diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 7dc34f7fe13d5f00a552065ac61931a906880ba8..442d482201c69b27f34b4ef184d9d925dac0cac1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -38,7 +38,7 @@ public class CyActivator extends AbstractCyActivator {
}
CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
- Core.registerApplicationManager(cyApplicationManager);
+ Core.setApplicationManager(cyApplicationManager);
CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
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 8d15d888412ed64bcfdf701f17d39db95b0e1391..9dd443be77506e2c718bcf4675a091ae5a7a79cf 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
@@ -14,9 +14,6 @@ public class Core {
private static CyApplicationManager cy;
- public static void registerApplicationManager(CyApplicationManager cyApplicationManager) {
- cy = cyApplicationManager;
- }
public static void performYoshiko(int timeLimit) {
CyNetwork currentNetwork = cy.getCurrentNetwork();
@@ -59,5 +56,16 @@ public class Core {
LibraryInterface.delete_LibraryInput(input);
}
+
+
+ //SETTER / GETTER METHODS
+
+ public static void setApplicationManager(CyApplicationManager cyApplicationManager) {
+ cy = cyApplicationManager;
+ }
+
+ public static CyNetwork getCurrentNetwork() {
+ return cy.getCurrentNetwork();
+ }
}
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 b9a430f28def8440dc9a9bae6e8ec9d1dd46ad31..e8fc5a9aeb123dea93490b868546e631578cb9f9 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
@@ -2,17 +2,23 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.io.File;
+import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+
public class YoshikoLoader {
- private static boolean libraryLoaded;
private static ConfigurationManager cm;
public static void loadLibrary(String libPath) {
+ //TODO: Java has no method to unload a native library :( This means, that reloading the library file on the fly is not possible
+
+ //Check 1: Library is already loaded
- if (libraryLoaded) {
+ if (isLibraryLoaded()) {
+ System.out.println("Library is already loaded!");
return;
}
+ //Attempt to load from a previously stored path
File f = new File (libPath);
if (!f.exists()) {
System.out.println("Could not find a previously saved yoshiko library path, needs to be set manually!");
@@ -24,7 +30,6 @@ public class YoshikoLoader {
System.load(libPath);
//update cfg
cm.getProperties().setProperty("pathToYoshiko", libPath);
- libraryLoaded = true;
}
catch(Exception e) {
e.printStackTrace();
@@ -34,7 +39,9 @@ public class YoshikoLoader {
//SETTER / GETTER
public static boolean isLibraryLoaded() {
- return libraryLoaded;
+
+ if (LibraryInterface.getVersionString() != null) return true;
+ return false;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ComfortPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ComfortPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..e2e320dbcfe5e42ec35c4e9e2e6cb7c3c86c8443
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ComfortPanel.java
@@ -0,0 +1,20 @@
+package de.hhu.ba.yoshikoWrapper.gui;
+
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+@SuppressWarnings("serial")
+public class ComfortPanel extends JPanel {
+
+ /**
+ * Comfort Function
+ * @param components The components that are to be added to this panel
+ */
+ protected void addAll(JComponent... components) {
+ for (JComponent c : components){
+ this.add(c);
+ }
+
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
new file mode 100644
index 0000000000000000000000000000000000000000..ba893825fcd140fcc01427755e2eb85c0264c16e
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
@@ -0,0 +1,19 @@
+package de.hhu.ba.yoshikoWrapper.gui;
+
+import javax.swing.JFormattedTextField;
+
+/**
+ * Provides a more strict input field that only accepts double
+ */
+@SuppressWarnings("serial")
+public class DoubleInputField extends JFormattedTextField{
+
+ public DoubleInputField() {
+ super(FormatHelper.getDoubleFormatter());
+ this.setColumns(8);
+ }
+
+ public int getTimeLimit() {
+ return Integer.parseInt(getText());
+ }
+}
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 9de27eae347737a6e1557162006e1188ccf86cef..dd448186bb2396aafb773173aeb941b8f1731a32 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
@@ -18,4 +18,16 @@ public class FormatHelper {
return formatter;
}
+ public static NumberFormatter getDoubleFormatter() {
+ NumberFormat format = NumberFormat.getInstance();
+ NumberFormatter formatter = new NumberFormatter(format);
+ formatter.setValueClass(Integer.class);
+ formatter.setMinimum(0);
+ formatter.setMaximum(Integer.MAX_VALUE);
+ formatter.setAllowsInvalid(false);
+ formatter.setCommitsOnValidEdit(true);
+
+ return formatter;
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/NumberInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java
similarity index 58%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/NumberInputField.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java
