Spohr
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+package de.hhu.ba.yoshikoWrapper.swing.components;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+
+@SuppressWarnings("serial")
+public class ClusterCountChooser extends JPanel {
+ private final IntegerInputField numSolutionsSetter;
+ private final JLabel label;
+
+ public ClusterCountChooser() {
+ //Swing Component init
+ numSolutionsSetter = new IntegerInputField();
+ label = new JLabel(LocalizationManager.get("nrClusters"));
+ SwingUtil.addAll(this,label, numSolutionsSetter);
+ }
+
+ @Override
+ public void setEnabled(boolean enabled) {
+ numSolutionsSetter.setEnabled(enabled);
+ }
+
+ public int getClusterCount() {
+ return numSolutionsSetter.getValueAsInt();
+ }
+}
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 38b0126b43ba7aa8fad14ff97da8fffa3b32cafb..4beef6ff2d19d37adaf29c52000d828a1307ad4e 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
@@ -27,8 +27,6 @@ import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.GroupLayout.Alignment;
-import org.cytoscape.model.CyColumn;
-
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
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 32d5906cf7fce2e4b63f8afa8f6092df11a75d13..32fd5d773f4e8c3c6129d5404e9c3329ea666fa9 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
@@ -359,6 +359,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
ret.usePartitionCuts = opModePanel.usePartitionCuts();
ret.solCount = opModePanel.getSolCount();
ret.disableMultiThreading = opModePanel.isMultiThreadingDisabled();
+ ret.clusterCount = opModePanel.getClusterCount();
return ret;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
index bda3f6f4b5c69a8a640831aa076d23df28e04fef..8a4287cc4e78b6d075456108f757a39d8ad70192 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
@@ -41,6 +41,8 @@ import javax.swing.GroupLayout.Alignment;
public class OperationModePanel extends JPanel{
//SWING COMPONENTS
+ private final JCheckBox useClusterCount;
+ private final ClusterCountChooser ccChooser;
private final JRadioButton useHeuristic;
private final JRadioButton useILP;
private final TimeLimitSetter timeLimitSetter;
@@ -53,6 +55,12 @@ public class OperationModePanel extends JPanel{
public OperationModePanel() {
+ useClusterCount = new JCheckBox(LocalizationManager.get("useClusterCount"));
+ ccChooser = new ClusterCountChooser();
+ ccChooser.setEnabled(false);
+
+ useClusterCount.addActionListener(ccSwitch);
+
heuristicGroup = new ButtonGroup();
useILP = new JRadioButton("Use Integer Linear Programming");
@@ -79,6 +87,8 @@ public class OperationModePanel extends JPanel{
useHeuristic.addActionListener(ilpHeuristicSwitch);
SwingUtil.addAll(this,
+ useClusterCount,
+ ccChooser,
useHeuristic,
useILP,
solutionNumberChooser,
@@ -97,6 +107,8 @@ public class OperationModePanel extends JPanel{
layout.setAutoCreateContainerGaps(true);
layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
+ .addComponent(useClusterCount, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(ccChooser, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useHeuristic, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useILP, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(solutionNumberChooser, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -107,6 +119,8 @@ public class OperationModePanel extends JPanel{
);
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addComponent(useClusterCount)
+ .addComponent(ccChooser)
.addComponent(useHeuristic)
.addComponent(useILP)
.addComponent(solutionNumberChooser)
@@ -137,13 +151,21 @@ public class OperationModePanel extends JPanel{
}
}
- ActionListener ilpHeuristicSwitch = new ActionListener() {
+ private ActionListener ilpHeuristicSwitch = new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
ilpHeuristicSwitch();
}
};
+ private ActionListener ccSwitch = new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ccChooser.setEnabled(useClusterCount.isSelected());
+ }
+
+ };
//SETTER GETTER
public int getTimeLimit() {
@@ -169,4 +191,8 @@ public class OperationModePanel extends JPanel{
public int getSolCount() {
return solutionNumberChooser.getSolCount();
}
+
+ public int getClusterCount() {
+ return useClusterCount.isSelected() ? ccChooser.getClusterCount() : -1;
+ }
}
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 dfb0eebb8bd3b79d670aff1c0e263905e3923105..d276d08c05343ca9a817a6aeeb697059abd0867f 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
@@ -43,7 +43,6 @@ import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.LayoutStyle;
import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
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 331c298188cd2a1912df5b54aecf9747d351ddce..4031bdf20b28d9edd4739319cd701153dceaf3c7 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -170,7 +170,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
parameterSet.snrMultFactor,
parameterSet.useHeuristic,
parameterSet.usePartitionCuts,
- parameterSet.useTriangleCuts
+ parameterSet.useTriangleCuts,
+ parameterSet.clusterCount
);
@@ -261,7 +262,13 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
}
+ /**
+ * Simple helper function that analyzes C++ results and identifies solutions that are not usable or meaningful
+ * @param result The ClusterEditingSolutions object generated in C++ by a Yoshiko run
+ * @throws Exception Throws an exception if the result is not usable
+ */
private void checkForInvalidSolutions(ClusterEditingSolutions result) throws Exception {
+ //TODO: Feasible might be the wrong word here
if (result == null) {
//There was no c_result object generated at all
throw new Exception(LocalizationManager.get("noFeasible"));
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index b20a177a70f2a91e877d6071906459d786118ec7..ce6dff546d03fce1a311296c3fbdec64096eb48d 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -74,6 +74,8 @@ optionpane_title = Yoshiko Info
noClustersSelected = You have not selected any clusters
notOptimal = Optimality not guaranteed
nrSolutions = Number of Solutions:
+nrClusters = Number of Clusters:
+useClusterCount = Define cluster count
operationMode = Operation Mode
optimal = Optimal Solution
paidCost = Paid a total modification cost of: