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 89b5f2675e5dc4fb406185476f75ada0c9c864fc..7fb128424d4b5922e08200058cf02885a9048315 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
@@ -23,6 +23,8 @@ public class Core {
public static void performYoshiko(
int timeLimit,
CyColumn weightColumn,
+ CyColumn permanentColumn,
+ CyColumn forbiddenColumn,
double insertionCostDefault,
double deletionCostDefault
)
@@ -45,6 +47,8 @@ public class Core {
currentNetwork,
nodeMap,
weightColumn,
+ permanentColumn,
+ forbiddenColumn,
deletionCostDefault
);
@@ -55,7 +59,6 @@ public class Core {
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);
@@ -63,6 +66,7 @@ public class Core {
for (long i=0;i<numberOfSolutions;i++) {
System.out.println("Processing solution "+(i+1)+" of "+numberOfSolutions);
String columnName = "YOSHIKO_SOLUTION_"+(i+1);
+ currentNetwork.getDefaultNodeTable().deleteColumn(columnName);
currentNetwork.getDefaultNodeTable().createColumn(columnName, String.class, false);
long numberOfClusters = LibraryInterface.ClusterEditingSolutions_getNumberOfClusters(solutions, i);
for (long k=0;k<numberOfClusters;k++) {
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 2776e294cda04c6800bf857f43c3a9bbc1af6527..cebd4e4e29532894f70e63993ed5a2d7c760cdf1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
@@ -21,6 +21,8 @@ public class NetworkParser {
CyNetwork net,
NodeMap nodeMap,
CyColumn weightColumn,
+ CyColumn permanentColumn,
+ CyColumn forbiddenColumn,
double deletionCostDefault
)
{
@@ -36,30 +38,53 @@ public class NetworkParser {
//Loop over edges
for (CyEdge e : edges) {
+
CyRow edgeEntry = net.getRow(e);
- //Set to default cost
+
+ //Parse editing costs
double weight = deletionCostDefault;
if (weightColumn != null){
+ System.out.println("Using column: "+weightColumn.getName());
try {
//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());
- weight = (double)edgeEntry.get(weightColumn.getName(), weightType);
+ logger.debug("Column has type: "+weightType.getName());
+ if (weightType == Integer.class) {
+ weight = (int)edgeEntry.get(weightColumn.getName(), weightType);
+ }
+ else if(weightType == Double.class) {
+ weight = (double)edgeEntry.get(weightColumn.getName(), weightType);
+ }
}
catch(Exception ex) {
+ ex.printStackTrace();
//Invalid entry (no entry)
logger.info("No valid edit costs defined for: "+edgeEntry.get("name", String.class)+", falling back to default value!");
}
}
+
+ //Parse Forbidden/Permanent markers
+ boolean forbidden = false;
+ boolean permanent = false;
+ if (permanentColumn != null) {
+ permanent = (boolean)edgeEntry.get(permanentColumn.getName(), boolean.class);
+ }
+ if (forbiddenColumn != null) {
+ forbidden = (boolean)edgeEntry.get(forbiddenColumn.getName(), boolean.class);
+ }
logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ " with weight:"+weight);
- LibraryInterface.LibraryInput_addEdge(generatedInput,
+ LibraryInterface.LibraryInput_addEdge(
+ generatedInput,
nodeMap.get(e.getSource()),
- nodeMap.get(e.getTarget())
- , weight);
+ nodeMap.get(e.getTarget()),
+ weight,
+ permanent,
+ forbidden
+ );
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
new file mode 100644
index 0000000000000000000000000000000000000000..f04fffb9510e66654e989f2464cc84d3fa61ef90
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
@@ -0,0 +1,121 @@
+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 org.cytoscape.application.CyApplicationManager;
+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 ColumnMapper extends ComfortPanel{
+
+ //Symbolic links
+ private CyApplicationManager cy;
+
+ //Swing components
+ private JComboBox<CyColumn> editingCostMapper;
+ private JComboBox<CyColumn> permanentMapper;
+ private JComboBox<CyColumn> forbiddenMapper;
+
+ private JCheckBox useMappingCost;
+ private JCheckBox useMappingPerm;
+ private JCheckBox useMappingForb;
+
+ public ColumnMapper() {
+ cy = Core.getApplicationManager();
+
+ //SWING COMPONENTS
+ editingCostMapper = new JComboBox<CyColumn>();
+ permanentMapper = new JComboBox<CyColumn>();
+ forbiddenMapper = new JComboBox<CyColumn>();
+
+ useMappingCost = new JCheckBox("Map modification costs");
+ useMappingPerm = new JCheckBox("Map edges as permanent");
+ useMappingForb = new JCheckBox("Map edges as forbidden");
+
+ useMappingCost.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"
+ );
+ this.addAll(useMappingCost,editingCostMapper,useMappingPerm,permanentMapper,useMappingForb,forbiddenMapper);
+ //Initial call to get table values
+ updateValues();
+ //Add a focus listener to update values
+ this.addFocusListener (new FocusListener() {
+
+ @Override
+ public void focusGained(FocusEvent e) {
+ updateValues();
+ }
+
+ @Override
+ public void focusLost(FocusEvent e) {}
+
+ });
+
+ }
+
+ public void updateValues() {
+
+ CyNetwork net = cy.getCurrentNetwork();
+
+ if (net != null) { //Check if a network is loaded
+
+ //Clear entries
+ editingCostMapper.removeAllItems();
+ for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+ //Only add columns with numeric values
+ if (c.getType() == Integer.class || c.getType() == Double.class) {
+ editingCostMapper.addItem(c);
+ }
+ }
+
+ forbiddenMapper.removeAllItems();
+ for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+ //Only add columns with boolean values
+ if (c.getType() == Boolean.class) {
+ editingCostMapper.addItem(c);