index 51cd3f4a014bb1f64772e697e636508e5307cdcd..fe400a19e488d7041dd581029ee72453551e431a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/NumberInputField.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java
@@ -5,16 +5,12 @@ import javax.swing.JFormattedTextField;
/**
* Provides a more strict input field that only accepts integers
*/
-public class NumberInputField extends JFormattedTextField{
+@SuppressWarnings("serial")
+public class IntegerInputField extends JFormattedTextField{
- /**
- * SerialVersionUID
- */
- private static final long serialVersionUID = -1144461027491991050L;
-
-
- public NumberInputField() {
+ public IntegerInputField() {
super(FormatHelper.getIntegerFormatter());
+ this.setColumns(8);
}
public int getTimeLimit() {
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 05a4de5ae137f03d88fc110fe3bc57fcd4620b48..a50e9be6eeb50fd133b3ec531b4510c726451259 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -5,11 +5,14 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
import javax.swing.Icon;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
-import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import de.hhu.ba.yoshikoWrapper.core.Core;
@@ -20,36 +23,58 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
* @author Philipp Spohr, Aug 6, 2017
*
*/
-public class MainPanel extends JPanel implements CytoPanelComponent {
+@SuppressWarnings("serial")
+public class MainPanel extends ComfortPanel implements CytoPanelComponent {
- /**
- * Unique identifier for serialization
- */
- private static final long serialVersionUID = 6214827920591046457L;
-
//SYMBOLIC LINKS
private MainPanel self = this; //for lambda function references
- //SWING COMPONENTS
+ //SWING COMPONENTS
private LibStatusPanel libStatusPanel;
private JButton searchLibButton;
private JLabel yoshikoVersionLabel;
+
+ private ModificationCostMapper modCostMapper;
+
+ private ButtonGroup heuristicGroup;
+ private JRadioButton useHeuristic;
+ private JRadioButton useILP;
+
private TimeLimitSetter timeLimitSetter;
+
+ private ReductionRulesChooser reductionRulesChooser;
+
+ private JCheckBox useTriangleCutsBox;
+ private JCheckBox usePartitionCutsBox;
+
+
/**
* Main constructor, creates a new Panel and initializes subcomponents
*/
public MainPanel() {
-
this.setLayout(new BoxLayout(this,BoxLayout.PAGE_AXIS));
- //SWING COMPONENT INITIALIZATION
+ //SWING COMPONENT INITIALIZATION
libStatusPanel = new LibStatusPanel();
libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
- this.add(libStatusPanel);
- searchLibButton = new JButton("SHOW YOSHIKO LIB");
+ yoshikoVersionLabel = new JLabel("YOSHIKO VERSION");
+ if (LibraryInterface.getVersionString() != null) {
+ yoshikoVersionLabel.setText(LibraryInterface.getVersionString());
+ }
+ searchLibButton = new JButton("POINT TO LIB");
+
+ modCostMapper = new ModificationCostMapper();
+
+ heuristicGroup = new ButtonGroup();
+ useILP = new JRadioButton("Use Integer Linear Programming");
+ useILP.setSelected(true);
+ useHeuristic = new JRadioButton("Use Heuristic");
+ heuristicGroup.add(useILP);
+ heuristicGroup.add(useHeuristic);
+
searchLibButton.addActionListener(new ActionListener() {
@Override
@@ -64,7 +89,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
}
});
- this.add(searchLibButton);
JButton runButton = new JButton("RUN");
runButton.addActionListener(new ActionListener() {
@@ -79,19 +103,35 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
}
});
- this.add(runButton);
+ reductionRulesChooser = new ReductionRulesChooser();
timeLimitSetter = new TimeLimitSetter();
- this.add(timeLimitSetter);
+ useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
+ usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
+
- yoshikoVersionLabel = new JLabel("YOSHIKO VERSION");
- this.add(yoshikoVersionLabel);
+ this.addAll(
+ libStatusPanel,
+ yoshikoVersionLabel,
+ searchLibButton,
+ modCostMapper,
+ useILP,
+ useHeuristic,
+ timeLimitSetter,
+ reductionRulesChooser,
+ useTriangleCutsBox,
+ usePartitionCutsBox,
+ runButton
+ );
this.setVisible(true);
}
+
+
+ //GETTER / SETTER
public Component getComponent() {
return this;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
new file mode 100644
index 0000000000000000000000000000000000000000..f5f145c2cf17d38b49505a0e10a0206b78c66c23
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
@@ -0,0 +1,68 @@
+package de.hhu.ba.yoshikoWrapper.gui;
+
+
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JPanel;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
+
+import de.hhu.ba.yoshikoWrapper.core.Core;
+
+@SuppressWarnings("serial") //will never be serialized
+public class ModificationCostMapper extends JPanel {
+
+ //Symbolic links
+ private CyNetwork net;
+
+ //Swing components
+ private JComboBox<CyColumn> tableFields;
+ private JCheckBox useMapping;
+
+ public ModificationCostMapper() {
+ tableFields = new JComboBox<CyColumn>();
+ useMapping = new JCheckBox("Map modification costs");
+ useMapping.setToolTipText(
+ "When you use this value you can assign a column in the edge table to represent the modification costs that are to be paid for deleting an edge."
+ +"You can also assign negative values if you have a complete graph to represent insertion costs."
+ +"Note: Any missing values are assumed to be the default values"
+ );
+ net = Core.getCurrentNetwork();
+ //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
+ this.addFocusListener(new FocusListener() {
+
+ @Override
+ public void focusGained(FocusEvent e) {
+ updateValues();
+ }
+
+ @Override
+ public void focusLost(FocusEvent e) {}
+
+ });
+
+ }
+
+ public void updateValues() {
+ //Clear entries
+ tableFields.removeAllItems();
+ for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+ tableFields.addItem(c);
+ }
+ }
+
+ public CyColumn getValue() {
+ if (useMapping.isSelected()) {
+ return tableFields.getItemAt(tableFields.getSelectedIndex());
+ }
+ return null;
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
new file mode 100644
index 0000000000000000000000000000000000000000..12273280c21033b3c82980575e73b1befab49d08
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
@@ -0,0 +1,54 @@
+package de.hhu.ba.yoshikoWrapper.gui;
+
+import java.awt.Component;
+
+import javax.swing.JCheckBox;
+
+@SuppressWarnings("serial")
+public class ReductionRulesChooser extends ComfortPanel{
+
+ private JCheckBox useCRule;
+ private JCheckBox useCCRule;
+ private JCheckBox useACRule;
+ private JCheckBox useHERule;
+ private JCheckBox usePDRRule;
+ private JCheckBox useSNRule;
+
+ public ReductionRulesChooser() {
+ //Initialize subcomponents
+ useCRule = new JCheckBox("Use Clique Rule");
+ useCCRule = new JCheckBox("Use Critical-Clique Rule");
+ useACRule = new JCheckBox("Use Almost-Clique Rule");
+ useHERule = new JCheckBox("Use Heavy-Edge 3 in 1 Rule");
+ usePDRRule = new JCheckBox("Use Parameter Dependent Reduction Rule");
+ useSNRule = new JCheckBox("Use Similar Neighborhood Rule");
+
+ this.addAll(
+ useCRule,
+ useCCRule,
+ useACRule,
+ useHERule,
+ usePDRRule,
+ useSNRule
+ );
+ //By default all reduction rules should be applied
+ for (Component c :this.getComponents()) {
+ ((JCheckBox)c).setSelected(true);
+ }
+ }
+
+
+ /** Creates a 6 Bit bitmask representing the currently selected choice of reduction rules.
+ * @return
+ */
+ public String getBitMask() {
+ String ret = "";
+ ret += (useCRule.isSelected() ? "1" : "0");
+ ret += (useCCRule.isSelected() ? "1" : "0");
+ ret += (useACRule.isSelected() ? "1" : "0");
+ ret += (useHERule.isSelected() ? "1" : "0");
+ ret += (usePDRRule.isSelected() ? "1" : "0");
+ ret += (useSNRule.isSelected() ? "1" : "0");
+ return ret;
+ }
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java
index 536f9a1d2e4fc6b6c8e5bb73220ce9dd72572d3e..c5445d6509f906abf71b60fb3c29cbee661afebc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java
@@ -4,21 +4,16 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JCheckBox;
-import javax.swing.JPanel;
-public class TimeLimitSetter extends JPanel{
-
- /**
- * Unique UID for serialization
- */
- private static final long serialVersionUID = 6617497954814566334L;
-
+@SuppressWarnings("serial")
+public class TimeLimitSetter extends ComfortPanel{
+
private JCheckBox checkBox;
- private NumberInputField numberField;
+ private IntegerInputField numberField;
public TimeLimitSetter() {
checkBox = new JCheckBox("Use time limit (s):");
- numberField = new NumberInputField();
+ numberField = new IntegerInputField();
numberField.setEnabled(false); //By default time limit is turned off
checkBox.addActionListener(
new ActionListener() {
@@ -31,8 +26,7 @@ public class TimeLimitSetter extends JPanel{
}
);
//REGISTER COMPONENTS
- this.add(checkBox);
- this.add(numberField);
+ this.addAll(checkBox,numberField);
}
public int getTimeLimit() {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java
index 312d9193351f22fd2d291114f1927339abba7452..af1b4ba45c3d45e8e18a4dea897dfc1baf319f6f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java
@@ -1,8 +1,4 @@
-/**
- *
- */
-/**
- * @author Philipp Spohr, Aug 6, 2017
+/**This package contains all Swing extensions and components (frontend)
*
*/
package de.hhu.ba.yoshikoWrapper.gui;
\ No newline at end of file