+ }
+ }
+
+ permanentMapper.removeAllItems();
+ for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+ //Only add columns with boolean values
+ if (c.getType() == Boolean.class) {
+ permanentMapper.addItem(c);
+ }
+ }
+
+ }
+ }
+
+ public CyColumn getEditingCostColumn() {
+ if (useMappingCost.isSelected()) {
+ return editingCostMapper.getItemAt(editingCostMapper.getSelectedIndex());
+ }
+ return null;
+ }
+
+ public CyColumn getForbiddenColumn() {
+ if (useMappingForb.isSelected()) {
+ return forbiddenMapper.getItemAt(forbiddenMapper.getSelectedIndex());
+ }
+ return null;
+ }
+
+ public CyColumn getPermanentColumn() {
+ if (useMappingPerm.isSelected()) {
+ return permanentMapper.getItemAt(permanentMapper.getSelectedIndex());
+ }
+ return null;
+ }
+
+}
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 54bd7474f9f96bb176f22c7e141df7d8f15b1a60..22456af30debbd9f33f794c0b89f8ec005e27e4c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
@@ -10,16 +10,15 @@ import org.cytoscape.model.CyColumn;
public class EditCostPanel extends ComfortPanel {
//SWING COMPONENTS
- private ModificationCostMapper modCostMapper;
+ private ColumnMapper columnMapper;
private DoubleInputField icField;
private DoubleInputField dcField;
private JLabel icLabel;
private JLabel dcLabel;
public EditCostPanel() {
-
//Initialize components
- modCostMapper = new ModificationCostMapper();
+ columnMapper = new ColumnMapper();
icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
icField.setText("-1.0");
@@ -28,7 +27,7 @@ public class EditCostPanel extends ComfortPanel {
dcLabel = new JLabel("Deletion Cost:");
icLabel.setLabelFor(icField);
dcLabel.setLabelFor(dcField);
- this.addAll(modCostMapper,icField,dcField,icLabel,dcLabel);
+ this.addAll(columnMapper,icField,dcField,icLabel,dcLabel);
//
this.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
@@ -37,7 +36,15 @@ public class EditCostPanel extends ComfortPanel {
//SETTER / GETTER
public CyColumn getWeightColumn() {
- return modCostMapper.getValue();
+ return columnMapper.getEditingCostColumn();
+ }
+
+ public CyColumn getPermanentColumn() {
+ return columnMapper.getPermanentColumn();
+ }
+
+ public CyColumn getForbiddenColumn() {
+ return columnMapper.getForbiddenColumn();
}
public double getDefaultInsertionCost() {
@@ -47,5 +54,7 @@ public class EditCostPanel extends ComfortPanel {
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 df06a396d5ba02c37be745d6988c335d077954d3..a403598585aba4b6504901daf6c6716b100a2fe5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
@@ -1,5 +1,6 @@
package de.hhu.ba.yoshikoWrapper.gui;
+import java.text.DecimalFormat;
import java.text.NumberFormat;
import javax.swing.text.NumberFormatter;
@@ -19,7 +20,7 @@ public class FormatHelper {
}
public static NumberFormatter getDoubleFormatter(double minValue, double maxValue) {
- NumberFormat format = NumberFormat.getInstance();
+ NumberFormat format = DecimalFormat.getInstance();
NumberFormatter formatter = new NumberFormatter(format);
formatter.setValueClass(Double.class);
formatter.setMinimum(minValue);
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 f870b9c5e3f945b27aa46eaa258c0c16dbf949b5..ff42424796102328cd159325577432127b49a4dc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -100,6 +100,8 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
Core.performYoshiko(
timeLimitSetter.getTimeLimit(),
ecPanel.getWeightColumn(),
+ ecPanel.getPermanentColumn(),
+ ecPanel.getForbiddenColumn(),
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
deleted file mode 100644
index fb110698557223cfcd19a9f27362d30190c745a3..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ModificationCostMapper.java
+++ /dev/null
@@ -1,76 +0,0 @@
-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 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{
-
- //Symbolic links
- private CyApplicationManager cy;
-
- //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"
- );
- cy = Core.getApplicationManager();
- this.addAll(useMapping,tableFields);
- //Initial call to get table values
- updateValues();
- //Add a focus listener to update values
- tableFields.addFocusListener (new FocusListener() {
-
- @Override
- public void focusGained(FocusEvent e) {
- updateValues();
- }
-
- @Override
- public void focusLost(FocusEvent e) {}
-
- });
-
- }
-
- public void updateValues() {
- //Clear entries
- tableFields.removeAllItems();
- CyNetwork net = cy.getCurrentNetwork();
- if (net != null) { //Check if a network is loaded
- for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
- //Only add columns with numeric values
- if (c.getType() == Integer.class || c.getType() == Double.class) {
- 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
index 12273280c21033b3c82980575e73b1befab49d08..6fd2b9706b5a4903f36877c8d953cff5f9d6e8fb 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
@@ -2,6 +2,7 @@ package de.hhu.ba.yoshikoWrapper.gui;
import java.awt.Component;
+import javax.swing.BoxLayout;
import javax.swing.JCheckBox;
@SuppressWarnings("serial")
@@ -15,6 +16,7 @@ public class ReductionRulesChooser extends ComfortPanel{
private JCheckBox useSNRule;
public ReductionRulesChooser() {
+ this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
//Initialize subcomponents
useCRule = new JCheckBox("Use Clique Rule");
useCCRule = new JCheckBox("Use Critical-Clique Rule");